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Everitt Maintainer: Torsten Hothorn Description: Functions, data sets, analyses and examples from the third edition of the book ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides). The publishers web page is ''. Depends: R (>= 3.0.0), tools Suggests: boot (>= 1.3-9), lattice (>= 0.20-23), MASS (>= 7.3-29), mgcv (>= 1.7-27), rpart (>= 4.1-4), survival (>= 2.37-4), ape (>= 3.0-11), coin (>= 1.1-3), flexmix (>= 2.3-11), Formula (>= 1.1-1), gamair (>= 0.0.8), gamlss.data (>= 4.2.6), gee (>= 4.13-18), KernSmooth (>= 2.23-10), lme4 (>= 1.0-5), maps (>= 2.3-6), maptools (>= 0.8-27), mboost (>= 2.2-3), mclust (>= 4.2), mlbench (>= 2.1-1), mice (>= 2.18), multcomp (>= 1.3-1), mvtnorm (>= 0.9-9996), partykit (>= 0.8-0), quantreg (>= 5.05), randomForest (>= 4.6-7), rmeta (>= 2.16), sandwich (>= 2.3-0), scatterplot3d (>= 0.3-34), sp (>= 1.0-14), TH.data (>= 1.0-2), vcd (>= 1.3-1), wordcloud (>= 2.4), HSAUR2 LazyData: yes License: GPL-2 Encoding: UTF-8 NeedsCompilation: no Packaged: 2021-10-18 14:49:48 UTC; hothorn Repository: CRAN Date/Publication: 2021-10-18 15:40:02 UTC HSAUR3/man/0000755000175000017500000000000014133301713012120 5ustar nileshnileshHSAUR3/man/roomwidth.Rd0000644000175000017500000000237712357775401014453 0ustar nileshnilesh\name{roomwidth} \alias{roomwidth} \docType{data} \title{ Students Estimates of Lecture Room Width } \description{ Lecture room width estimated by students in two different units. } \usage{data("roomwidth")} \format{ A data frame with 113 observations on the following 2 variables. \describe{ \item{unit}{a factor with levels \code{feet} and \code{metres}.} \item{width}{the estimated width of the lecture room.} } } \details{ Shortly after metric units of length were officially introduced in Australia, each of a group of 44 students was asked to guess, to the nearest metre, the width of the lecture hall in which they were sitting. Another group of 69 students in the same room was asked to guess the width in feet, to the nearest foot. The data were collected by Professor T. Lewis and are taken from Hand et al (1994). The main question is whether estimation in feet and in metres gives different results. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("roomwidth", package = "HSAUR3") convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) boxplot(I(width * convert) ~ unit, data = roomwidth) } \keyword{datasets} HSAUR3/man/aspirin.Rd0000644000175000017500000000163512357775401014100 0ustar nileshnilesh\name{aspirin} \alias{aspirin} \docType{data} \title{ Aspirin Data } \description{ Efficacy of Aspirin in preventing death after a myocardial infarct. } \usage{data("aspirin")} \format{ A data frame with 7 observations on the following 4 variables. \describe{ \item{\code{dp}}{number of deaths after placebo.} \item{\code{tp}}{total number subjects treated with placebo.} \item{\code{da}}{number of deaths after Aspirin.} \item{\code{ta}}{total number of subjects treated with Aspirin.} } } \details{ The data were collected for a meta-analysis of the effectiveness of Aspirin (versus placebo) in preventing death after a myocardial infarction. } \source{ J. L. Fleiss (1993), The statistical basis of meta-analysis. \emph{Statistical Methods in Medical Research} \bold{2}, 121--145. } \examples{ data("aspirin", package = "HSAUR3") aspirin } \keyword{datasets} HSAUR3/man/Smoking_SchairerSchoeniger1944.Rd0000644000175000017500000000154312357775401020211 0ustar nileshnilesh\name{Smoking_SchairerSchoeniger1944} \alias{Smoking_SchairerSchoeniger1944} \docType{data} \title{ Smoking and Lung Cancer (II) } \description{ Number of smokers in a case-control study. } \usage{data(Smoking_SchairerSchoeniger1944)} \format{ The format is: table [1:5, 1:7] 3 11 31 19 29 2 0 4 6 3 ... - attr(*, "dimnames")=List of 2 ..$ Smoking : chr [1:5] "Nonsmoker" "Moderate smoker" "Medium smoker" "Heavy smoker" ... ..$ Diagnosis: chr [1:7] "Lung cancer" "Lip cancer" "Throat cancer" "Stomach cancer" ... } \source{ E. Schairer and E. Sch\"oninger (1944), Lungenkrebs und Tabakverbrauch, \emph{Zeitschrift fuer Krebsforschung}, \bold{54}(4), 261-269 } \references{ Richard Doll (1998), Uncovering the effects of smoking: historical perspective. \emph{Statistical Methods in Medical Research}, \bold{7}(87), 87-117 } \keyword{datasets} HSAUR3/man/toothpaste.Rd0000644000175000017500000000255012357775401014622 0ustar nileshnilesh\name{toothpaste} \alias{toothpaste} \docType{data} \title{ Toothpaste Data } \description{ Meta-analysis of studies comparing two different toothpastes. } \usage{data("toothpaste")} \format{ A data frame with 9 observations on the following 7 variables. \describe{ \item{\code{Study}}{the identifier of the study.} \item{\code{nA}}{number of subjects using toothpaste A.} \item{\code{meanA}}{mean DMFS index of subjects using toothpaste A.} \item{\code{sdA}}{standard deviation of DMFS index of subjects using toothpaste A.} \item{\code{nB}}{number of subjects using toothpaste B.} \item{\code{meanB}}{mean DMFS index of subjects using toothpaste B.} \item{\code{sdB}}{standard deviation of DMFS index of subjects using toothpaste B.} } } \details{ The data are the results of nine randomised trials comparing two different toothpastes for the prevention of caries development. The outcomes in each trial was the change, from baseline, in the decayed, missing (due to caries) and filled surface dental index (DMFS). } \source{ B. S. Everitt and A. Pickles (2000), \emph{Statistical Aspects of the Design and Analysis of Clinical Trials}, Imperial College Press, London. } \examples{ data("toothpaste", package = "HSAUR3") toothpaste } \keyword{datasets} HSAUR3/man/bp.Rd0000644000175000017500000000135212357775401013030 0ustar nileshnilesh\name{bp} \alias{bp} \docType{data} \title{ Lowering Blood Pressure Data } \description{ Lowering a patient's blood pressure during surgery, using a hypotensive drug. } \usage{data(bp)} \format{ A data frame with 53 observations on the following 3 variables. \describe{ \item{\code{logdose}}{the logarithm (base 10) of the dose of drug in milligrams} \item{\code{bloodp}}{average systolic blood pressure achieved while the drug was being administered} \item{\code{recovtime}}{time in minutes before the patient's systolic blood pressure returned to 100mm of mercury} } } \source{ J. D. Robertson and P. Armitage (1959) Comparison of Two Hypotensive Agents, \emph{Anaesthesia}, \bold{14}(1), 53--64 } \keyword{datasets} HSAUR3/man/men1500m.Rd0000644000175000017500000000151312357775401013670 0ustar nileshnilesh\name{men1500m} \alias{men1500m} \docType{data} \title{ Winners of the Olympic Men's 1500m } \description{ The data gives the winners of the men's 1500m race for the Olympic Games 1896 to 2004. } \usage{data("men1500m")} \format{ A data frame with 25 observations on the following 5 variables. \describe{ \item{\code{year}}{the olympic year.} \item{\code{venue}}{city where the games took place.} \item{\code{winner}}{winner of men's 1500m race.} \item{\code{country}}{country the winner came from.} \item{\code{time}}{time (in seconds) of the winner.} } } \examples{ data("men1500m", package = "HSAUR3") op <- par(las = 2) plot(time ~ year, data = men1500m, axes = FALSE) yrs <- seq(from = 1896, to = 2004, by = 4) axis(1, at = yrs, labels = yrs) axis(2) box() par(op) } \keyword{datasets} HSAUR3/man/CHFLS.Rd0000644000175000017500000001647414033271372013270 0ustar nileshnilesh\name{CHFLS} \alias{CHFLS} \docType{data} \title{ Chinese Health and Family Life Survey } \description{ The Chinese Health and Family Life Survey sampled $60$ villages and urban neighborhoods chosen in such a way as to represent the full geographical and socioeconomic range of contemporary China. } \usage{data("CHFLS")} \format{ A data frame with 1534 observations on the following 10 variables. \describe{ \item{\code{R_region}}{a factor with levels \code{Coastal South}, \code{Coastal East}, \code{Inlands}, \code{North}, \code{Northeast}, \code{Central West}.} \item{\code{R_age}}{age of the responding woman.} \item{\code{R_edu}}{education level of the responding woman, an ordered factor with levels \code{Never attended school} < \code{Elementary school} < \code{Junior high school} < \code{Senior high school} < \code{Junior college} < \code{University}.} \item{\code{R_income}}{monthly income of the responding woman.} \item{\code{R_health}}{self-reported health status, an ordered factor with levels \code{Poor} < \code{Not good} < \code{Fair} < \code{Good} < \code{Excellent}.} \item{\code{R_height}}{height of the responding woman.} \item{\code{R_happy}}{self-reportet happiness of the responding woman, an ordered factor with levels \code{Very unhappy} < \code{Not too happy} < \code{Somewhat happy} < \code{Very happy}.} \item{\code{A_height}}{height of the woman's partner.} \item{\code{A_edu}}{level of education of the woman's partner, an ordered factor with levels \code{Never attended school} < \code{Elementary school} < \code{Junior high school} < \code{Senior high school} < \code{Junior college} < \code{University}.} \item{\code{A_income}}{montjly income of the woman's partner.} } } \details{ Contemporary China is on the leading edge of a sexual revolution, with tremendous regional and generational differences that provide unparalleled natural experiments for analysis of the antecedents and outcomes of sexual behavior. The Chinese Health and Family Life Study, conducted 1999--2000 as a collaborative research project of the Universities of Chicago, Beijing, and North Carolina, provides a baseline from which to anticipate and track future changes. Specifically, this study produces a baseline set of results on sexual behavior and disease patterns, using a nationally representative probability sample. The Chinese Health and Family Life Survey sampled 60 villages and urban neighborhoods chosen in such a way as to represent the full geographical and socioeconomic range of contemporary China excluding Hong Kong and Tibet. Eighty-three individuals were chosen at random for each location from official registers of adults aged between 20 and 64 years to target a sample of 5000 individuals in total. Here, we restrict our attention to women with current male partners for whom no information was missing, leading to a sample of 1534 women. The data have been extracted as given in the example section. } \source{ \url{https://sscs.uchicago.edu} } \references{ William L. Parish, Edward O. Laumann, Myron S. Cohen, Suiming Pan, Heyi Zheng, Irving Hoffman, Tianfu Wang, and Kwai Hang Ng. (2003), Population-Based Study of Chlamydial Infection in China: A Hidden Epidemic. \emph{Journal of the American Medican Association}, \bold{289}(10), 1265--1273. } \examples{ \dontrun{ ### for a description see http://popcenter.uchicago.edu/data/chfls.shtml library("TH.data") load(file.path(path.package(package="TH.data"), "rda", "CHFLS.rda")) tmp <- chfls1[, c("REGION6", "ZJ05", "ZJ06", "A35", "ZJ07", "ZJ16M", "INCRM", "JK01", "JK02", "JK20", "HY04", "HY07", "A02", "AGEGAPM", "A07M", "A14", "A21", "A22M", "A23", "AX16", "INCAM", "SEXNOW", "ZW04")] names(tmp) <- c("Region", "Rgender", ### gender of respondent "Rage", ### age of respondent "RagestartA", ### age of respondent at beginning of relationship ### with partner A "Redu", ### education of respondent "RincomeM", ### rounded monthly income of respondent "RincomeComp", ### inputed monthly income of respondent "Rhealth", ### health condition respondent "Rheight", ### respondent's height "Rhappy", ### respondent's happiness "Rmartial", ### respondent's marital status "RhasA", ### R has current A partner "Agender", ### gender of partner A "RAagegap", ### age gap "RAstartage", ### age at marriage "Aheight", ### height of partner A "Aedu", ### education of partner A "AincomeM", ### rounded partner A income "AincomeEst", ### estimated partner A income "orgasm", ### orgasm frequency "AincomeComp", ### imputed partner A income "Rsexnow", ### has sex last year "Rhomosexual") ### R is homosexual ### code missing values tmp$AincomeM[tmp$AincomeM < 0] <- NA tmp$RincomeM[tmp$RincomeM < 0] <- NA tmp$Aheight[tmp$Aheight < 0] <- NA olevels <- c("never", "rarely", "sometimes", "often", "always") tmpA <- subset(tmp, Rgender == "female" & Rhomosexual != "yes" & orgasm \%in\% olevels) ### 1534 subjects dim(tmpA) CHFLS <- tmpA[, c("Region", "Rage", "Redu", "RincomeComp", "Rhealth", "Rheight", "Rhappy", "Aheight", "Aedu", "AincomeComp")] names(CHFLS) <- c("R_region", "R_age", "R_edu", "R_income", "R_health", "R_height", "R_happy", "A_height", "A_edu", "A_income") levels(CHFLS$R_region) <- c("Coastal South", "Coastal Easth", "Inlands", "North", "Northeast", "Central West") CHFLS$R_edu <- ordered(as.character(CHFLS$R_edu), levels = c("no school", "primary", "low mid", "up mid", "j col", "univ/grad")) levels(CHFLS$R_edu) <- c("Never attended school", "Elementary school", "Junior high school", "Senior high school", "Junior college", "University") CHFLS$A_edu <- ordered(as.character(CHFLS$A_edu), levels = c("no school", "primary", "low mid", "up mid", "j col", "univ/grad")) levels(CHFLS$A_edu) <- c("Never attended school", "Elementary school", "Junior high school", "Senior high school", "Junior college", "University") CHFLS$R_health <- ordered(as.character(CHFLS$R_health), levels = c("poor", "not good", "fair", "good", "excellent")) levels(CHFLS$R_health) <- c("Poor", "Not good", "Fair", "Good", "Excellent") CHFLS$R_happy <- ordered(as.character(CHFLS$R_happy), levels = c("v unhappy", "not too", "relatively", "very")) levels(CHFLS$R_happy) <- c("Very unhappy", "Not too happy", "Relatively happy", "Very happy") } } \keyword{datasets} HSAUR3/man/smoking.Rd0000644000175000017500000000410712357775401014077 0ustar nileshnilesh\name{smoking} \alias{smoking} \docType{data} \title{ Nicotine Gum and Smoking Cessation } \description{ Data from a meta-analysis on nicotine gum and smoking cessation } \usage{data("smoking")} \format{ A data frame with 26 observations (studies) on the following 4 variables. \describe{ \item{\code{qt}}{the number of treated subjetcs who stopped smoking.} \item{\code{tt}}{the totla number of treated subjects.} \item{\code{qc}}{the number of subjetcs who stopped smoking without being treated.} \item{\code{tc}}{the total number of subject not being treated.} } } \details{ Cigarette smoking is the leading cause of preventable death in the United States and kills more Americans than AIDS, alcohol, illegal drug use, car accidents, fires, murders and suicides combined. It has been estimated that 430,000 Americans die from smoking every year. Fighting tobacco use is, consequently, one of the major public health goals of our time and there are now many programs available designed to help smokers quit. One of the major aids used in these programs is nicotine chewing gum, which acts as a substitute oral activity and provides a source of nicotine that reduces the withdrawal symptoms experienced when smoking is stopped. But separate randomized clinical trials of nicotine gum have been largely inconclusive, leading Silagy (2003) to consider combining the results studies found from an extensive literature search. The results of these trials in terms of numbers of people in the treatment arm and the control arm who stopped smoking for at least 6 months after treatment are given here. } \source{ C. Silagy (2003), Nicotine replacement therapy for smoking cessation (Cochrane Review). \emph{The Cochrane Library}, \bold{4}, John Wiley \& Sons, Chichester. } \examples{ data("smoking", package = "HSAUR3") boxplot(smoking$qt/smoking$tt, smoking$qc/smoking$tc, names = c("Treated", "Control"), ylab = "Percent Quitters") } \keyword{datasets} HSAUR3/man/clouds.Rd0000644000175000017500000000503612357775401013723 0ustar nileshnilesh\name{clouds} \alias{clouds} \docType{data} \title{ Cloud Seeding Data } \description{ Data from an experiment investigating the use of massive amounts of silver iodide (100 to 1000 grams per cloud) in cloud seeding to increase rainfall. } \usage{data("clouds")} \format{ A data frame with 24 observations on the following 7 variables. \describe{ \item{seeding}{a factor indicating whether seeding action occured (\code{no} or \code{yes}).} \item{time}{number of days after the first day of the experiment.} \item{sne}{suitability criterion.} \item{cloudcover}{the percentage cloud cover in the experimental area, measured using radar.} \item{prewetness}{the total rainfall in the target area one hour before seeding (in cubic metres times \code{1e+8}).} \item{echomotion}{a factor showing whether the radar echo was \code{moving} or \code{stationary}.} \item{rainfall}{the amount of rain in cubic metres times \code{1e+8}.} } } \details{ Weather modification, or cloud seeding, is the treatment of individual clouds or storm systems with various inorganic and organic materials in the hope of achieving an increase in rainfall. Introduction of such material into a cloud that contains supercooled water, that is, liquid water colder than zero Celsius, has the aim of inducing freezing, with the consequent ice particles growing at the expense of liquid droplets and becoming heavy enough to fall as rain from clouds that otherwise would produce none. The data available in \code{cloud} were collected in the summer of 1975 from an experiment to investigate the use of massive amounts of silver iodide 100 to 1000 grams per cloud) in cloud seeding to increase rainfall. In the experiment, which was conducted in an area of Florida, 24 days were judged suitable for seeding on the basis that a measured suitability criterion (\code{SNE}). } \source{ W. L. Woodley, J. Simpson, R. Biondini and J. Berkeley (1977), Rainfall results 1970-75: Florida area cumulus experiment. \emph{Science} \bold{195}, 735--742. R. D. Cook and S. Weisberg (1980), Characterizations of an empirical influence function for detecting influential cases in regression. \emph{Technometrics} \bold{22}, 495--508. } \examples{ data("clouds", package = "HSAUR3") layout(matrix(1:2, nrow = 2)) boxplot(rainfall ~ seeding, data = clouds, ylab = "Rainfall") boxplot(rainfall ~ echomotion, data = clouds, ylab = "Rainfall") } \keyword{datasets} HSAUR3/man/skulls.Rd0000644000175000017500000000306312357775401013745 0ustar nileshnilesh\name{skulls} \alias{skulls} \docType{data} \title{ Egyptian Skulls } \description{ Measurements made on Egyptian skulls from five epochs. } \usage{data("skulls")} \format{ A data frame with 150 observations on the following 5 variables. \describe{ \item{\code{epoch}}{the epoch the skull as assigned to, a factor with levels \code{c4000BC} \code{c3300BC}, \code{c1850BC}, \code{c200BC}, and \code{cAD150}, where the years are only given approximately, of course.} \item{\code{mb}}{maximum breaths of the skull.} \item{\code{bh}}{basibregmatic heights of the skull.} \item{\code{bl}}{basialiveolar length of the skull.} \item{\code{nh}}{nasal heights of the skull.} } } \details{ The question is whether the measurements change over time. Non-constant measurements of the skulls over time would indicate interbreeding with immigrant populations. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("skulls", package = "HSAUR3") means <- tapply(1:nrow(skulls), skulls$epoch, function(i) apply(skulls[i,colnames(skulls)[-1]], 2, mean)) means <- matrix(unlist(means), nrow = length(means), byrow = TRUE) colnames(means) <- colnames(skulls)[-1] rownames(means) <- levels(skulls$epoch) pairs(means, panel = function(x, y) { text(x, y, levels(skulls$epoch)) }) } \keyword{datasets} HSAUR3/man/rearrests.Rd0000644000175000017500000000175512357775401014450 0ustar nileshnilesh\name{rearrests} \alias{rearrests} \docType{data} \title{ Rearrests of Juvenile Felons } \description{ Rearrests of juventile felons by type of court in which they were tried. } \usage{data("rearrests")} \format{ A two-way classification, see \code{\link{table}}. } \details{ The data (taken from Agresti, 1996) arise from a sample of juveniles convicted of felony in Florida in 1987. Matched pairs were formed using criteria such as age and the number of previous offences. For each pair, one subject was handled in the juvenile court and the other was transferred to the adult court. Whether or not the juvenile was rearrested by the end of 1988 was then noted. Here the question of interest is whether the true proportions rearrested were identical for the adult and juvenile court assignments? } \source{ A. Agresti (1996). \emph{An Introduction to Categorical Data Analysis}. Wiley, New York. } \examples{ data("rearrests", package = "HSAUR3") rearrests } \keyword{datasets} HSAUR3/man/Smoking_Wassink1945.Rd0000644000175000017500000000143412357775401016061 0ustar nileshnilesh\name{Smoking_Wassink1945} \alias{Smoking_Wassink1945} \docType{data} \title{ Smoking and Lung Cancer (III) } \description{ Number of smokers in a case-control study. } \usage{data(Smoking_Wassink1945)} \format{ The format is: table [1:4, 1:2] 6 18 36 74 19 36 25 20 - attr(*, "dimnames")=List of 2 ..$ Smoking : chr [1:4] "Nonsmoker" "Moderate smoker" "Heavy smoker" "Very heavy smoker" ..$ Diagnosis: chr [1:2] "Lung cancer" "Healthy control" } \source{ W. F. Wassink (1945), Ontstaansvoorwaarden voor Longkanker, \emph{Nederlands Tijdschrift voor Geneeskunde}, \bold{92}, 3732--3747 } \references{ Richard Doll (1998), Uncovering the effects of smoking: historical perspective. \emph{Statistical Methods in Medical Research}, \bold{7}(87), 87-117 } \keyword{datasets} HSAUR3/man/pottery.Rd0000644000175000017500000000206212357775401014134 0ustar nileshnilesh\name{pottery} \alias{pottery} \docType{data} \title{ Romano-British Pottery Data } \description{ Chemical composition of Romano-British pottery. } \usage{data("pottery")} \format{ A data frame with 45 observations on the following 9 chemicals. \describe{ \item{Al2O3}{aluminium trioxide.} \item{Fe2O3}{iron trioxide.} \item{MgO}{magnesium oxide.} \item{CaO}{calcium oxide.} \item{Na2O}{natrium oxide.} \item{K2O}{calium oxide.} \item{TiO2}{titanium oxide.} \item{MnO}{mangan oxide.} \item{BaO}{barium oxide.} \item{kiln}{site at which the pottery was found.} } } \details{ The data gives the chemical composition of specimens of Romano-British pottery, determined by atomic absorption spectrophotometry, for nine oxides. } \source{ A. Tubb and N. J. Parker and G. Nickless (1980), The analysis of Romano-British pottery by atomic absorption spectrophotometry. \emph{Archaeometry}, \bold{22}, 153--171. } \examples{ data("pottery", package = "HSAUR3") plot(pottery) } \keyword{datasets} HSAUR3/man/water.Rd0000644000175000017500000000302212357775401013545 0ustar nileshnilesh\name{water} \alias{water} \docType{data} \title{ Mortality and Water Hardness } \description{ The mortality and drinking water hardness for 61 cities in England and Wales. } \usage{data("water")} \format{ A data frame with 61 observations on the following 4 variables. \describe{ \item{location}{a factor with levels \code{North} and \code{South} indicating whether the town is as north as Derby.} \item{town}{the name of the town.} \item{mortality}{averaged annual mortality per 100.000 male inhabitants.} \item{hardness}{calcium concentration (in parts per million).} } } \details{ The data were collected in an investigation of environmental causes of disease. They show the annual mortality per 100,000 for males, averaged over the years 1958-1964, and the calcium concentration (in parts per million) in the drinking water for 61 large towns in England and Wales. The higher the calcium concentration, the harder the water. Towns at least as far north as Derby are identified in the table. Here there are several questions that might be of interest including, are mortality and water hardness related, and do either or both variables differ between northern and southern towns? } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("water", package = "HSAUR3") plot(mortality ~ hardness, data = water, col = as.numeric(water$location)) } \keyword{datasets} HSAUR3/man/EFT.Rd0000644000175000017500000000111612357775401013043 0ustar nileshnilesh\name{EFT} \alias{EFT} \docType{data} \title{ Embedded Figures Test Data } \description{ Embedded figures test for 24 school children. } \usage{data(EFT)} \format{ A data frame with 24 observations on the following 3 variables. \describe{ \item{\code{group}}{a factor with levels \code{row} \code{corner}} \item{\code{time}}{time to complete the pattern} \item{\code{EFT}}{Embedded Figures Test} } } \source{ M. Aitkin, D. Anderson, B. Francis, and J. Hinde (1989), \emph{Statistical Modelling in GLIM}, Oxford University Press, New York, USA } \keyword{datasets} HSAUR3/man/waves.Rd0000644000175000017500000000245712357775401013563 0ustar nileshnilesh\name{waves} \alias{waves} \docType{data} \title{ Electricity from Wave Power at Sea } \description{ Measurements of root mean square bending moment by two different mooring methods. } \usage{data("waves")} \format{ A data frame with 18 observations on the following 2 variables. \describe{ \item{method1}{Root mean square bending moment in Newton metres, mooring method 1} \item{method2}{Root mean square bending moment in Newton metres, mooring method 2} } } \details{ In a design study for a device to generate electricity from wave power at sea, experiments were carried out on scale models in a wave tank to establish how the choice of mooring method for the system affected the bending stress produced in part of the device. The wave tank could simulate a wide range of sea states and the model system was subjected to the same sample of sea states with each of two mooring methods, one of which was considerably cheaper than the other. The question of interest is whether bending stress differs for the two mooring methods. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("waves", package = "HSAUR3") plot(method1 ~ method2, data = waves) } \keyword{datasets} HSAUR3/man/foster.Rd0000644000175000017500000000212312357775401013726 0ustar nileshnilesh\name{foster} \alias{foster} \docType{data} \title{ Foster Feeding Experiment } \description{ The data are from a foster feeding experiment with rat mothers and litters of four different genotypes. The measurement is the litter weight after a trial feeding period. } \usage{data("foster")} \format{ A data frame with 61 observations on the following 3 variables. \describe{ \item{\code{litgen}}{genotype of the litter, a factor with levels \code{A}, \code{B}, \code{I}, and \code{J}.} \item{\code{motgen}}{genotype of the mother, a factor with levels \code{A}, \code{B}, \code{I}, and \code{J}.} \item{\code{weight}}{the weight of the litter after a feeding period.} } } \details{ Here the interest lies in uncovering the effect of genotype of mother and litter on litter weight. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("foster", package = "HSAUR3") plot.design(foster) } \keyword{datasets} HSAUR3/man/plasma.Rd0000644000175000017500000000360712357775401013711 0ustar nileshnilesh\name{plasma} \alias{plasma} \docType{data} \title{ Blood Screening Data } \description{ The erythrocyte sedimentation rate and measurements of two plasma proteins (fibrinogen and globulin). } \usage{data("plasma")} \format{ A data frame with 32 observations on the following 3 variables. \describe{ \item{\code{fibrinogen}}{the fibrinogen level in the blood.} \item{\code{globulin}}{the globulin level in the blood.} \item{\code{ESR}}{the erythrocyte sedimentation rate, either less or greater 20 mm / hour. } } } \details{ The erythrocyte sedimentation rate (ESR) is the rate at which red blood cells (erythrocytes) settle out of suspension in blood plasma, when measured under standard conditions. If the ESR increases when the level of certain proteins in the blood plasma rise in association with conditions such as rheumatic diseases, chronic infections and malignant diseases, its determination might be useful in screening blood samples taken form people suspected to being suffering from one of the conditions mentioned. The absolute value of the ESR is not of great importance rather it is whether it is less than 20mm/hr since lower values indicate a healthy individual. The question of interest is whether there is any association between the probability of an ESR reading greater than 20mm/hr and the levels of the two plasma proteins. If there is not then the determination of ESR would not be useful for diagnostic purposes. } \source{ D. Collett and A. A. Jemain (1985), Residuals, outliers and influential observations in regression analysis. \emph{Sains Malaysiana}, \bold{4}, 493--511. } \examples{ data("plasma", package = "HSAUR3") layout(matrix(1:2, ncol = 2)) boxplot(fibrinogen ~ ESR, data = plasma, varwidth = TRUE) boxplot(globulin ~ ESR, data = plasma, varwidth = TRUE) } \keyword{datasets} HSAUR3/man/schizophrenia2.Rd0000644000175000017500000000306412357775401015361 0ustar nileshnilesh\name{schizophrenia2} \alias{schizophrenia2} \docType{data} \title{ Schizophrenia Data } \description{ Though disorder and early onset of schizophrenia. } \usage{data("schizophrenia2")} \format{ A data frame with 220 observations on the following 4 variables. \describe{ \item{\code{subject}}{the patient ID, a factor with levels \code{1} to \code{44}.} \item{\code{onset}}{the time of onset of the disease, a factor with levels \code{< 20 yrs} and \code{> 20 yrs}.} \item{\code{disorder}}{whether thought disorder was \code{absent} or \code{present}, the response variable.} \item{\code{month}}{month after hospitalisation.} } } \details{ The data were collected in a follow-up study of women patients with schizophrenia. The binary response recorded at 0, 2, 6, 8 and 10 months after hospitalisation was thought disorder (absent or present). The single covariate is the factor indicating whether a patient had suffered early or late onset of her condition (age of onset less than 20 years or age of onset 20 years or above). The question of interest is whether the course of the illness differs between patients with early and late onset? } \source{ Davis (2002), \emph{Statistical Methods for the Analysis of Repeated Measurements}, Springer, New York. } \examples{ data("schizophrenia2", package = "HSAUR3") mosaicplot(xtabs( ~ onset + month + disorder, data = schizophrenia2)) } \keyword{datasets} HSAUR3/man/pistonrings.Rd0000644000175000017500000000164012357775401015006 0ustar nileshnilesh\name{pistonrings} \alias{pistonrings} \docType{data} \title{ Piston Rings Failures } \description{ Number of failures of piston rings in three legs of four steam-driven compressors. } \usage{data("pistonrings")} \format{ A two-way classification, see \code{\link{table}}. } \details{ The data are given in form of a \code{\link{table}}. The table gives the number of piston-ring failures in each of three legs of four steam-driven compressors located in the same building. The compressors have identical design and are oriented in the same way. The question of interest is whether the two classification variables (compressor and leg) are independent. } \source{ S. J. Haberman (1973), The analysis of residuals in cross-classificed tables. \emph{Biometrics} \bold{29}, 205--220. } \examples{ data("pistonrings", package = "HSAUR3") mosaicplot(pistonrings) } \keyword{datasets} HSAUR3/man/USstates.Rd0000644000175000017500000000144612357775401014206 0ustar nileshnilesh\name{USstates} \alias{USstates} \docType{data} \title{ US States } \description{ Socio-demographic variables for ten US states. } \usage{data(USstates)} \format{ A data frame with 10 observations on the following 7 variables. \describe{ \item{\code{Population}}{population size divided by 1000} \item{\code{Income}}{average per capita income} \item{\code{Illiteracy}}{illiteracy rate (per cent population)} \item{\code{Life.Expectancy}}{life expectancy (years)} \item{\code{Homicide}}{homicide rate (per 1000)} \item{\code{Graduates}}{percentage of high school graduates} \item{\code{Freezing}}{average number of days per below freezing} } } \details{ The data set contains values of seven socio-demographic variables for ten states in the USA. } \keyword{datasets} HSAUR3/man/gardenflowers.Rd0000644000175000017500000000112612357775401015270 0ustar nileshnilesh\name{gardenflowers} \alias{gardenflowers} \docType{data} \title{ Garden Flowers Data} \description{ The dissimilarity matrix of 18 species of garden flowers. } \usage{data("gardenflowers")} \format{ An object of class \code{\link{dist}}. } \details{ The dissimilarity was computed based on certain characteristics of the flowers. } \source{ L. Kaufman and P. J. Rousseeuw (1990), \emph{Finding groups in data: an introduction to cluster analysis}, John Wiley \& Sons, New York. } \examples{ data("gardenflowers", package = "HSAUR3") gardenflowers } \keyword{datasets} HSAUR3/man/CYGOB1.Rd0000644000175000017500000000222312357775401013351 0ustar nileshnilesh\name{CYGOB1} \alias{CYGOB1} \docType{data} \title{ CYG OB1 Star Cluster Data } \description{ Energy output and surface termperature for Star Cluster CYG OB1. } \usage{data("CYGOB1")} \format{ A data frame with 47 observations on the following 2 variables. \describe{ \item{\code{logst}}{log survface termperature of the star.} \item{\code{logli}}{log light intensity of the star.} } } \details{ The Hertzsprung-Russell (H-R) diagram forms the basis of the theory of stellar evolution. The diagram is essentially a plot of the energy output of stars plotted against their surface temperature. Data from the H-R diagram of Star Cluster CYG OB1, calibrated according to VanismaGreve1972 are given here. } \source{ F. Vanisma and J. P. De Greve (1972), Close binary systems before and after mass transfer. \emph{Astrophysics and Space Science}, \bold{87}, 377--401. D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("CYGOB1", package = "HSAUR3") plot(logst ~ logli, data = CYGOB1) } \keyword{datasets} HSAUR3/man/polyps.Rd0000644000175000017500000000330712357775401013757 0ustar nileshnilesh\name{polyps} \alias{polyps} \docType{data} \title{ Familial Andenomatous Polyposis } \description{ Data from a placebo-controlled trial of a non-steroidal anti-inflammatory drug in the treatment of familial andenomatous polyposis (FAP). } \usage{data("polyps")} \format{ A data frame with 20 observations on the following 3 variables. \describe{ \item{\code{number}}{number of colonic polyps at 12 months.} \item{\code{treat}}{treatment arms of the trail, a factor with levels \code{placebo} and \code{drug}.} \item{\code{age}}{the age of the patient.} } } \details{ Giardiello et al. (1993) and Piantadosi (1997) describe the results of a placebo-controlled trial of a non-steroidal anti-inflammatory drug in the treatment of familial andenomatous polyposis (FAP). The trial was halted after a planned interim analysis had suggested compelling evidence in favour of the treatment. Here we are interested in assessing whether the number of colonic polyps at 12 months is related to treatment and age of patient. } \source{ F. M. Giardiello, S. R. Hamilton, A. J. Krush, S. Piantadosi, L. M. Hylind, P. Celano, S. V. Booker, C. R. Robinson and G. J. A. Offerhaus (1993), Treatment of colonic and rectal adenomas with sulindac in familial adenomatous polyposis. \emph{New England Journal of Medicine}, \bold{328}(18), 1313--1316. S. Piantadosi (1997), \emph{Clinical Trials: A Methodologic Perspective}. John Wiley \& Sons, New York. } \examples{ data("polyps", package = "HSAUR3") plot(number ~ age, data = polyps, pch = as.numeric(polyps$treat)) legend(40, 40, legend = levels(polyps$treat), pch = 1:2, bty = "n") } \keyword{datasets} HSAUR3/man/voting.Rd0000644000175000017500000000177512357775401013746 0ustar nileshnilesh\name{voting} \alias{voting} \docType{data} \title{ House of Representatives Voting Data } \description{ Voting results for 15 congressmen from New Jersey. } \usage{data("voting")} \format{ A 15 times 15 matrix. } \details{ Romesburg (1984) gives a set of data that shows the number of times 15 congressmen from New Jersey voted differently in the House of Representatives on 19 environmental bills. Abstentions are not recorded. } \source{ H. C. Romesburg (1984), \emph{Cluster Analysis for Researchers}. Lifetime Learning Publications, Belmont, Canada. } \examples{ data("voting", package = "HSAUR3") require("MASS") voting_mds <- isoMDS(voting) plot(voting_mds$points[,1], voting_mds$points[,2], type = "n", xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(voting_mds$points[,1])*1.2) text(voting_mds$points[,1], voting_mds$points[,2], labels = colnames(voting)) voting_sh <- Shepard(voting[lower.tri(voting)], voting_mds$points) } \keyword{datasets} HSAUR3/man/Smoking_DollHill1950.Rd0000644000175000017500000000154412357775401016143 0ustar nileshnilesh\name{Smoking_DollHill1950} \alias{Smoking_DollHill1950} \docType{data} \title{ Smoking and Lung Cancer (IV) } \description{ Number of smokers in a case-control study. } \usage{data(Smoking_DollHill1950)} \format{ The format is: table [1:6, 1:2, 1:2] 2 33 250 196 136 32 27 55 293 190 ... - attr(*, "dimnames")=List of 3 ..$ Smoking : chr [1:6] "Nonsmoker" "1-" "5-" "15-" ... ..$ Diagnosis: chr [1:2] "Lung cancer" "Other" ..$ Sex : chr [1:2] "Male" "Female" } \details{ This is Table V from Doll and Hill (1950). } \source{ Richard Doll and A. Bradford Hill (1950), Smoking and Carcinoma of the Lung, \emph{British Medical Journal}, \bold{2}, 739-748 } \references{ Richard Doll (1998), Uncovering the effects of smoking: historical perspective. \emph{Statistical Methods in Medical Research}, \bold{7}(87), 87-117 } \keyword{datasets} HSAUR3/man/watervoles.Rd0000644000175000017500000000265612357775401014632 0ustar nileshnilesh\name{watervoles} \alias{watervoles} \docType{data} \title{ Water Voles Data } \description{ Percentage incidence of the 13 characteristics of water voles in 14 areas. } \usage{data("watervoles")} \format{ A dissimilarity matrix for the following 14 variables, i.e, areas: \code{Surrey}, \code{Shropshire}, \code{Yorkshire}, \code{Perthshire}, \code{Aberdeen}, \code{Elean Gamhna}, \code{Alps}, \code{Yugoslavia}, \code{Germany}, \code{Norway}, \code{Pyrenees I}, \code{Pyrenees II}, \code{North Spain}, and \code{South Spain}. } \details{ Corbet et al. (1970) report a study of water voles (genus Arvicola) in which the aim was to compare British populations of these animals with those in Europe, to investigate whether more than one species might be present in Britain. The original data consisted of observations of the presence or absence of 13 characteristics in about 300 water vole skulls arising from six British populations and eight populations from the rest of Europe. The data are the percentage incidence of the 13 characteristics in each of the 14 samples of water vole skulls. } \source{ G. B. Corbet, J. Cummins, S. R. Hedges, W. J. Krzanowski (1970), The taxonomic structure of British water voles, genus \emph{Arvicola}. \emph{Journal of Zoology}, \bold{61}, 301--316. } \examples{ data("watervoles", package = "HSAUR3") watervoles } \keyword{datasets} HSAUR3/man/mastectomy.Rd0000644000175000017500000000163612357775401014621 0ustar nileshnilesh\name{mastectomy} \alias{mastectomy} \docType{data} \title{ Survival Times after Mastectomy of Breast Cancer Patients } \description{ Survival times in months after mastectomy of women with breast cancer. The cancers are classified as having metastized or not based on a histochemical marker. } \usage{data("mastectomy")} \format{ A data frame with 42 observations on the following 3 variables. \describe{ \item{time}{survival times in months.} \item{event}{a logical indicating if the event was observed (\code{TRUE}) or if the survival time was censored (\code{FALSE}).} \item{metastasized}{a factor at levels \code{yes} and \code{no}.} } } \source{ B. S. Everitt and S. Rabe-Hesketh (2001), \emph{Analysing Medical Data using S-PLUS}, Springer, New York, USA. } \examples{ data("mastectomy", package = "HSAUR3") table(mastectomy$metastasized) } \keyword{datasets} HSAUR3/man/students.Rd0000644000175000017500000000231212357775401014275 0ustar nileshnilesh\name{students} \alias{students} \docType{data} \title{ Student Risk Taking } \description{ Students were administered two parallel forms of a test after a random assignment to three different treatments. } \usage{data("students")} \format{ A data frame with 35 observations on the following 3 variables. \describe{ \item{\code{treatment}}{a factor with levels \code{AA}, \code{C}, and \code{NC}.} \item{\code{low}}{the result of the first test.} \item{\code{high}}{the result of the second test.} } } \details{ The data arise from a large study of risk taking (Timm, 2002). Students were randomly assigned to three different treatments labelled AA, C and NC. Students were administered two parallel forms of a test called \code{low} and \code{high}. The aim is to carry out a test of the equality of the bivariate means of each treatment population. } \source{ N. H. Timm (2002), \emph{Applied Multivariate Analysis}. Springer, New York. } \examples{ data("students", package = "HSAUR3") layout(matrix(1:2, ncol = 2)) boxplot(low ~ treatment, data = students, ylab = "low") boxplot(high ~ treatment, data = students, ylab = "high") } \keyword{datasets} HSAUR3/man/suicides.Rd0000644000175000017500000000120612357775401014235 0ustar nileshnilesh\name{suicides} \alias{suicides} \docType{data} \title{ Crowd Baiting Behaviour and Suicides } \description{ Data from a study carried out to investigate the causes of jeering or baiting behaviour by a crowd when a person is threatening to commit suicide by jumping from a high building. } \usage{data("suicides")} \format{ A two-way classification, see \code{\link{table}}. } \source{ L. Mann (1981), The baiting crowd in episodes of threatened suicide. \emph{Journal of Personality and Social Psychology}, \bold{41}, 703--709. } \examples{ data("suicides", package = "HSAUR3") mosaicplot(suicides) } \keyword{datasets} HSAUR3/man/birthdeathrates.Rd0000644000175000017500000000107212357775401015603 0ustar nileshnilesh\name{birthdeathrates} \alias{birthdeathrates} \docType{data} \title{ Birth and Death Rates Data } \description{ Birth and death rates for 69 countries. } \usage{data("birthdeathrates")} \format{ A data frame with 69 observations on the following 2 variables. \describe{ \item{\code{birth}}{birth rate.} \item{\code{death}}{death rate.} } } \source{ J. A. Hartigan (1975), \emph{Clustering Algorithms}. John Wiley & Sons, New York. } \examples{ data("birthdeathrates", package = "HSAUR3") plot(birthdeathrates) } \keyword{datasets} HSAUR3/man/Forbes2000.Rd0000644000175000017500000000224713732061231014140 0ustar nileshnilesh\name{Forbes2000} \alias{Forbes2000} \docType{data} \title{ The Forbes 2000 Ranking of the World's Biggest Companies (Year 2004) } \description{ The Forbes 2000 list is a ranking of the world's biggest companies, measured by sales, profits, assets and market value. } \usage{data("Forbes2000")} \format{ A data frame with 2000 observations on the following 8 variables. \describe{ \item{rank}{the ranking of the company.} \item{name}{the name of the company.} \item{country}{a factor giving the country the company is situated in.} \item{category}{a factor describing the products the company produces.} \item{sales}{the amount of sales of the company in billion USD.} \item{profits}{the profit of the company in billion USD.} \item{assets}{the assets of the company in billion USD.} \item{marketvalue}{the market value of the company in billion USD.} } } \source{ \url{https://www.forbes.com}, assessed on November 26th, 2004. } \examples{ data("Forbes2000", package = "HSAUR3") summary(Forbes2000) ### number of countries length(levels(Forbes2000$country)) ### number of industries length(levels(Forbes2000$category)) } \keyword{datasets} HSAUR3/man/schooldays.Rd0000644000175000017500000000346012357775401014601 0ustar nileshnilesh\name{schooldays} \alias{schooldays} \docType{data} \title{ Days not Spent at School } \description{ Data from a sociological study, the number of days absent from school is the response variable. } \usage{data("schooldays")} \format{ A data frame with 154 observations on the following 5 variables. \describe{ \item{\code{race}}{race of the child, a factor with levels \code{aboriginal} and \code{non-aboriginal}.} \item{\code{gender}}{the gender of the child, a factor with levels \code{female} and \code{male}.} \item{\code{school}}{the school type, a factor with levels \code{F0} (primary), \code{F1} (first), \code{F2} (second) and \code{F3} (third form).} \item{\code{learner}}{how good is the child in learning things, a factor with levels \code{average} and \code{slow}.} \item{\code{absent}}{number of days absent from school.} } } \details{ The data arise from a sociological study of Australian Aboriginal and white children reported by Quine (1975). In this study, children of both sexes from four age groups (final grade in primary schools and first, second and third form in secondary school) and from two cultural groups were used. The children in age group were classified as slow or average learners. The response variable was the number of days absent from school during the school year. (Children who had suffered a serious illness during the years were excluded.) } \source{ S. Quine (1975), Achievement Orientation of Aboriginal and White Adolescents. Doctoral Dissertation, Australian National University, Canberra. } \examples{ data("schooldays", package = "HSAUR3") plot.design(schooldays) } \keyword{datasets} HSAUR3/man/Lanza.Rd0000644000175000017500000000474612357775401013506 0ustar nileshnilesh\name{Lanza} \alias{Lanza} \docType{data} \title{ Prevention of Gastointestinal Damages } \description{ Data from four randomised clinical trials on the prevention of gastointestinal damages by Misoprostol reported by Lanza et al. (1987, 1988a,b, 1989). } \usage{data("Lanza")} \format{ A data frame with 198 observations on the following 3 variables. \describe{ \item{\code{study}}{a factor with levels \code{I}, \code{II}, \code{III}, and \code{IV} describing the study number.} \item{\code{treatment}}{a factor with levels \code{Misoprostol} \code{Placebo}} \item{\code{classification}}{an ordered factor with levels \code{1} < \code{2} < \code{3} < \code{4} < \code{5} describing an ordered response variable.} } } \details{ The response variable is defined by the number of haemorrhages or erosions. } \source{ F. L. Lanza (1987), A double-blind study of prophylactic effect of misoprostol on lesions of gastric and duodenal mucosa induced by oral administration of tolmetin in healthy subjects. \emph{British Journal of Clinical Practice}, May suppl, 91--101. F. L. Lanza, R. L. Aspinall, E. A. Swabb, R. E. Davis, M. F. Rack, A. Rubin (1988a), Double-blind, placebo-controlled endoscopic comparison of the mucosal protective effects of misoprostol versus cimetidine on tolmetin-induced mucosal injury to the stomach and duodenum. \emph{Gastroenterology}, \bold{95}(2), 289--294. F. L. Lanza, K. Peace, L. Gustitus, M. F. Rack, B. Dickson (1988b), A blinded endoscopic comparative study of misoprostol versus sucralfate and placebo in the prevention of aspirin-induced gastric and duodenal ulceration. \emph{American Journal of Gastroenterology}, \bold{83}(2), 143--146. F. L. Lanza, D. Fakouhi, A. Rubin, R. E. Davis, M. F. Rack, C. Nissen, S. Geis (1989), A double-blind placebo-controlled comparison of the efficacy and safety of 50, 100, and 200 micrograms of misoprostol QID in the prevention of ibuprofen-induced gastric and duodenal mucosal lesions and symptoms. \emph{American Journal of Gastroenterology}, \bold{84}(6), 633--636. } \examples{ data("Lanza", package = "HSAUR3") layout(matrix(1:4, nrow = 2)) pl <- tapply(1:nrow(Lanza), Lanza$study, function(indx) mosaicplot(table(Lanza[indx,"treatment"], Lanza[indx,"classification"]), main = "", shade = TRUE)) } \keyword{datasets} HSAUR3/man/planets.Rd0000644000175000017500000000243012357775401014073 0ustar nileshnilesh\name{planets} \alias{planets} \docType{data} \title{ Exoplanets Data } \description{ Data on planets outside the Solar System. } \usage{data("planets")} \format{ A data frame with 101 observations from 101 exoplanets on the following 3 variables. \describe{ \item{mass}{Jupiter mass of the planet.} \item{period}{period in earth days.} \item{eccen}{the radial eccentricity of the planet.} } } \details{ From the properties of the exoplanets found up to now it appears that the theory of planetary development constructed for the planets of the Solar System may need to be reformulated. The exoplanets are not at all like the nine local planets that we know so well. A first step in the process of understanding the exoplanets might be to try to classify them with respect to their known properties. } \source{ M. Mayor and P. Frei (2003). \emph{New Worlds in the Cosmos: The Discovery of Exoplanets}. Cambridge University Press, Cambridge, UK. } \examples{ data("planets", package = "HSAUR3") require("scatterplot3d") scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen), type = "h", highlight.3d = TRUE, angle = 55, scale.y = 0.7, pch = 16) } \keyword{datasets} HSAUR3/man/HSAURtable.Rd0000644000175000017500000000414712357775401014326 0ustar nileshnilesh\name{HSAURtable} \alias{HSAURtable} \alias{toLatex.tabtab} \alias{toLatex.dftab} \alias{HSAURtable.table} \alias{HSAURtable.data.frame} \title{ Produce LaTeX Tables } \description{ Generate \code{longtable} LaTeX environments. } \usage{ HSAURtable(object, ...) \method{HSAURtable}{table}(object, xname = deparse(substitute(object)), pkg = NULL, ...) \method{HSAURtable}{data.frame}(object, xname = deparse(substitute(object)), pkg = NULL, nrows = NULL, ...) \method{toLatex}{tabtab}(object, caption = NULL, label = NULL, topcaption = TRUE, index = TRUE, ...) \method{toLatex}{dftab}(object, pcol = 1, caption = NULL, label = NULL, rownames = FALSE, topcaption = TRUE, index = TRUE, ...) } \arguments{ \item{object}{ an object of \code{table} or \code{data.frame}. } \item{xname}{ the name of the object. } \item{pkg}{ the package \code{object} comes from, optionally. } \item{nrows}{ the number of rows actually printed for a \code{data.frame}.} \item{caption}{ the (optional) caption of the table without label. } \item{label}{ the (optional) label to be defined for this table. } \item{pcol}{ the number of parallel columns. } \item{rownames}{ logical, should the rownames be printed in the first row without column name? } \item{topcaption}{ logical, should the captions be placed on top (default) of the table?} \item{index}{ logical, should an index entry be generated?} \item{\dots}{ additional arguments, currently ignored. } } \details{ Based on the data in \code{object}, an object from which a Latex table (in a \code{longtable} environment) may be constructed (via \code{\link[utils]{toLatex}}) is generated. } \value{ An object of class \code{tabtab} or \code{dftab} for which \code{\link[utils]{toLatex}} methods are available. \code{toLatex} produces objects of class \code{Latex}, a character vector, essentially. } \examples{ data("rearrests", package = "HSAUR3") toLatex(HSAURtable(rearrests), caption = "Rearrests of juvenile felons.", label = "rearrests_tab") } \keyword{misc} HSAUR3/man/heptathlon.Rd0000644000175000017500000000361412357775401014600 0ustar nileshnilesh\name{heptathlon} \alias{heptathlon} \docType{data} \title{ Olympic Heptathlon Seoul 1988 } \description{ Results of the olympic heptathlon competition, Seoul, 1988. } \usage{data("heptathlon")} \format{ A data frame with 25 observations on the following 8 variables. \describe{ \item{\code{hurdles}}{results 100m hurdles.} \item{\code{highjump}}{results high jump.} \item{\code{shot}}{results shot.} \item{\code{run200m}}{results 200m race.} \item{\code{longjump}}{results long jump.} \item{\code{javelin}}{results javelin.} \item{\code{run800m}}{results 800m race.} \item{\code{score}}{total score.} } } \details{ The first combined Olympic event for women was the pentathlon, first held in Germany in 1928. Initially this consisted of the shot putt, long jump, 100m, high jump and javelin events held over two days. The pentathlon was first introduced into the Olympic Games in 1964, when it consisted of the 80m hurdles, shot, high jump, long jump and 200m. In 1977 the 200m was replaced by the 800m and from 1981 the IAAF brought in the seven-event heptathlon in place of the pentathlon, with day one containing the events-100m hurdles, shot, high jump, 200m and day two, the long jump, javelin and 800m. A scoring system is used to assign points to the results from each event and the winner is the woman who accumulates the most points over the two days. The event made its first Olympic appearance in 1984. In the 1988 Olympics held in Seoul, the heptathlon was won by one of the stars of women's athletics in the USA, Jackie Joyner-Kersee. The results for all 25 competitors are given here. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("heptathlon", package = "HSAUR3") plot(heptathlon) } \keyword{datasets} HSAUR3/man/respiratory.Rd0000644000175000017500000000414212357775401015012 0ustar nileshnilesh\name{respiratory} \alias{respiratory} \docType{data} \title{ Respiratory Illness Data } \description{ The respiratory status of patients recruited for a randomised clinical multicenter trial. } \usage{data("respiratory")} \format{ A data frame with 555 observations on the following 7 variables. \describe{ \item{\code{centre}}{the study center, a factor with levels \code{1} and \code{2}.} \item{\code{treatment}}{the treatment arm, a factor with levels \code{placebo} and \code{treatment}.} \item{\code{gender}}{a factor with levels \code{female} and \code{male}.} \item{\code{age}}{the age of the patient.} \item{\code{status}}{the respiratory status (response variable), a factor with levels \code{poor} and \code{good}.} \item{\code{month}}{the month, each patient was examined at months \code{0}, \code{1}, \code{2}, \code{3} and \code{4}.} \item{\code{subject}}{the patient ID, a factor with levels \code{1} to \code{111}.} } } \details{ In each of two centres, eligible patients were randomly assigned to active treatment or placebo. During the treatment, the respiratory status (categorised \code{poor} or \code{good}) was determined at each of four, monthly visits. The trial recruited 111 participants (54 in the active group, 57 in the placebo group) and there were no missing data for either the responses or the covariates. The question of interest is to assess whether the treatment is effective and to estimate its effect. Note that the data are in long form, i.e, repeated measurments are stored as additional rows in the data frame. } \source{ C. S. Davis (1991), Semi-parametric and non-parametric methods for the analysis of repeated measurements with applications to clinical trials. \emph{Statistics in Medicine}, \bold{10}, 1959--1980. } \examples{ data("respiratory", package = "HSAUR3") mosaicplot(xtabs( ~ treatment + month + status, data = respiratory)) } \keyword{datasets} HSAUR3/man/meteo.Rd0000644000175000017500000000207212357775401013540 0ustar nileshnilesh\name{meteo} \alias{meteo} \docType{data} \title{ Meteorological Measurements for 11 Years } \description{ Several meteorological measurements for a period between 1920 and 1931. } \usage{data("meteo")} \format{ A data frame with 11 observations on the following 6 variables. \describe{ \item{\code{year}}{the years.} \item{\code{rainNovDec}}{rainfall in November and December (mm).} \item{\code{temp}}{average July temperature.} \item{\code{rainJuly}}{rainfall in July (mm).} \item{\code{radiation}}{radiation in July (millilitres of alcohol).} \item{\code{yield}}{average harvest yield (quintals per hectare).} } } \details{ Carry out a principal components analysis of both the covariance matrix and the correlation matrix of the data and compare the results. Which set of components leads to the most meaningful interpretation? } \source{ B. S. Everitt and G. Dunn (2001), \emph{Applied Multivariate Data Analysis}, 2nd edition, Arnold, London. } \examples{ data("meteo", package = "HSAUR3") meteo } \keyword{datasets} HSAUR3/man/GHQ.Rd0000644000175000017500000000237612357775401013055 0ustar nileshnilesh\name{GHQ} \alias{GHQ} \docType{data} \title{ General Health Questionnaire } \description{ Data from an psychiatric screening questionnaire } \usage{data("GHQ")} \format{ A data frame with 22 observations on the following 4 variables. \describe{ \item{\code{GHQ}}{the General Health Questionnaire score.} \item{\code{gender}}{a factor with levels \code{female} and \code{male}} \item{\code{cases}}{the number of diseased subjects.} \item{\code{non.cases}}{the number of healthy subjects.} } } \details{ The data arise from a study of a psychiatric screening questionnaire called the GHQ (General Health Questionnaire, see Goldberg, 1972). Here the main question of interest is to see how caseness is related to gender and GHQ score. } \source{ D. Goldberg (1972). \emph{The Detection of Psychiatric Illness by Questionnaire}, Oxford University Press, Oxford, UK. } \examples{ data("GHQ", package = "HSAUR3") male <- subset(GHQ, gender == "male") female <- subset(GHQ, gender == "female") layout(matrix(1:2, ncol = 2)) barplot(t(as.matrix(male[,c("cases", "non.cases")])), main = "Male", xlab = "GHC score") barplot(t(as.matrix(male[,c("cases", "non.cases")])), main = "Female", xlab = "GHC score") } \keyword{datasets} HSAUR3/man/household.Rd0000644000175000017500000000202512357775401014417 0ustar nileshnilesh\name{household} \alias{household} \docType{data} \title{ Household Expenditure Data } \description{ Survey data on household expenditure on four commodity groups. } \usage{data("household")} \format{ A data frame with 40 observations on the following 5 variables. \describe{ \item{\code{housing}}{expenditure on housing, including fuel and light.} \item{\code{food}}{expenditure on foodstuffs, including alcohol and tobacco.} \item{\code{goods}}{expenditure on other goods, including clothing, footwear and durable goods.} \item{\code{service}}{expenditure on services, including transport and vehicles.} \item{\code{gender}}{a factor with levels \code{female} and \code{male}} } } \details{ The data are part of a data set collected from a survey of household expenditure and give the expenditure of 20 single men and 20 single women on four commodity groups. The units of expenditure are Hong Kong dollars, } \source{ FIXME } \examples{ data("household", package = "HSAUR3") } \keyword{datasets} HSAUR3/man/phosphate.Rd0000644000175000017500000000205212357775401014420 0ustar nileshnilesh\name{phosphate} \alias{phosphate} \docType{data} \title{ Phosphate Level Data } \description{ Plasma inorganic phosphate levels from 33 subjects. } \usage{data("phosphate")} \format{ A data frame with 33 observations on the following 9 variables. \describe{ \item{\code{group}}{a factor with levels \code{control} and \code{obese}.} \item{\code{t0}}{baseline phosphate level}, \item{\code{t0.5}}{phosphate level after 1/2 an hour.} \item{\code{t1}}{phosphate level after one an hour.} \item{\code{t1.5}}{phosphate level after 1 1/2 hours.} \item{\code{t2}}{phosphate level after two hours.} \item{\code{t3}}{phosphate level after three hours.} \item{\code{t4}}{phosphate level after four hours.} \item{\code{t5}}{phosphate level after five hours.} } } \source{ C. S. Davis (2002), \emph{Statistical Methods for the Analysis of Repeated Measurements}, Springer, New York. } \examples{ data("phosphate", package = "HSAUR3") plot(t0 ~ group, data = phosphate) } \keyword{datasets} HSAUR3/man/schizophrenia.Rd0000644000175000017500000000245512357775401015302 0ustar nileshnilesh\name{schizophrenia} \alias{schizophrenia} \docType{data} \title{ Age of Onset of Schizophrenia Data } \description{ Data on sex differences in the age of onset of schizophrenia. } \usage{data("schizophrenia")} \format{ A data frame with 251 observations on the following 2 variables. \describe{ \item{\code{age}}{age at the time of diagnosis.} \item{\code{gender}}{a factor with levels \code{female} and \code{male}} } } \details{ A sex difference in the age of onset of schizophrenia was noted by Kraepelin (1919). Subsequently epidemiological studies of the disorder have consistently shown an earlier onset in men than in women. One model that has been suggested to explain this observed difference is know as the subtype model which postulates two type of schizophrenia, one characterised by early onset, typical symptoms and poor premorbid competence, and the other by late onset, atypical symptoms, and good premorbid competence. The early onset type is assumed to be largely a disorder of men and the late onset largely a disorder of women. } \source{ E. Kraepelin (1919), \emph{Dementia Praecox and Paraphrenia}. Livingstone, Edinburgh. } \examples{ data("schizophrenia", package = "HSAUR3") boxplot(age ~ gender, data = schizophrenia) } \keyword{datasets} HSAUR3/man/agefat.Rd0000644000175000017500000000220012357775401013647 0ustar nileshnilesh\name{agefat} \alias{agefat} \docType{data} \title{ Total Body Composision Data } \description{ Age and body fat percentage of 25 normal adults. } \usage{data("agefat")} \format{ A data frame with 25 observations on the following 3 variables. \describe{ \item{\code{age}}{the age of the subject.} \item{\code{fat}}{the body fat percentage.} \item{\code{gender}}{a factor with levels \code{female} and \code{male}.} } } \details{ The data come from a study investigating a new methods of measuring body composition (see Mazess et al, 1984), and give the body fat percentage (percent fat), age and gender for 25 normal adults aged between 23 and 61 years. The questions of interest are how are age and percent fat related, and is there any evidence that the relationship is different for males and females. } \source{ R. B. Mazess, W. W. Peppler and M. Gibbons (1984), Total body composition by dual-photon (153Gd) absorptiometry. \emph{American Journal of Clinical Nutrition}, \bold{40}, 834--839. } \examples{ data("agefat", package = "HSAUR3") plot(fat ~ age, data = agefat) } \keyword{datasets} HSAUR3/man/birds.Rd0000644000175000017500000000150212357775401013527 0ustar nileshnilesh\name{birds} \alias{birds} \docType{data} \title{ Birds in Paramo Vegetation Data } \description{ The data were originally derived from a study which investigated numbers of bird species in isolated islands of paramo vegetation in the northern Andes. } \usage{data(birds)} \format{ A data frame with 14 observations on the following 5 variables. \describe{ \item{\code{N}}{number of species} \item{\code{AR}}{area of island in thousands of square km} \item{\code{EL}}{elevation in thousands of m} \item{\code{Dec}}{distance from Ecuador in km} \item{\code{DNI}}{distance to the nearest island in km} } } \source{ F. Vuilleumier (1970), Insular biogeography in continental regions. I. The northern Andes of South America. \emph{The American Naturalist} \bold{104}, 373--388 } \keyword{datasets} HSAUR3/man/epilepsy.Rd0000644000175000017500000000350712357775401014265 0ustar nileshnilesh\name{epilepsy} \alias{epilepsy} \docType{data} \title{ Epilepsy Data } \description{ A randomised clinical trial investigating the effect of an anti-epileptic drug. } \usage{data("epilepsy")} \format{ A data frame with 236 observations on the following 6 variables. \describe{ \item{\code{treatment}}{the treatment group, a factor with levels \code{placebo} and \code{Progabide}.} \item{\code{base}}{the number of seizures before the trial.} \item{\code{age}}{the age of the patient.} \item{\code{seizure.rate}}{the number of seizures (response variable).} \item{\code{period}}{treatment period, an ordered factor with levels \code{1} to \code{4}.} \item{\code{subject}}{the patient ID, a factor with levels \code{1} to \code{59}.} } } \details{ In this clinical trial, 59 patients suffering from epilepsy were randomized to groups receiving either the anti-epileptic drug Progabide or a placebo in addition to standard chemotherapy. The numbers of seizures suffered in each of four, two-week periods were recorded for each patient along with a baseline seizure count for the 8 weeks prior to being randomized to treatment and age. The main question of interest is whether taking progabide reduced the number of epileptic seizures compared with placebo. } \source{ P. F. Thall and S. C. Vail (1990), Some covariance models for longitudinal count data with overdispersion. \emph{Biometrics}, \bold{46}, 657--671. } \examples{ data("epilepsy", package = "HSAUR3") library(lattice) dotplot(I(seizure.rate / base) ~ period | subject, data = epilepsy, subset = treatment == "Progabide") dotplot(I(seizure.rate / base) ~ period | subject, data = epilepsy, subset = treatment == "Progabide") } \keyword{datasets} HSAUR3/man/backpain.Rd0000644000175000017500000000322512357775401014200 0ustar nileshnilesh\name{backpain} \alias{backpain} \docType{data} \title{ Driving and Back Pain Data} \description{ A case-control study to investigate whether driving a car is a risk factor for low back pain resulting from acute herniated lumbar intervertebral discs (AHLID). } \usage{data("backpain")} \format{ A data frame with 434 observations on the following 4 variables. \describe{ \item{\code{ID}}{a factor which identifies matched pairs.} \item{\code{status}}{a factor with levels \code{case} and \code{control}.} \item{\code{driver}}{a factor with levels \code{no} and \code{yes}.} \item{\code{suburban}}{a factor with levels \code{no} and \code{yes} indicating a suburban resident.} } } \details{ These data arise from a study reported in Kelsey and Hardy (1975) which was designed to investigate whether driving a car is a risk factor for low back pain resulting from acute herniated lumbar intervertebral discs (AHLID). A case-control study was used with cases selected from people who had recently had X-rays taken of the lower back and had been diagnosed as having AHLID. The controls were taken from patients admitted to the same hospital as a case with a condition unrelated to the spine. Further matching was made on age and sex and a total of 217 matched pairs were recruited, consisting of 89 female pairs and 128 male pairs. } \source{ Jennifer L. Kelsey and Robert J. Hardy (1975), Driving of Motor Vehicles as a Risk Factor for Acute Herniated Lumbar Intervertebral Disc. \emph{American Journal of Epidemiology}, \bold{102}(1), 63--73. } \examples{ data("backpain", package = "HSAUR3") summary(backpain) } \keyword{datasets} HSAUR3/man/womensrole.Rd0000644000175000017500000000245212357775401014623 0ustar nileshnilesh\name{womensrole} \alias{womensrole} \docType{data} \title{ Womens Role in Society } \description{ Data from a survey from 1974 / 1975 asking both female and male responders about their opinion on the statement: Women should take care of running their homes and leave running the country up to men. } \usage{data("womensrole")} \format{ A data frame with 42 observations on the following 4 variables. \describe{ \item{\code{education}}{years of education.} \item{\code{gender}}{a factor with levels \code{Male} and \code{Female}.} \item{\code{agree}}{number of subjects in agreement with the statement.} \item{\code{disagree}}{number of subjects in disagreement with the statement.} } } \details{ The data are from Haberman (1973) and also given in Collett (2003). The questions here are whether the response of men and women differ. } \source{ S. J. Haberman (1973), The analysis of residuals in cross-classificed tables. \emph{Biometrics}, \bold{29}, 205--220. D. Collett (2003), \emph{Modelling Binary Data}. Chapman and Hall / CRC, London. 2nd edition. } \examples{ data("womensrole", package = "HSAUR3") summary(subset(womensrole, gender == "Female")) summary(subset(womensrole, gender == "Male")) } \keyword{datasets} HSAUR3/man/polyps3.Rd0000644000175000017500000000274712357775401014051 0ustar nileshnilesh\name{polyps3} \alias{polyps3} \docType{data} \title{ Familial Andenomatous Polyposis } \description{ Data from a placebo-controlled trial of a non-steroidal anti-inflammatory drug in the treatment of familial andenomatous polyposis (FAP). } \usage{data("polyps3")} \format{ A data frame with 22 observations on the following 5 variables. \describe{ \item{\code{gender}}{a factor with levels \code{female} and \code{male}.} \item{\code{treatment}}{a factor with levels \code{placebo} and \code{active}.} \item{\code{baseline}}{the baseline number of polyps.} \item{\code{age}}{the age of the patient.} \item{\code{number3m}}{the number of polyps after three month.} } } \details{ The data arise from the same study as the \code{\link{polyps}} data. Here, the number of polyps after three months are given. } \source{ F. M. Giardiello, S. R. Hamilton, A. J. Krush, S. Piantadosi, L. M. Hylind, P. Celano, S. V. Booker, C. R. Robinson and G. J. A. Offerhaus (1993), Treatment of colonic and rectal adenomas with sulindac in familial adenomatous polyposis. \emph{New England Journal of Medicine}, \bold{328}(18), 1313--1316. S. Piantadosi (1997), \emph{Clinical Trials: A Methodologic Perspective}. John Wiley \& Sons, New York. } \examples{ data("polyps3", package = "HSAUR3") plot(number3m ~ age, data = polyps3, pch = as.numeric(polyps3$treatment)) legend("topright", legend = levels(polyps3$treatment), pch = 1:2, bty = "n") } \keyword{datasets} HSAUR3/man/UStemp.Rd0000644000175000017500000000102612357775401013642 0ustar nileshnilesh\name{UStemp} \alias{UStemp} \docType{data} \title{ Temperatures in 22 US cities } \description{ Lowest temperatures in Fahrenheit in 22 US cities in four months. } \usage{data(UStemp)} \format{ A data frame with 22 observations on the following 4 variables. \describe{ \item{\code{January}}{lowest temperature in Fahrenheit} \item{\code{April}}{lowest temperature in Fahrenheit} \item{\code{July}}{lowest temperature in Fahrenheit} \item{\code{October}}{lowest temperature in Fahrenheit} } } \keyword{datasets} HSAUR3/man/orallesions.Rd0000644000175000017500000000113312357775401014756 0ustar nileshnilesh\name{orallesions} \alias{orallesions} \docType{data} \title{ Oral Lesions in Rural India } \description{ The distribution of the oral lesion site found in house-to-house surveys in three geographic regions of rural India. } \usage{data("orallesions")} \format{ A two-way classification, see \code{\link{table}}. } \source{ Cyrus R. Mehta and Nitin R. Patel (2003), \emph{StatXact-6: Statistical Software for Exact Nonparametric Inference}, Cytel Software Cooperation, Cambridge, USA. } \examples{ data("orallesions", package = "HSAUR3") mosaicplot(orallesions) } \keyword{datasets} HSAUR3/man/toenail.Rd0000644000175000017500000000372112357775401014064 0ustar nileshnilesh\name{toenail} \alias{toenail} \docType{data} \title{ Toenail Infection Data } \description{ Results of a clinical trial to compare two competing oral antifungal treatments for toenail infection. } \usage{data("toenail")} \format{ A data frame with 1908 observations on the following 5 variables. \describe{ \item{\code{patientID}}{a unique identifier for each patient in the trial.} \item{\code{outcome}}{degree of separation of the nail plate from the nail bed (onycholysis).} \item{\code{treatment}}{a factor with levels \code{itraconazole} and \code{terbinafine}.} \item{\code{time}}{the time in month when the visit actually took place.} \item{\code{visit}}{number of visit attended.} } } \details{ De Backer et al. (1998) describe a clinical trial to compare two competing oral antifungal treatments for toenail infection (dermatophyte onychomycosis). A total of 378 patients were randomly allocated into two treatment groups, one group receiving 250mg per day of terbinafine and the other group 200mg per day of itraconazole. Patients were evaluated at seven visits, intended to be at weeks 0, 4, 8, 12, 24, 36, and 48 for the degree of separation of the nail plate from the nail bed (onycholysis) dichotomized into \code{moderate or severe} and \code{none or mild}. But patients did not always arrive exactly at the scheduled time and the exact time in months that they did attend was recorded. The data is not balanced since not all patients attended for all seven planned visits. } \source{ M. D. Backer and C. D. Vroey and E. Lesaffre and I. Scheys and P. D. Keyser (1998), Twelve weeks of continuous oral therapy for toenail onychomycosis caused by dermatophytes: A double-blind comparative trial of terbinafine 250 mg/day versus itraconazole 200 mg/day. \emph{Journal of the American Academy of Dermatology}, \bold{38}, S57--S63. } \examples{ data("toenail", package = "HSAUR3") } \keyword{datasets} HSAUR3/man/bladdercancer.Rd0000644000175000017500000000206312357775401015200 0ustar nileshnilesh\name{bladdercancer} \alias{bladdercancer} \docType{data} \title{ Bladder Cancer Data } \description{ Data arise from 31 male patients who have been treated for superficial bladder cancer, and give the number of recurrent tumours during a particular time after the removal of the primary tumour, along with the size of the original tumour. } \usage{data("bladdercancer")} \format{ A data frame with 31 observations on the following 3 variables. \describe{ \item{\code{time}}{the duration.} \item{\code{tumorsize}}{a factor with levels \code{<=3cm} and \code{>3cm}.} \item{\code{number}}{number of recurrent tumours.} } } \details{ The aim is the estimate the effect of size of tumour on the number of recurrent tumours. } \source{ G. U. H. Seeber (1998), Poisson Regression. In: \emph{Encyclopedia of Biostatistics} (P. Armitage and T. Colton, eds), John Wiley \& Sons, Chichester. } \examples{ data("bladdercancer", package = "HSAUR3") mosaicplot(xtabs(~ number + tumorsize, data = bladdercancer)) } \keyword{datasets} HSAUR3/man/USairpollution.Rd0000644000175000017500000000244712357775401015426 0ustar nileshnilesh\name{USairpollution} \alias{USairpollution} \docType{data} \title{ Air Pollution in US Cities } \description{ Air pollution data of 41 US cities. } \usage{data("USairpollution")} \format{ A data frame with 41 observations on the following 7 variables. \describe{ \item{\code{SO2}}{SO2 content of air in micrograms per cubic metre.} \item{\code{temp}}{average annual temperature in Fahrenheit.} \item{\code{manu}}{number of manufacturing enterprises employing 20 or more workers.} \item{\code{popul}}{population size (1970 census); in thousands.} \item{\code{wind}}{average annual wind speed in miles per hour.} \item{\code{precip}}{average annual precipitation in inches.} \item{\code{predays}}{average number of days with precipitation per year.} } } \details{ The annual mean concentration of sulphur dioxide, in micrograms per cubic metre, is a measure of the air pollution of the city. The question of interest here is what aspects of climate and human ecology as measured by the other six variables in the data determine pollution? } \source{ R. R. Sokal and F. J. Rohlf (1981), \emph{Biometry}, W. H. Freeman, San Francisco (2nd edition). } \examples{ data("USairpollution", package = "HSAUR3") } \keyword{datasets} HSAUR3/man/suicides2.Rd0000644000175000017500000000157512357775401014330 0ustar nileshnilesh\name{suicides2} \alias{suicides2} \docType{data} \title{ Male Suicides Data } \description{ Number of suicides in different age groups and countries. } \usage{data("suicides2")} \format{ A data frame with 15 observations on the following 5 variables. \describe{ \item{\code{A25.34}}{number of suicides (per 100000 males) between 25 and 34 years old.} \item{\code{A35.44}}{number of suicides (per 100000 males) between 35 and 44 years old.} \item{\code{A45.54}}{number of suicides (per 100000 males) between 45 and 54 years old.} \item{\code{A55.64}}{number of suicides (per 100000 males) between 55 and 64 years old.} \item{\code{A65.74}}{number of suicides (per 100000 males) between 65 and 74 years old.} } } \details{ Each of the numbers gives the number of suicides per 100000 male inhabitants of the countries given by the row names. } \keyword{datasets} HSAUR3/man/weightgain.Rd0000644000175000017500000000224312357775401014555 0ustar nileshnilesh\name{weightgain} \alias{weightgain} \docType{data} \title{ Gain in Weight of Rats } \description{ The data arise from an experiment to study the gain in weight of rats fed on four different diets, distinguished by amount of protein (low and high) and by source of protein (beef and cereal). } \usage{data("weightgain")} \format{ A data frame with 40 observations on the following 3 variables. \describe{ \item{\code{source}}{source of protein given, a factor with levels \code{Beef} and \code{Cereal}.} \item{\code{type}}{amount of protein given, a factor with levels \code{High} and \code{Low}.} \item{\code{weightgain}}{weigt gain in grams.} } } \details{ Ten rats are randomized to each of the four treatments. The question of interest is how diet affects weight gain. } \source{ D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994). \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London. } \examples{ data("weightgain", package = "HSAUR3") interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain) } \keyword{datasets} HSAUR3/man/BtheB.Rd0000644000175000017500000000475112357775401013421 0ustar nileshnilesh\name{BtheB} \alias{BtheB} \docType{data} \title{ Beat the Blues Data } \description{ Data from a clinical trial of an interactive multimedia program called `Beat the Blues'. } \usage{data("BtheB")} \format{ A data frame with 100 observations of 100 patients on the following 8 variables. \describe{ \item{drug}{did the patient take anti-depressant drugs (\code{No} or \code{Yes}).} \item{length}{the length of the current episode of depression, a factor with levels \code{<6m} (less than six months) and \code{>6m} (more than six months).} \item{treatment}{treatment group, a factor with levels \code{TAU} (treatment as usual) and \code{BtheB} (Beat the Blues)} \item{bdi.pre}{Beck Depression Inventory II before treatment.} \item{bdi.2m}{Beck Depression Inventory II after two months.} \item{bdi.3m}{Beck Depression Inventory II after one month follow-up.} \item{bdi.5m}{Beck Depression Inventory II after three months follow-up.} \item{bdi.8m}{Beck Depression Inventory II after six months follow-up.} } } \details{ Longitudinal data from a clinical trial of an interactive, multimedia program known as "Beat the Blues" designed to deliver cognitive behavioural therapy to depressed patients via a computer terminal. Patients with depression recruited in primary care were randomised to either the Beating the Blues program, or to "Treatment as Usual (TAU)". Note that the data are stored in the wide form, i.e., repeated measurments are represented by additional columns in the data frame. } \source{ J. Proudfoot, D. Goldberg, A. Mann, B. S. Everitt, I. Marks and J. A. Gray, (2003). Computerized, interactive, multimedia cognitive-behavioural program for anxiety and depression in general practice. \emph{Psychological Medicine}, \bold{33}(2), 217--227. } \examples{ data("BtheB", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) ylim <- range(BtheB[,grep("bdi", names(BtheB))], na.rm = TRUE) boxplot(subset(BtheB, treatment == "TAU")[,grep("bdi", names(BtheB))], main = "Treated as usual", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) boxplot(subset(BtheB, treatment == "BtheB")[,grep("bdi", names(BtheB))], main = "Beat the Blues", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) } \keyword{datasets} HSAUR3/man/USmelanoma.Rd0000644000175000017500000000221612357775401014470 0ustar nileshnilesh\name{USmelanoma} \alias{USmelanoma} \docType{data} \title{ USA Malignant Melanoma Data } \description{ USA mortality rates for white males due to malignant melanoma 1950-1969. } \usage{data("USmelanoma")} \format{ A data frame with 48 observations on the following 5 variables. \describe{ \item{\code{mortality}}{number of white males died due to malignant melanoma 1950-1969 per one million inhabitants.} \item{\code{latitude}}{latitude of the geographic centre of the state.} \item{\code{longitude}}{longitude of the geographic centre of each state.} \item{\code{ocean}}{a binary variable indicating contiguity to an ocean at levels \code{no} or \code{yes}.} } } \details{ Fisher and van Belle (1993) report mortality rates due to malignant melanoma of the skin for white males during the period 1950-1969, for each state on the US mainland. Questions of interest about these data include how do the mortality rates compare for ocean and non-ocean states? } \source{ Fisher and van Belle (1993) } \examples{ data("USmelanoma", package = "HSAUR3") } \keyword{datasets} HSAUR3/man/Smoking_Mueller1940.Rd0000644000175000017500000000231012357775401016034 0ustar nileshnilesh\name{Smoking_Mueller1940} \alias{Smoking_Mueller1940} \docType{data} \title{Smoking and Lung Cancer (I) } \description{ Number of smokers in a case-control study. } \usage{data(Smoking_Mueller1940)} \format{ The format is: table [1:5, 1:2] 25 18 13 27 3 4 5 22 41 14 - attr(*, "dimnames")=List of 2 ..$ Smoking_type: chr [1:5] "Extreme smoker" "Very heavy smoker" "Heavy smoker" "Moderate smoker" ... ..$ Group : chr [1:2] "Lung cancer" "Healthy control" } \details{ Extreme smoker: 10-15 cigars, >35 cigarettes, or >50 g pipe tobacco/day. Very heavy smoker: 7-9 cigars, 26-35 cigarettes, or 36-50 g pipe tobacco/day. Heavy smoker: 4-6 cigars, 16-25 cigarettes, or 21-35 g pipe tobacco/day. Moderate smoker: 1-3 cigars, 1-15 cigarettes, or 1-20 g pipe tobacco/day. } \source{ Franz-Hermann Mueller (1940), Tabakmissbrauch und Lungencarcinom. \emph{Zeitschrift fuer Krebsforschung} \bold{49}(1), 57-85. } \references{ Richard Doll (1998), Uncovering the effects of smoking: historical perspective. \emph{Statistical Methods in Medical Research}, \bold{7}(87), 87-117 } \examples{ data(Smoking_Mueller1940) ## maybe str(Smoking_Mueller1940) ; plot(Smoking_Mueller1940) ... } \keyword{datasets} HSAUR3/man/BCG.Rd0000644000175000017500000000541012357775401013021 0ustar nileshnilesh\name{BCG} \alias{BCG} \docType{data} \title{ BCG Vaccine Data } \description{ A meta-analysis on the efficacy of BCG vaccination against tuberculosis (TB). } \usage{data("BCG")} \format{ A data frame with 13 observations on the following 7 variables. \describe{ \item{\code{Study}}{an identifier of the study.} \item{\code{BCGTB}}{the number of subjects suffering from TB after a BCG vaccination.} \item{\code{BCGVacc}}{the number of subjects with BCG vaccination.} \item{\code{NoVaccTB}}{the number of subjects suffering from TB without BCG vaccination.} \item{\code{NoVacc}}{the total number of subjects without BCG vaccination.} \item{\code{Latitude}}{geographic position of the place the study was undertaken.} \item{\code{Year}}{the year the study was undertaken.} } } \details{ Bacille Calmette Guerin (BCG) is the most widely used vaccination in the world. Developed in the 1930s and made of a live, weakened strain of Mycobacterium bovis, the BCG is the only vaccination available against tuberculosis today. Colditz et al. (1994) report data from 13 clinical trials of BCG vaccine each investigating its efficacy in the treatment of tuberculosis. The number of subjects suffering from TB with or without BCG vaccination are given here. In addition, the data contains the values of two other variables for each study, namely, the geographic latitude of the place where the study was undertaken and the year of publication. These two variables will be used to investigate and perhaps explain any heterogeneity among the studies. } \source{ G. A. Colditz, T. F. Brewer, C. S. Berkey, M. E. Wilson, E. Burdick, H. V. Fineberg and F. Mosteller (1994), Efficacy of BCG vaccine in the prevention of tuberculosis. Meta-analysis of the published literature. \emph{Journal of the American Medical Association}, \bold{271}(2), 698--702. } \examples{ data("BCG", package = "HSAUR3") ### sort studies w.r.t. sample size BCG <- BCG[order(rowSums(BCG[,2:5])),] ### to long format BCGlong <- with(BCG, data.frame(Freq = c(BCGTB, BCGVacc - BCGTB, NoVaccTB, NoVacc - NoVaccTB), infected = rep(rep(factor(c("yes", "no")), rep(nrow(BCG), 2)), 2), vaccined = rep(factor(c("yes", "no")), rep(nrow(BCG) * 2, 2)), study = rep(factor(Study, levels = as.character(Study)), 4))) ### doubledecker plot library("vcd") doubledecker(xtabs(Freq ~ study + vaccined + infected, data = BCGlong)) } \keyword{datasets} HSAUR3/vignettes/0000755000175000017500000000000014133304614013360 5ustar nileshnileshHSAUR3/vignettes/Ch_errata.Rnw0000644000175000017500000001672314133304452015751 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Errata} \setcounter{chapter}{21} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Errata]{Errata} %\bibliographystyle{LaTeXBibTeX/refstyle} %\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_gam.Rnw0000644000175000017500000006234514133304452015240 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Generalized Additive Models} %%\VignetteDepends{mgcv,rpart,wordcloud,mboost} \setcounter{chapter}{9} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("mgcv") library("mboost") library("rpart") library("wordcloud") @ \chapter[Scatterplot Smoothers and Additive Models]{Scatterplot Smoothers and Generalized Additive Models: The Men's Olympic 1500m, Air Pollution in the US, Risk Factors for Kyphosis, and Women's Role in %' Society \label{GAM}} \section{Introduction} \section{Scatterplot Smoothers and Generalized Additive Models} \section{Analysis Using \R{}} \subsection{Olympic 1500m Times} To begin we will construct a scatterplot of winning time against the year the games were held. The \R{} code and the resulting plot are shown in Figure~\ref{GAM-men1500m-plot}. There is a very clear downward trend in the times over the years, and, in addition there is a very clear outlier namely the winning time for 1896. We shall remove this time from the data set and now concentrate on the remaining times. First we will fit a simple linear regression to the data and plot the fit onto the scatterplot. The code and the resulting plot are shown in Figure~\ref{GAM-men1500m-lm}. Clearly the linear regression model captures in general terms the downward trend in the times. Now we can add the fits given by the lowess smoother and by a cubic spline smoother; the resulting graph and the extra \R{} code needed are shown in Figure~\ref{GAM-men1500m-smooth}. Both non-parametric fits suggest some distinct departure from linearity, and clearly point to a quadratic model being more sensible than a linear model here. And fitting a parametric model that includes both a linear and a quadratic effect for the year gives a prediction curve very similar to the non-parametric curves; see Figure~\ref{GAM-men1500m-quad}. Here use of the non-parametric smoothers has effectively diagnosed our linear model and pointed the way to using a more suitable parametric model; this is often how such non-parametric models can be used most effectively. For these data, of course, it is clear that the simple linear model cannot be suitable if the investigator is interested in predicting future times since even the most basic knowledge of human physiology will tell us that times cannot continue to go down. There must be some lower limit to the time man can run 1500m. But in other situations use of the non-parametric smoothers may point to a parametric model that could not have been identified \emph{a priori}. \begin{figure} \begin{center} <>= plot(time ~ year, data = men1500m, xlab = "Year", ylab = "Winning time (sec)") @ \caption{Scatterplot of year and winning time. \label{GAM-men1500m-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= men1500m1900 <- subset(men1500m, year >= 1900) men1500m_lm <- lm(time ~ year, data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") abline(men1500m_lm) @ \caption{Scatterplot of year and winning time with fitted values from a simple linear model. \label{GAM-men1500m-lm}} \end{center} \end{figure} \begin{figure} \begin{center} <>= x <- men1500m1900$year y <- men1500m1900$time men1500m_lowess <- lowess(x, y) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m_lowess, lty = 2) men1500m_cubic <- gam(y ~ s(x, bs = "cr")) lines(x, predict(men1500m_cubic), lty = 3) @ \caption{Scatterplot of year and winning time with fitted values from a smooth non-parametric model. \label{GAM-men1500m-smooth}} \end{center} \end{figure} \begin{figure} \begin{center} <>= men1500m_lm2 <- lm(time ~ year + I(year^2), data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m1900$year, predict(men1500m_lm2)) @ \caption{Scatterplot of year and winning time with fitted values from a quadratic model. \label{GAM-men1500m-quad}} \end{center} \end{figure} It is of some interest to look at the predictions of winning times in future Olympics from both the linear and quadratic models. For example, for 2008 and 2012 the predicted times and their $95\%$ confidence intervals can be found using the following code \newpage <>= predict(men1500m_lm, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") predict(men1500m_lm2, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") @ \newpage For predictions far into the future both the quadratic and the linear model fail; we leave readers to get some more predictions to see what happens. We can compare the first prediction with the time actually recorded by the winner of the men's 1500m in Beijing 2008, Rashid Ramzi from Brunei, who won the event in $212.94$ seconds. The confidence interval obtained from the simple linear model does not include this value but the confidence interval for the prediction derived from the quadratic model does. \subsection{Air Pollution in US Cities} Unfortunately, we cannot fit an additive model for describing the $\text{SO}_2$ concentration based on all six covariates because this leads to more parameters than cities, i.e., more parameters than observations when using the default parameterization of \Rpackage{mgcv}. Thus, before we can apply the \Rcmd{gam} function from package \Rpackage{mgcv}, we have to decide which covariates should enter the model and which subset of these covariates should be allowed to deviate from a linear regression relationship. As briefly discussed in Section~\ref{GAM:VS}, we can fit an additive model using the iterative boosting algorithm as described by \cite{HSAUR:BuehlmannHothorn2007}. The complexity of the model is determined by an AIC criterion, which can also be used to determine an appropriate number of boosting iterations to choose. The methodology is available from package \Rpackage{mboost} \citep{PKG:mboost}. We start with a small number of boosting iterations ($100$ by default) and compute the AIC of the corresponding $100$ models: <>= library("mboost") USair_boost <- gamboost(SO2 ~ ., data = USairpollution) USair_aic <- AIC(USair_boost) USair_aic @ The AIC suggests that the boosting algorithm should be stopped after $\Sexpr{mstop(USair_aic)}$ iterations. The partial contributions of each covariate to the predicted $\text{SO}_2$ concentration are given in Figure~\ref{GAM-USairpollution-boostplot}. The plot indicates that all six covariates enter the model and the selection of a subset of covariates for modeling isn't appropriate in this case. However, the number of manufacturing enterprises seems to add linearly to the $\text{SO}_2$ concentration, which simplifies the model. Moreover, the average annual precipitation contribution seems to deviate from zero only for some extreme observations and one might refrain from using the covariate at all. \begin{figure} \begin{center} <>= USair_gam <- USair_boost[mstop(USair_aic)] layout(matrix(1:6, ncol = 3)) plot(USair_gam, ask = FALSE) @ \caption{Partial contributions of six exploratory covariates to the predicted $\text{SO}_2$ concentration. \label{GAM-USairpollution-boostplot}} \end{center} \end{figure} As always, an inspection of the model fit via a residual plot is worth the effort. Here, we plot the fitted values against the residuals and label the points with the name of the corresponding city using the \Rcmd{textplot} function from package \Rpackage{wordcloud}. Figure~\ref{GAM-USairpollution-residplot} shows at least two extreme observations. Chicago has a very large observed and fitted $\text{SO}_2$ concentration, which is due to the huge number of inhabitants and manufacturing plants (see Figure~\ref{GAM-USairpollution-boostplot} also). One smaller city, Providence, is associated with a rather large positive residual indicating that the actual $\text{SO}_2$ concentration is underestimated by the model. In fact, this small town has a rather high $\text{SO}_2$ concentration which is hardly explained by our model. Overall, the model doesn't fit the data very well, so we should avoid overinterpreting the model structure too much. In addition, since each of the six covariates contributes to the model, we aren't able to select a smaller subset of the covariates for modeling and thus fitting a model using \Rcmd{gam} is still complicated (and will not add much knowledge anyway). \begin{figure} \begin{center} <>= SO2hat <- predict(USair_gam) SO2 <- USairpollution$SO2 plot(SO2hat, SO2 - SO2hat, type = "n", xlim = c(-20, max(SO2hat) * 1.1), ylim = range(SO2 - SO2hat) * c(2, 1)) textplot(SO2hat, SO2 - SO2hat, rownames(USairpollution), show.lines = FALSE, new = FALSE) abline(h = 0, lty = 2, col = "grey") @ \caption{Residual plot of $\text{SO}_2$ concentration. \label{GAM-USairpollution-residplot}} \end{center} \end{figure} \subsection{Risk Factors for Kyphosis} \index{Spinogram} Before modeling the relationship between kyphosis and the three exploratory variables age, starting vertebral level of the surgery, and number of vertebrae involved, we investigate the partial associations by so-called \stress{spinograms}, as introduced in \Sexpr{ch("DAGD")}. The numeric exploratory covariates are discretized and their empirical relative frequencies are plotted against the conditional frequency of kyphosis in the corresponding group. Figure~\ref{GAM-kyphosis-plot} shows that kyphosis is absent in very young or very old children, children with a small starting vertebral level, and high number of vertebrae involved. \begin{figure} \begin{center} <>= layout(matrix(1:3, nrow = 1)) spineplot(Kyphosis ~ Age, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Number, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Start, data = kyphosis, ylevels = c("present", "absent")) @ \caption{Spinograms of the three exploratory variables and response variable \Robject{kyphosis}. \label{GAM-kyphosis-plot}} \end{center} \end{figure} The logistic additive model needed to describe the conditional probability of kyphosis given the exploratory variables can be fitted using function \Rcmd{gam}. Here, the dimension of the basis ($k$) has to be modified for \Robject{Number} and \Robject{Start} since these variables are heavily tied. As for generalized linear models, the \Robject{family} argument determines the type of model to be fitted, a logistic model in our case: <>= (kyphosis_gam <- gam(Kyphosis ~ s(Age, bs = "cr") + s(Number, bs = "cr", k = 3) + s(Start, bs = "cr", k = 3), family = binomial, data = kyphosis)) @ The partial contributions of each covariate to the conditional probability of kyphosis with confidence bands are shown in Figure~\ref{GAM-kyphosis-gamplot}. In essence, the same conclusions as drawn from Figure~\ref{GAM-kyphosis-plot} can be stated here. The risk of kyphosis being present decreases with higher starting vertebral level and lower number of vertebrae involved. Children about $100$ months old are under higher risk compared to younger or older children. \begin{figure} \begin{center} <>= trans <- function(x) binomial()$linkinv(x) layout(matrix(1:3, nrow = 1)) plot(kyphosis_gam, select = 1, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 2, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 3, shade = TRUE, trans = trans) @ \caption{Partial contributions of three exploratory variables with confidence bands. \label{GAM-kyphosis-gamplot}} \end{center} \end{figure} \subsection{Women's Role in Society} %' In Chapter~\ref{GLM}, we saw that a logistic regression with an interaction between gender and level of education described the data better than a main-effects only model. Using an additive logistic regression model, we can fit separate, possibly nonlinear, functions of levels of education to both genders: <>= data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ s(education, by = gender) womensrole_gam <- gam(fm1, data = womensrole, family = binomial()) @ The resulting model is best inspected by a plot (Figure~\ref{GAM-womensrole-gamplot}). For males, the log-odds of agreement decreases linearly with each additional year of education. For females, the log-odds is more or less constant up to five years of education and only then begins to decrease. After 15 years, there seems to be no further impact on the log-odds. When we plot the resulting fitted probabilities in a way similar to Figure~\ref{GLM-role2plot}, we see that the interaction is even more pronounced in the additive compared to the linear model. The flat curve for women with less than five years of education can be explained by the rather large variability of the answers in this area but the plateau to the right is due to two groups of highly educated women with a rather large proportion of agreement. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(womensrole_gam, select = 1, shade = TRUE) plot(womensrole_gam, select = 1, shade = TRUE) @ \caption{Effects of level of education for males (right) and females (left) on the log-odds scale derived from an additive logistic regression model. The shaded area denotes confidence bands. \label{GAM-womensrole-gamplot}} \end{center} \end{figure} <>= myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } @ \begin{figure} \begin{center} <>= myplot(predict(womensrole_gam, type = "response")) @ \caption{Effects of level of education for males (right) and females (left) on the log-odds scale derived from an additive logistic regression model. The shaded area denotes confidence bands. \label{GAM-womensrole-probplot}} \end{center} \end{figure} \section{Summary of Findings} \begin{description} \item[Olympic 1500m times] Here the use of a generalized additive model suggested that a quadratic model might best describe the data. When such a model was fitted it made reasonable predictions of the winner's times in the Olympic Games of 2008 and 2012. \item[Air pollution data] Finding a suitable model for these data was problematic because of the outliers in the data and the high correlations between some pairs of explanatory variables. Except for wind, the fitted partial contributions are well approximated by a linear function for most of the observations and it might be questioned if the more complex additive model is really needed. \item[Kyphosis] The risk of kyphosis being present decreases with higher starting vertebral level and lower number of vertebrae involved. Children about 100 months old are under higher risk compared to younger or older children. \item[Women's role in society] For males, the log-odds of agreement decreases linearly with each additional year of education. For females, the log-odds is more or less constant up to five years of education and only then begins to decrease. After $15$ years, there seems to be no further impact on the log-odds. \end{description} \section{Final Comments} Additive models offer flexible modeling tools for regression problems. They stand between generalized linear models, where the regression relationship is assumed to be linear, and more complex models like random forests (see \Sexpr{ch("RP")}) where the regression relationship remains unspecified. Smooth functions describing the influence of covariates on the response can be easily interpreted. Variable selection is a technically difficult problem in this class of models; boosting methods are one possibility to deal with this problem. \section*{Exercises} \begin{description} \exercise Consider the body fat data introduced in \Sexpr{ch("RP")}, Table~\ref{RP-bodyfat-tab}. First fit a generalized additive model assuming normal errors using function \Rcmd{gam}. Are all potential covariates informative? Check the results against a generalized additive model that underwent AIC-based variable selection (fitted using function \Rcmd{gamboost}). \exercise Again fit an additive model to the body fat data, but this time for a log-transformed response. Compare the two models, which one is more appropriate? \exercise Try to fit a logistic additive model to the glaucoma data discussed in \Sexpr{ch("RP")}. Which covariates should enter the model and how is their influence on the probability of suffering from glaucoma? \exercise Investigate the use of different types of scatterplot smoothers on the Hubble data in Table~\ref{MLR-hubble-tab} in Chapter~\ref{MLR-hubble-tab}. \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_graphical_display.Rnw0000644000175000017500000010257514133304452020153 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Data Analysis using Graphical Displays} %%\VignetteDepends{lattice, maps, maptools, sp} \setcounter{chapter}{1} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} \chapter[Data Analysis Using Graphical Displays]{Data Analysis Using Graphical Displays: Malignant Melanoma in the US and Chinese Health and \\ Family Life \label{DAGD}} \section{Introduction} \section{Initial Data Analysis} \section{Analysis Using \R{}} \subsection{Malignant Melanoma} \index{Boxplot|(} \index{Histogram|(} \index{Scatterplot|(} We might begin to examine the malignant melanoma data in Table~\ref{DAGD-USmelanoma-tab} by constructing a histogram or boxplot for \stress{all} the mortality rates in Figure~\ref{DAGD-USmelanoma-histbox}. The \Rcmd{plot}, \Rcmd{hist} and \Rcmd{boxplot} functions have already been introduced in \Sexpr{ch("AItR")} and we want to produce a plot where both techniques are applied at once. The \Rcmd{layout} function organizes two independent plots on one plotting device, for example on top of each other. Using this relatively simple technique (more advanced methods will be introduced later) we have to make sure that the $x$-axis is the same in both graphs. This can be done by computing a plausible range of the data, later to be specified in a plot via the \Rcmd{xlim} argument: <>= xr <- range(USmelanoma$mortality) * c(0.9, 1.1) xr @ Now, plotting both the histogram and the boxplot requires setting up the plotting device with equal space for two independent plots on top of each other. Calling the \Rcmd{layout} function on a matrix with two cells in two rows, containing the numbers one and two, leads to such a partitioning. The \Rcmd{boxplot} function is called first on the mortality data and then the \Rcmd{hist} function, where the range of the $x$-axis in both plots is defined by $(\Sexpr{xr[1]}, \Sexpr{xr[2]})$. One tiny problem to solve is the size of the margins; their defaults are too large for such a plot. As with many other graphical parameters, one can adjust their value for a specific plot using function \Rcmd{par}. The \R{} code and the resulting display are given in Figure~\ref{DAGD-USmelanoma-histbox}. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 2)) par(mar = par("mar") * c(0.8, 1, 1, 1)) boxplot(USmelanoma$mortality, ylim = xr, horizontal = TRUE, xlab = "Mortality") hist(USmelanoma$mortality, xlim = xr, xlab = "", main = "", axes = FALSE, ylab = "") axis(1) @ \caption{Histogram (top) and boxplot (bottom) of malignant melanoma mortality rates. \label{DAGD-USmelanoma-histbox}} \end{center} \end{figure} Both the histogram and the boxplot in Figure~\ref{DAGD-USmelanoma-histbox} indicate a certain skewness of the mortality distribution. Looking at the characteristics of all the mortality rates is a useful beginning but for these data we might be more interested in comparing mortality rates for ocean and non-ocean states. So we might construct two histograms or two boxplots. Such a \stress{parallel boxplot}, visualizing the conditional distribution of a numeric variable in groups as given by a categorical variable, are easily computed using the \Rcmd{boxplot} function. The continuous response variable and the categorical independent variable are specified via a \Rclass{formula} as described in \Sexpr{ch("AItR")}. Figure~\ref{DAGD-USmelanoma-boxocean} shows such parallel boxplots, as by default produced the \Rcmd{plot} function for such data, for the mortality in ocean and non-ocean states and leads to the impression that the mortality is increased in east or west coast states compared to the rest of the country. \begin{figure} \begin{center} <>= plot(mortality ~ ocean, data = USmelanoma, xlab = "Contiguity to an ocean", ylab = "Mortality") @ \caption{Parallel boxplots of malignant melanoma mortality rates by contiguity to an ocean. \label{DAGD-USmelanoma-boxocean}} \end{center} \end{figure} Histograms are generally used for two purposes: counting and displaying the distribution of a variable; according to \cite{HSAUR:Wilkinson1992}, `they are effective for neither'. Histograms can often be misleading for displaying distributions because of their dependence on the number of classes chosen. An alternative is to formally estimate the density function of a variable and then plot the resulting estimate; details of density estimation are given in \Sexpr{ch("DE")} but for the ocean and non-ocean states the two density estimates can be produced and plotted as shown in Figure~\ref{DAGD-USmelanoma-dens} which supports the impression from Figure~\ref{DAGD-USmelanoma-boxocean}. For more details on such density estimates we refer to \Sexpr{ch("DE")}. \begin{figure} \begin{center} <>= dyes <- with(USmelanoma, density(mortality[ocean == "yes"])) dno <- with(USmelanoma, density(mortality[ocean == "no"])) plot(dyes, lty = 1, xlim = xr, main = "", ylim = c(0, 0.018), xlab = "Mortality") lines(dno, lty = 2) legend("topleft", lty = 1:2, legend = c("Coastal State", "Land State"), bty = "n") @ \caption{Estimated densities of malignant melanoma mortality rates by contiguity to an ocean. \label{DAGD-USmelanoma-dens}} \end{center} \end{figure} Now we might move on to look at how mortality rates are related to the geographic location of a state as represented by the latitude and longitude of the center of the state. Here the main graphic will be the scatterplot. The simple $xy$ scatterplot has been in use since at least the eighteenth century and has many virtues -- indeed according to \cite{HSAUR:Tufte1983}: \begin{quote} The relational graphic -- in its barest form the scatterplot and its variants -- is the greatest of all graphical designs. It links at least two variables, encouraging and even imploring the viewer to assess the possible causal relationship between the plotted variables. It confronts causal theories that $x$ causes $y$ with empirical evidence as to the actual relationship between $x$ and $y$. \end{quote} Let's begin with simple scatterplots of mortality rate against longitude %%' and mortality rate against latitude which can be produced by the code preceding Figure~\ref{DAGD-USmelanoma-xy}. Again, the \Rcmd{layout} function is used for partitioning the plotting device, now resulting in two side-by-side plots. The argument to \Rcmd{layout} is now a matrix with only one row but two columns containing the numbers one and two. In each cell, the \Rcmd{plot} function is called for producing a scatterplot of the variables given in the \Rclass{formula}. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) plot(mortality ~ longitude, data = USmelanoma, ylab = "Mortality", xlab = "Longitude") plot(mortality ~ latitude, data = USmelanoma, ylab = "Mortality", xlab = "Latitude") @ \caption{Scatterplot of malignant melanoma mortality rates by geographical location. \label{DAGD-USmelanoma-xy}} \end{center} \end{figure} Since mortality rate is clearly related only to latitude we can now produce scatterplots of mortality rate against latitude separately for ocean and non-ocean states. Instead of producing two displays, one can choose different plotting symbols for either states. This can be achieved by specifying a vector of integers or characters to the \Rcmd{pch}, where the $i$th element of this vector defines the plot symbol of the $i$th observation in the data to be plotted. For the sake of simplicity, we convert the \Robject{ocean} factor to an \Rclass{integer} vector containing the numbers one for land states and two for ocean states. As a consequence, land states can be identified by the dot symbol and ocean states by triangles. It is useful to add a legend to such a plot, most conveniently by using the \Rcmd{legend} function. This function takes three arguments: a string indicating the position of the legend in the plot, a character vector of labels to be printed and the corresponding plotting symbols (referred to by integers). In addition, the display of a bounding box is anticipated (\Rcmd{bty = "n"}). \begin{figure} \begin{center} <>= plot(mortality ~ latitude, data = USmelanoma, pch = (1:2)[ocean], ylab = "Mortality", xlab = "Latitude") legend("topright", legend = c("Land state", "Coast state"), pch = 1:2, bty = "n") @ \caption{Scatterplot of malignant melanoma mortality rates against latitude. \label{DAGD-USmelanoma-lat}} \end{center} \end{figure} The scatterplot in Figure~\ref{DAGD-USmelanoma-lat} highlights that the mortality is lowest in the northern land states. Coastal states show a higher mortality than land states at roughly the same latitude. The highest mortalities can be observed for the south coastal states with latitude less than $32^\circ$, say, that is <>= subset(USmelanoma, latitude < 32) @ Alternatively, we also may simply want to look at a color-coded map of the United States, where each state is plotted in a color that corresponds to its mortality rate. It is fairly simple to set-up such a plot using the \Rpackage{sp} family of packages \citep{PKG:sp}. We start with loading a map of the mainland states, basically a number of polygons: <>= library("sp") library("maps") library("maptools") states <- map("state", plot = FALSE, fill = TRUE) @ It is of course important to match the mortality rates to the corresponding state. We therefore create unique names of the states in lower-case letters for both the polygons and the mortality data <>= IDs <- sapply(strsplit(states$names, ":"), function(x) x[1]) rownames(USmelanoma) <- tolower(rownames(USmelanoma)) @ Now we are ready to merge these two objects into a so-called \Rclass{SpatialPolygonsDataFrame} object. We first create a \Rclass{SpatialPolygons} object from the map in the correct reference system (WGS84, in our case) and then merge the polygons with the data <>= us1 <- map2SpatialPolygons(states, IDs=IDs, proj4string = CRS("+proj=longlat +datum=WGS84")) us2 <- SpatialPolygonsDataFrame(us1, USmelanoma) @ The resulting object \Robject{us2} can now be plotted using the \Rcmd{spplot} function, see Figure~\ref{DAGD-USmelanoma-long-lat}. The colors correspond to the mortality rate, as shown in the color legend to the right of the map. We see that darker grey values corresponding to higher mortality rates appear in the southern costal states, both on the east and the west coast in good agreement with our earlier results. \begin{figure} \begin{center} <>= spplot(us2, "mortality", col.regions = rev(grey.colors(100))) @ \caption{Map of the United States of America showing malignant melanoma mortality rates. \label{DAGD-USmelanoma-long-lat}} \end{center} \end{figure} Up to now we have primarily focused on the visualization of continuous variables. We now extend our focus to the visualization of categorical variables. \index{Boxplot|)} \index{Histogram|)} \index{Scatterplot|)} \subsection{Chinese Health and Family Life} \index{Barchart|(} \index{Spineplot|(} \index{Spinogram|(} One part of the questionnaire the Chinese Health and Family Life Survey focuses on is the self-reported health status. Two questions are interesting for us. The first one is `Generally speaking, do you consider the condition of your health to be excellent, good, fair, not good, or poor?'. The second question is `Generally speaking, in the past twelve months, how happy were you?'. The distribution of such variables is commonly visualized using barcharts where for each category the total or relative number of observations is displayed. Such a barchart can conveniently be produced by applying the \Rcmd{barplot} function to a tabulation of the data. The empirical density of the variable \Robject{R\_happy} is computed by the \Rcmd{xtabs} function for producing (contingency) tables; the resulting barchart is given in Figure~\ref{DAGD-CHFLS-happy}. \begin{figure} <>= barplot(xtabs(~ R_happy, data = CHFLS)) @ \caption{Bar chart of happiness. \label{DAGD-CHFLS-happy}} \end{figure} The visualization of two categorical variables could be done by conditional barcharts, i.e., barcharts of the first variable within the categories of the second variable. An attractive alternative for displaying such two-way tables are \stress{spineplots} \citep{HSAUR:Friendly1994,HSAUR:HofmannTheus2005,HSAUR:Chenetal2008}; the meaning of the name will become clear when looking at such a plot in Figure~\ref{DAGD-CHFLS-health_happy}. Before constructing such a plot, we produce a two-way table of the health status and self-reported happiness using the \Rcmd{xtabs} function: <>= xtabs(~ R_happy + R_health, data = CHFLS) @ <>= hh <- xtabs(~ R_health + R_happy, data = CHFLS) @ A \stress{spineplot} is a group of rectangles, each representing one cell in the two-way contingency table. The area of the rectangle is proportional with the number of observations in the cell. Here, we produce a mosaic plot of health status and happiness in Figure~\ref{DAGD-CHFLS-health_happy}. \begin{figure} <>= plot(R_happy ~ R_health, data = CHFLS, ylab = "Happiness", xlab = "Health") @ \caption{Spineplot of health status and happiness. \label{DAGD-CHFLS-health_happy}} \end{figure} Consider the right upper cell in Figure~\ref{DAGD-CHFLS-health_happy}, i.e., the $\Sexpr{hh["Excellent", "Very happy"]}$ very happy women with excellent health status. The width of the right-most bar corresponds to the frequency of women with excellent health status. The length of the top-right rectangle corresponds to the conditional frequency of very happy women given their health status is excellent. Multiplying these two quantities gives the area of this cell which corresponds to the frequency of women who are both very happy and enjoy an excellent health status. The conditional frequency of very happy women increases with increasing health status, whereas the conditional frequency of very unhappy or not too happy women decreases. When the association of a categorical and a continuous variable is of interest, say the monthly income and self-reported happiness, one might use parallel boxplots to visualize the distribution of the income depending on happiness. If we were studying self-reported happiness as response and income as independent variable, however, this would give a representation of the conditional distribution of income given happiness, but we are interested in the conditional distribution of happiness given income. One possibility to produce a more appropriate plot is called \stress{spinogram}. Here, the continuous $x$-variable is categorized first. Within each of these categories, the conditional frequencies of the response variable are given by stacked barcharts, in a way similar to spineplots. For happiness depending on log-income (since income is naturally skewed we use a log-transformation of the income) it seems that the proportion of unhappy and not too happy women decreases with increasing income whereas the proportion of very happy women stays rather constant. In contrast to spinograms, where bins, as in a histogram, are given on the $x$-axis, a \stress{conditional density plot} uses the original $x$-axis for a display of the conditional density of the categorical response given the independent variable. \begin{figure} <>= layout(matrix(1:2, ncol = 2)) plot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") cdplot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") @ \caption{Spinogram (left) and conditional density plot (right) of happiness depending on log-income. \label{DAGD-CHFLS-happy_income}} \end{figure} \index{Barchart|)} \index{Spineplot|)} \index{Spinogram|)} \index{Trellis plot|(} For our last example we return to scatterplots for inspecting the association between a woman's monthly income and the income of her partner. Both income variables have been computed and partially imputed from other self-reported variables and are only rough assessments of the real income. Moreover, the data itself is numeric but heavily tied, making it difficult to produce `correct' scatterplots because points will overlap. A relatively easy trick is to jitter the observation by adding a small random noise to each point in order to avoid overlapping plotting symbols. In addition, we want to study the relationship between both monthly incomes conditional on the woman's education. Such conditioning plots are called \stress{trellis} plots and are implemented in the package \Rpackage{lattice} \citep{PKG:lattice, HSAUR:Sarkar2008}. We utilize the \Rcmd{xyplot} function from package \Rpackage{lattice} to produce a scatterplot. The formula reads as already explained with the exception that a third \stress{conditioning} variable, \Robject{R\_edu} in our case, is present. For each level of education, a separate scatterplot will be produced. The plots are directly comparable since the axes remain the same for all plots. \begin{figure} <>= library("lattice") xyplot(jitter(log(R_income + 0.5)) ~ jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, pch = 19, col = rgb(.1, .1, .1, .1), ylab = "log(Wife's income + .5)", xlab = "log(Husband's income + .5)") @ <>= library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) xyplot(jitter(log(R_income + 0.5)) ~ jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, pch = 19, col = rgb(.1, .1, .1, .1), ylab = "log(Wife's income + .5)", xlab = "log(Husband's income + .5)") @ \caption{Scatterplot of jittered log-income of wife and husband, conditional on the wife's education. \label{DAGD-CHFLS-RAincome3}} \end{figure} The plot shown in Figure~\ref{DAGD-CHFLS-RAincome3} reveals several interesting issues. Some observations are positioned on a straight line with slope one, most probably an artifact of missing value imputation by linear models (as described in the data dictionary, see the documentation \texttt{?CHFLS}). Four constellations can be identified: both partners have zero income, the partner has no income, the woman has no income or both partners have a positive income. For couples where the woman has a university degree, the income of both partners is relatively high (except for two couples where only the woman has income). A small number of former junior college students live in relationships where only the man has income, the income of both partners seems only slightly positively correlated for the remaining couples. For lower levels of education, all four constellations are present. The frequency of couples where only the man has some income seems larger than the other way around. Ignoring the observations on the straight line, there is almost no association between the income of both partners. \index{Trellis plot|)} \section{Summary of Findings} Using relatively straightforward graphical techniques only on the two sets of data considered in this chapter we have been able to uncover a number of important features of each data set; \begin{description} \item[Melanoma mortality] Mortality is related only to the latitude of a state not to its longitude, mortality is higher for costal states than for land states, and the highest mortality is observed in the south costal states with latitude less than 32 degrees. \item[Health and family life] We saw that happiness depends on health status. Women reported to be very happy more often when they also reported a good or excellent health status. The dependency of happiness on the income of the women seems to be less clear, but we conclude that, conditional on education, the income of wives and their husbands is highly correlated. \end{description} \section{Final Comments} Producing publication-quality graphics is one of the major strengths of the \R{} system and almost anything is possible since graphics are programmable in \R{}. Naturally, this chapter can be only a very brief introduction to some commonly used displays and the reader is referred to specialized books, most important \cite{HSAUR:Murrell2005}, \cite{HSAUR:Sarkar2008}, and \cite{HSAUR:Chenetal2008}. Interactive 3D-graphics are available from package \Rpackage{rgl} \citep{PKG:rgl}. \section*{Exercises} \begin{description} \exercise The data in Table~\ref{DAGD-household-tab} are part of a data set collected from a survey of household expenditure and give the expenditure of $20$ single men and $20$ single women on four commodity groups. The units of expenditure are Hong Kong dollars, and the four commodity groups are \begin{description} \item[\Robject{housing}] housing, including fuel and light, \item[\Robject{food}] foodstuffs, including alcohol and tobacco, \item[\Robject{goods}] other goods, including clothing, footwear, and durable goods, \item[\Robject{service}] services, including transport and vehicles. \end{description} The aim of the survey was to investigate how the division of household expenditure between the four commodity groups depends on total expenditure and to find out whether this relationship differs for men and women. Use appropriate graphical methods to answer these questions and state your conclusions. <>= data("household", package = "HSAUR3") toLatex(HSAURtable(household), caption = paste("Household expenditure for single men and women."), label = "DAGD-household-tab") @ \exercise The data set shown in Table~\ref{DAGD-USstates-tab} contains values of seven variables for ten states in the US. The seven variables are \begin{description} \item[\Robject{Population}] population size divided by $1000$, \item[\Robject{Income}] average per capita income, \item[\Robject{Illiteracy}] illiteracy rate (\% population), \item[\Robject{Life.Expectancy}] life expectancy (years), \item[\Robject{Homicide}] homicide rate (per $1000$), \item[\Robject{Graduates}] percentage of high school graduates, \item[\Robject{Freezing}] average number of days per below freezing. \end{description} With these data \begin{enumerate} \item Construct a scatterplot matrix of the data labeling the points by state name (using function \Rcmd{text}). \item Construct a plot of life expectancy and homicide rate conditional on average per capita income. \end{enumerate} \begin{sidewaystable} \vspace*{12.5cm} \begin{center} <>= data("USstates", package = "HSAUR3") toLatex(HSAURtable(USstates), caption = paste("Socio-demographic variables for ten US states."), label = "DAGD-USstates-tab") @ \end{center} \end{sidewaystable} \exercise Mortality rates per $100,000$ from male suicides for a number of age groups and a number of countries are given in Table~\ref{DAGD-suicides2-tab}. Construct side-by-side box plots for the data from different age groups, and comment on what the graphic tells us about the data. <>= data("suicides2", package = "HSAUR3") toLatex(HSAURtable(suicides2), caption = paste("Mortality rates per $100,000$ from male suicides."), label = "DAGD-suicides2-tab", rownames = TRUE) @ \exercise \cite{HSAUR:FluryRiedwyl1988} report data that give various length measurements on $200$ Swiss bank notes. The data are available from package \Rpackage{mclust} \citep{PKG:mclust}; a sample of ten bank notes is given in Table~\ref{DAGD-banknote-tab}. <>= data("banknote", package = "mclust") banknote$Status <- NULL banknote <- banknote[c(1:5, 101:200),] toLatex(HSAURtable(banknote, pkg = "mclust", nrow = 10), caption = paste("Swiss bank note data."), label = "DAGD-banknote-tab", rownames = FALSE) @ Use whatever graphical techniques you think are appropriate to investigate whether there is any `pattern' or structure in the data. Do you observe something suspicious? \exercise The data in Table~\ref{DAGD-birds-tab} were originally derived from a study reported in \cite{HSAUR:Vuilleumier1970} which investigated numbers of bird species in isolated `islands' of paramo vegetation in the northern Andes. The aim of the study was to investigate how the number of species (\Robject{N}) is related to four other variables, \Robject{AR} (area of `island' in thousands of square km), \Robject{EL} (elevation in thousands of m), \Robject{Dec} (distance from Ecuador in km) and \Robject{DNI} (distance to the nearest `island' in km). Begin by constructing a scatterplot matrix of the data differentiating the islands on each panel by a different plotting symbol and on each diagonal panel showing the histogram of the associated variable. What can you conclude from this plot about how N is related to the other four variables? <>= data("birds", package = "HSAUR3") toLatex(HSAURtable(birds), caption = paste("Birds in paramo vegetation."), label = "DAGD-birds-tab", rownames = TRUE) @ \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_introduction_to_R.Rnw0000644000175000017500000015624114133304452020177 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{An Introduction to R} %%\VignetteDepends{sandwich} \setcounter{chapter}{0} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter{An Introduction to \R{} \label{AItR}} \setcounter{page}{1} \section{What is \R{}?} The \R{} system for statistical computing is an environment for data analysis and graphics. %% #Z %% and an implementation of the \R{} programming language. The root of \R{} is the \S{} language, developed by John Chambers and colleagues \citep{HSAUR:Becker+Chambers+Wilks:1988,HSAUR:Chambers+Hastie:1992,HSAUR:Chambers:1998} at Bell Laboratories (formerly AT\&T, now owned by Lucent Technologies) starting in the 1960s. The \S{} language was designed and developed as a programming language for data analysis tasks but in fact it is a full-featured programming language in its current implementations. The development of the \R{} system for statistical computing is heavily influenced by the open source idea: The base distribution of \R{} \index{Base distribution} and a large number of user-contributed extensions are available under the terms of the Free Software Foundation's GNU General %%' Public License in source code form. \index{GNU General Public License} This licence has two major implications for the data analyst working with \R. The complete source code is available and thus the practitioner can investigate the details of the implementation of a special method, make changes, and distribute modifications to colleagues. As a side effect, the \R{} system for statistical computing is available to everyone. All scientists, including, in particular, those working in developing countries, now have access to state-of-the-art tools for statistical data analysis without additional costs. With the help of the \R{} system for statistical computing, research really becomes reproducible when both the data and the results of all data analysis steps reported in a paper are available to the readers through an \R{} transcript file. \R{} is most widely used for teaching undergraduate and graduate statistics classes at universities all over the world because students can freely use the statistical computing tools. The base distribution of \R{} is maintained by a small group of statisticians, the \R{} Development Core Team. A huge amount of additional functionality is implemented in add-on packages \index{Add-on package} authored and maintained by a large group of volunteers. The main source of information about the \R{} system is the World Wide Web with the official home page of the \R{} project being \curl{http://www.R-project.org} All resources are available from this page: the \R{} system itself, a collection of add-on packages, manuals, documentation, and more. The intention of this chapter is to give a rather informal introduction to basic concepts and data manipulation techniques for the \R{} novice. Instead of a rigid treatment of the technical background, the most common tasks are illustrated by practical examples and it is our hope that this will enable readers to get started without too many problems. \section{Installing \R{}} \index{Base system|(} The \R{} system for statistical computing consists of two major parts: the base system and a collection of user-contributed add-on packages. The \R{} language is implemented in the base system. Implementations of statistical and graphical procedures are separated from the base system and are organized in the form of \stress{packages}. A package is \index{Add-on package} a collection of functions, examples, and documentation. The functionality of a package is often focused on a special statistical methodology. Both the base system and packages are distributed via the Comprehensive \R{} Archive Network (CRAN) accessible under \curl{http://CRAN.R-project.org} \index{Comprehensive R Archive Network (CRAN)@Comprehensive \R{} Archive Network (CRAN)} \subsection{The Base System and the First Steps \label{AItR:Base}} The base system is available in source form and in precompiled form for various Unix systems, Windows platforms and Mac OS X. For the data analyst, it is sufficient to download the precompiled binary distribution and install it locally. Windows users follow the link \curl{http://CRAN.R-project.org/bin/windows/base/release.htm} download the corresponding file (currently named \file{\Sexpr{HSAUR3:::exename()}}), execute it locally, and follow the instructions given by the installer. \index{Base system|)} \begin{wrapfigure}{lH}[0cm]{2cm} \includegraphics[width=1.95cm]{graphics/Rlogo_bw} \end{wrapfigure} Depending on the operating system, \R{} can be started either by typing `\texttt{R}' on the shell (Unix systems) or by clicking on the %' \R{} symbol (as shown left) created by the installer (Windows). \R{} comes without any frills and on start up shows simply a short introductory message including the version number and a prompt `\texttt{>}': %' \index{Prompt} <>= HSAUR3:::Rwelcome() @ <>= options(prompt = "> ") @ One can change the appearance of the prompt by <>= options(prompt = "R> ") @ and we will use the prompt \Rarg{R>} for the display of the code examples throughout this book. A \texttt{+} sign at the very beginning of a line indicates a continuing command after a newline. Essentially, the \R{} system evaluates commands typed on the \R{} prompt and returns the results of the computations. The end of a command is indicated by the return key. Virtually all introductory texts on \R{} start with an example using \R{} as a pocket calculator, and so do we: <>= x <- sqrt(25) + 2 @ This simple statement asks the \R{} interpreter to calculate $\sqrt{25}$ and then to add $2$. The result of the operation is assigned to an \R{} object \index{Object} with variable name \Robject{x}. The assignment operator \Roperator{<-} binds the value of its right-hand side to a variable name on the left-hand side. The value of the object \Robject{x} can be inspected simply by typing <>= x @ which, implicitly, calls the \Rcmd{print} method: <>= print(x) @ \subsection{Packages} \index{Add-on package|(} The base distribution already comes with some high-priority add-on packages, namely \begin{center} <>= colwidth <- 4 ip <- installed.packages(priority = "high") pkgs <- unique(ip[,"Package"]) pkgs <- paste("\\Rpackage{", pkgs, "}", sep = "") nrows <- ceiling(length(pkgs) / colwidth) pkgs <- c(pkgs, rep("", colwidth * nrows - length(pkgs))) cat(paste(c("\\begin{tabular}{", paste(rep("l", colwidth), collapse=""), "}"), collapse = ""), "\n", file = "tables/rec.tex", append = FALSE) for (i in 1:nrows) { cat(paste(pkgs[(1:colwidth) + (i-1)*colwidth], collapse = " & "), file = "tables/rec.tex", append = TRUE) cat("\\\\ \n", file = "tables/rec.tex", append = TRUE) } cat("\\end{tabular}\n", file = "tables/rec.tex", append = TRUE) rm(ip, nrows) @ \input{tables/rec} \end{center} Some of the packages listed here %% #Z %% are maintained by members of the \R{} core development team and implement standard statistical functionality, for example linear models, classical tests, a huge collection of high-level plotting functions or tools for survival analysis; many of these will be described and used in later chapters. Others provide basic infrastructure, for example for graphic systems, code analysis tools, graphical-user interfaces or other utilities. <>= cp <- available.packages(contriburl = "http://CRAN.r-project.org/src/contrib") ncp <- sum(!rownames(cp) %in% pkgs) rm(cp, pkgs) @ Packages not included in the base distribution can be installed directly from the \R{} prompt. At the time of writing this chapter, $\Sexpr{ncp}$ user-contributed packages covering almost all fields of statistical methodology were available. Certain so-called `task views' for special topics, such as statistics in the social sciences, environmetrics, robust statistics, etc., describe important and helpful packages and are available from \curl{http://CRAN.R-project.org/web/views/} <>= rm(ncp, colwidth, i) @ Given that an Internet connection is available, a package is installed by supplying the name of the package to the function \Rcmd{install.packages}. If, for example, add-on functionality for robust estimation of covariance matrices via sandwich estimators \index{Sandwich estimator} is required (for example in \Sexpr{ch("ALDII")}), the \Rpackage{sandwich} package \citep{PKG:sandwich} can be downloaded and installed via <>= install.packages("sandwich") @ The package functionality is available after \stress{attaching} the package by <>= library("sandwich") @ A comprehensive list of available packages can be obtained from \curl{http://CRAN.R-project.org/web/packages/} Note that on Windows operating systems, precompiled versions of packages are downloaded and installed. %%Currently, the service of overnight compilation of all packages on %%CRAN for the Windows platform is kindly offered by Uwe Ligges from the %%University of Dortmund, Germany. In contrast, packages are compiled locally before they are installed on Unix systems. \index{Add-on package|)} \section{Help and Documentation \label{AItR:HDN}} \index{Help system|(} Roughly, three different forms of documentation for the \R{} system for statistical computing may be distinguished: online help that comes with the base distribution or packages, electronic manuals, and publications work in the form of books, etc. The help system is a collection of manual pages describing each user-visible function and data set that comes with \R{}. A manual page is shown in a pager or Web browser when the name of the function we would like to get help for is supplied to the \Rcmd{help} function <>= help("mean") @ or, for short, \begin{Verbatim} R> ?mean \end{Verbatim} Each manual page consists of a general description, the argument list of the documented function with a description of each single argument, information about the return value of the function and, optionally, references, cross-links and, in most cases, executable examples. The function \Rcmd{help.search} is helpful for searching within manual pages. An overview on documented topics in an add-on package is given, for example for the \Rpackage{sandwich} package, by <>= help(package = "sandwich") @ Often a package comes along with an additional document describing the package functionality and giving examples. Such a document is called a \Rclass{vignette} \citep{HSAUR:Leisch2003,HSAUR:Gentleman2005}. For example, the \Rpackage{sandwich} package vignette is opened using <>= vignette("sandwich", package = "sandwich") @ More extensive documentation is available electronically from the collection of manuals at \curl{http://CRAN.R-project.org/manuals.html} For the beginner, at least the first and the second document of the following four manuals \citep{HSAUR:AItR,HSAUR:RDIE,HSAUR:RIA,HSAUR:WRE} are mandatory: \begin{description} \item[An Introduction to R] A more formal introduction to data analysis with \R{} than this chapter. \item[R Data Import/Export] A very useful description of how to read and write various external data formats. \item[R Installation and Administration] Hints for installing \R{} on special platforms. \item[Writing \R{} Extensions] The authoritative source on how to write \R{} programs and packages. \end{description} Both printed and online publications are available, the most important ones are \booktitle{Modern Applied Statistics with \S{}} \citep{HSAUR:VenablesRipley2002}, \booktitle{Introductory Statistics with \R{}} \citep{HSAUR:Dalgaard2002}, \booktitle{\R{} Graphics} \citep{HSAUR:Murrell2005} and the \R{} Newsletter, freely available from \curl{http://CRAN.R-project.org/doc/Rnews/} In case the electronically available documentation and the answers to frequently asked questions (FAQ), available from \curl{http://CRAN.R-project.org/faqs.html} \index{Frequently asked questions (FAQ)} have been consulted but a problem or question remains unsolved, the \texttt{r-help} email list is the right place to get answers to well-thought-out questions. It is helpful to read the posting guide \curl{http://www.R-project.org/posting-guide.html} before starting to ask. \index{Help system|)} \section{Data Objects in \R{}} \index{Forbes 2000 ranking|(} The data handling and manipulation techniques explained in this chapter will be illustrated by means of a data set of $2000$ world leading companies, the Forbes 2000 list for the year 2004 collected by \booktitle{Forbes Magazine}. This list is originally available from \curl{http://www.forbes.com} and, as an \R{} data object, it is part of the \Rpackage{HSAUR3} package (\textit{Source}: From Forbes.com, New York, New York, 2004. With permission.). In a first step, we make the data available for computations within \R. The \Rcmd{data} function searches for data objects of the specified name (\Robject{"Forbes2000"}) in the package specified via the \Rarg{package} argument and, if the search was successful, attaches the data object to the global environment: \index{Forbes2000 data@\Robject{Forbes2000} data} <>= data("Forbes2000", package = "HSAUR3") ls() @ <>= x <- c("x", "Forbes2000") print(x) @ The output of the \Rcmd{ls} function lists the names of all objects currently stored in the global environment, and, as the result of the previous command, a variable named \Robject{Forbes2000} is available for further manipulation. The variable \Robject{x} arises from the pocket calculator example in Subsection~\ref{AItR:Base}. As one can imagine, printing a list of $2000$ companies via <>= print(Forbes2000) @ <>= print(Forbes2000[1:3,]) cat("...\n") @ will not be particularly helpful in gathering some initial information about the data; it is more useful to look at a description of their structure found by using the following command <>= str(Forbes2000) @ <>= str(Forbes2000, vec.len = 2, strict.width = "cut", width = 60) @ The output of the \Rcmd{str} function tells us that \Robject{Forbes2000} is an object of class \Rclass{data.frame}, the most important data structure for handling tabular statistical data in \R. As expected, information about $2000$ observations, i.e., companies, are stored in this object. For each observation, the following eight variables are available: \begin{description} \item[\Robject{rank}] the ranking of the company, \item[\Robject{name}] the name of the company, \item[\Robject{country}] the country the company is situated in, \item[\Robject{category}] a category describing the products the company produces, \item[\Robject{sales}] the amount of sales of the company in billion US dollars, \item[\Robject{profits}] the profit of the company in billion US dollars, \item[\Robject{assets}] the assets of the company in billion US dollars, \item[\Robject{marketvalue}] the market value of the company in billion US dollars. \end{description} A similar but more detailed description is available from the help page for the \Robject{Forbes2000} object: <>= help("Forbes2000") @ or \begin{Verbatim} R> ?Forbes2000 \end{Verbatim} All information provided by \Rcmd{str} can be obtained by specialized functions as well and we will now have a closer look at the most important of these. The \R{} language is an object-oriented programming language, \index{Object-oriented programming language} so every object is an instance of a class. The name of the class of an object can be determined by <>= class(Forbes2000) @ Objects of class \Rclass{data.frame} represent data the traditional table-oriented way. Each row is associated with one single observation and each column corresponds to one variable. The dimensions of such a table can be extracted using the \Rcmd{dim} function <>= dim(Forbes2000) @ Alternatively, the numbers of rows and columns can be found using <>= nrow(Forbes2000) ncol(Forbes2000) @ The results of both statements show that \Robject{Forbes2000} has $\Sexpr{nrow(Forbes2000)}$ rows, i.e., observations, the companies in our case, with eight variables describing the observations. The variable names are accessible from <>= names(Forbes2000) @ The values of single variables can be extracted from the \Robject{Forbes2000} object by their names, for example the ranking of the companies <>= class(Forbes2000[,"rank"]) @ is stored as an integer variable. Brackets \Robject{[]} always indicate a subset \index{Subset} of a larger object, in our case a single variable extracted from the whole table. Because \Rclass{data.frame}s have two dimensions, observations and variables, the comma is required in order to specify that we want a subset of the second dimension, i.e., the variables. The rankings for all $\Sexpr{nrow(Forbes2000)}$ companies are represented in a \Rclass{vector} structure the length of which is given by <>= length(Forbes2000[,"rank"]) @ A \Rclass{vector} is the elementary structure for data handling in \R{} and is a set of simple elements, all being objects of the same class. For example, a simple vector of the numbers one to three can be constructed by one of the following commands <>= 1:3 c(1,2,3) seq(from = 1, to = 3, by = 1) @ The unique names of all $\Sexpr{nrow(Forbes2000)}$ companies are stored in a character vector \index{character vector@\Rclass{character} vector} <>= class(Forbes2000[,"name"]) length(Forbes2000[,"name"]) @ and the first element of this vector is <>= Forbes2000[,"name"][1] @ Because the companies are ranked, Citigroup is the world's largest %' company according to the Forbes 2000 list. Further details on vectors and subsetting are given in Section~\ref{AItR:BDM}. Nominal measurements are represented by \Rclass{factor} variables in \R, such as the category of the company's business segment %%' <>= class(Forbes2000[,"category"]) @ Objects of class \Rclass{factor} and \Rclass{character} basically differ in the way their values are stored internally. Each element of a vector of class \Rclass{character} is stored as a \Rclass{character} variable whereas an integer variable indicating the level of a \Rclass{factor} is saved for \Rclass{factor} objects. In our case, there are <>= nlevels(Forbes2000[,"category"]) @ different levels, i.e., business categories, which can be extracted by <>= levels(Forbes2000[,"category"]) @ <>= levels(Forbes2000[,"category"])[1:3] cat("...\n") @ As a simple summary statistic, the frequencies of the levels of such a \Rclass{factor} variable can be found from <>= table(Forbes2000[,"category"]) @ <>= table(Forbes2000[,"category"])[1:3] cat("...\n") @ The sales, assets, profits, and market value variables are of type \Robject{numeric}, the natural data type for continuous or discrete measurements, for example <>= class(Forbes2000[,"sales"]) @ and simple summary statistics such as the mean, median, and range can be found from <>= median(Forbes2000[,"sales"]) mean(Forbes2000[,"sales"]) range(Forbes2000[,"sales"]) @ The \Rcmd{summary} method can be applied to a numeric vector to give a set of useful summary statistics, namely the minimum, maximum, mean, median, and the $25\%$ and $75\%$ quartiles; for example <>= summary(Forbes2000[,"sales"]) @ \section{Data Import and Export} \index{Data import and export|(} In the previous section, the data from the Forbes 2000 list of the world's largest %%' companies were loaded into \R{} from the \Rpackage{HSAUR3} package but we will now explore practically more relevant ways to import data into the \R{} system. The most frequent data formats the data analyst is confronted with are comma separated files, \index{Comma separated files} \EXCEL{} spreadsheets, \index{Excel spreadsheets@\EXCEL{} spreadsheets} files in \SPSS{} format \index{SPSS file format@\SPSS{} file format} and a variety of \SQL{} data base engines. \index{SQL data bases@\SQL{} data bases} Querying data bases is a nontrivial task and requires additional knowledge about querying languages, and we therefore refer to the \booktitle{\R{} Data Import/Export} manual -- see Section~\ref{AItR:HDN}. <>= pkgpath <- system.file(package = "HSAUR2") mywd <- getwd() filep <- file.path(pkgpath, "rawdata") setwd(filep) @ We assume that a comma-separated file containing the Forbes 2000 list is available as \file{Forbes2000.csv} (such a file is part of the \Rpackage{HSAUR3} source package in directory \file{HSAUR3/inst/rawdata}). When the fields are separated by commas and each row begins with a name (a text format typically created by \EXCEL{}), we can read in the data as follows using the \Rcmd{read.table} function <>= csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1) @ The argument \Rarg{header = TRUE} indicates that the entries in the first line of the text file \Robject{"Forbes2000.csv"} should be interpreted as variable names. Columns are separated by a comma (\Rcmd{sep = ","}), users of continental versions of \EXCEL{} should take care of the character symbol coding for decimal points (by default \Rcmd{dec = "."}). Finally, the first column should be interpreted as row names but not as a variable (\Rarg{row.names = 1}). Alternatively, the function \Rcmd{read.csv} can be used to read comma-separated files. The function \Rcmd{read.table} by default guesses the class of each variable from the specified file. In our case, character variables are stored as factors <>= class(csvForbes2000[,"name"]) @ which is only suboptimal since the names of the companies are unique. However, we can supply the types for each variable to the \Rarg{colClasses} argument <>= csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1, colClasses = c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric")) class(csvForbes2000[,"name"]) @ and check if this object is identical to our previous Forbes 2000 list object <>= all.equal(csvForbes2000, Forbes2000) @ The argument \Rarg{colClasses} expects a character vector of length equal to the number of columns in the file. Such a vector can be supplied by the \Rcmd{c} function that combines the objects given in the parameter list into a \Rclass{vector} <>= classes <- c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric") length(classes) class(classes) @ An \R{} interface to the open data base connectivity (ODBC) standard \index{Open data base connectivity standard (ODBC)} is available in package \Rpackage{RODBC} and its functionality can be used to access \EXCEL{} and \ACCESS{} files directly: <>= library("RODBC") cnct <- odbcConnectExcel("Forbes2000.xls") sqlQuery(cnct, "select * from \"Forbes2000\\$\"") @ The function \Rcmd{odbcConnectExcel} opens a connection to the specified \EXCEL{} or \ACCESS{} file which can be used to send \SQL{} queries to the data base engine and retrieve the results of the query. <>= setwd(mywd) @ Files in \SPSS{} format are read in a way similar to reading comma-separated files, using the function \Rcmd{read.spss} from package \Rpackage{foreign} (which comes with the base distribution). Exporting data from \R{} is now rather straightforward. A comma-separated file readable by \EXCEL{} can be constructed from a \Rclass{data.frame} object via <>= write.table(Forbes2000, file = "Forbes2000.csv", sep = ",", col.names = NA) @ The function \Rcmd{write.csv} is one alternative and the functionality implemented in the \Rpackage{RODBC} package can be used to write data directly into \EXCEL{} spreadsheets as well. \index{Saving R objects@Saving \R{} objects} Alternatively, when data should be saved for later processing in \R{} only, \R{} objects of arbitrary kind can be stored into an external binary file via <>= save(Forbes2000, file = "Forbes2000.rda") @ where the extension \file{.rda} is standard. We can get the file names of all files with extension \file{.rda} from the working directory <>= list.files(pattern = "\\.rda") @ and we can load the contents of the file into \R{} by <>= load("Forbes2000.rda") @ \index{Data import and export|)} \section{Basic Data Manipulation \label{AItR:BDM}} \index{Data manipulation|(} The examples shown in the previous section have illustrated the importance of \Rclass{data.frame}s for storing and handling tabular data in \R. Internally, a \Rclass{data.frame} is a \Rclass{list} of vectors of a common length $n$, the number of rows of the table. Each of those vectors represents the measurements of one variable and we have seen that we can access such a variable by its name, for example the names of the companies <>= companies <- Forbes2000[,"name"] @ Of course, the \Robject{companies} vector is of class \Rclass{character} and of length $\Sexpr{length(companies)}$. A subset \index{Subset} of the elements of the vector \Robject{companies} can be extracted using the \Rcmd{[]} subset operator. For example, the largest of the $2000$ companies listed in the Forbes 2000 list is <>= companies[1] @ and the top three companies can be extracted utilizing an integer vector of the numbers one to three: <>= 1:3 companies[1:3] @ In contrast to indexing with positive integers, negative indexing returns \index{negative indexing} all elements that are \stress{not} part of the index vector given in brackets. For example, all companies except those with numbers four to two thousand, i.e., the top three companies, are again <>= companies[-(4:2000)] @ The complete information about the top three companies can be printed in a similar way. Because \Rclass{data.frame}s have a concept of rows and columns, we need to separate the subsets corresponding to rows and columns by a comma. The statement <>= Forbes2000[1:3, c("name", "sales", "profits", "assets")] @ extracts the variables \Robject{name}, \Robject{sales}, \Robject{profits} and \Robject{assets} for the three largest companies. Alternatively, a single variable can be extracted from a \Rclass{data.frame} by <>= companies <- Forbes2000$name @ which is equivalent to the previously shown statement <>= companies <- Forbes2000[,"name"] @ We might be interested in extracting the largest companies with respect to an alternative ordering. The three top-selling companies can be computed along the following lines. First, we need to compute the ordering of the companies' sales %%' <>= order_sales <- order(Forbes2000$sales) @ which returns the indices of the ordered elements of the numeric vector \Robject{sales}. Consequently the three companies with the lowest sales are <>= companies[order_sales[1:3]] @ The indices of the three top sellers are the elements $1998, 1999$ and $2000$ of the integer vector \Robject{order\_sales} <>= Forbes2000[order_sales[c(2000, 1999, 1998)], c("name", "sales", "profits", "assets")] @ Another way of selecting vector elements is the use of a logical vector being \Robject{TRUE} when the corresponding element is to be selected and \Robject{FALSE} otherwise. The companies with assets of more than $1000$ billion US dollars are <>= Forbes2000[Forbes2000$assets > 1000, c("name", "sales", "profits", "assets")] @ where the expression \Robject{Forbes2000\$assets > 1000} indicates a logical vector of length $2000$ with <>= table(Forbes2000$assets > 1000) @ elements being either \Robject{FALSE} or \Robject{TRUE}. In fact, for some of the companies the measurement of the \Robject{profits} variable are missing. In \R, missing values are treated by a special symbol, \Robject{NA}, indicating \index{NA symbol@\Robject{NA} symbol} that this measurement is not available. \index{Missing values} The observations with profit information missing can be obtained via <>= na_profits <- is.na(Forbes2000$profits) table(na_profits) Forbes2000[na_profits, c("name", "sales", "profits", "assets")] @ where the function \Rcmd{is.na} returns a logical vector being \Robject{TRUE} when the corresponding element of the supplied vector is \Robject{NA}. A more comfortable approach is available when we want to remove all observations with at least one missing value from a \Rclass{data.frame} object. The function \Rcmd{complete.cases} takes a \Rclass{data.frame} and returns a logical vector being \Robject{TRUE} when the corresponding observation does not contain any missing value: <>= table(complete.cases(Forbes2000)) @ Subsetting \Rclass{data.frame}s driven by logical expressions may induce a lot of typing which can be avoided. The \Rcmd{subset} function takes a \Rclass{data.frame} as first argument and a logical expression as second argument. For example, we can select a subset of the Forbes 2000 list consisting of all companies situated in the United Kingdom by <>= UKcomp <- subset(Forbes2000, country == "United Kingdom") dim(UKcomp) @ i.e., $\Sexpr{nrow(UKcomp)}$ of the $2000$ companies are from the UK. Note that it is not necessary to extract the variable \Robject{country} from the \Rclass{data.frame} \Robject{Forbes2000} when formulating the logical expression with \Rcmd{subset}. \index{Data manipulation|)} \section{Computing with Data} \subsection{Simple Summary Statistics} Two functions are helpful for getting an overview about \R{} objects: \Rcmd{str} and \Rcmd{summary}, where \Rcmd{str} is more detailed about data types and \Rcmd{summary} gives a collection of sensible summary statistics. For example, applying the \Rcmd{summary} method to the \Robject{Forbes2000} data set, <>= summary(Forbes2000) @ results in the following output <>= summary(Forbes2000) @ From this output we can immediately see that most of the companies are situated in the US and that most of the companies are working in the banking sector as well as that negative profits, or losses, up to $\Sexpr{abs(round(min(Forbes2000$profits, na.rm = TRUE)))}$ billion US dollars occur. Internally, \Rcmd{summary} is a so-called \stress{generic function} \index{Generic function} with methods for a multitude of classes, i.e., \Rcmd{summary} can be applied to objects of different classes and will report sensible results. Here, we supply a \Rclass{data.frame} object to \Rcmd{summary} where it is natural to apply \Rcmd{summary} to each of the variables in this \Rclass{data.frame}. Because a \Rclass{data.frame} is a \Rclass{list} with each variable being an element of that \Rclass{list}, the same effect can be achieved by <>= lapply(Forbes2000, summary) @ \index{apply family@\Rcmd{apply} family} The members of the \Rcmd{apply} family help to solve recurring tasks for each element of a \Rclass{data.frame}, \Rclass{matrix}, \Rclass{list} or for each level of a \Rclass{factor}. It might be interesting to compare the profits in each of the $\Sexpr{nlevels(Forbes2000$category)}$ categories. To do so, we first compute the median profit for each category from <>= mprofits <- tapply(Forbes2000$profits, Forbes2000$category, median, na.rm = TRUE) @ a command that should be read as follows. For each level of the factor \Robject{category}, determine the corresponding elements of the numeric vector \Robject{profits} and supply them to the \Rcmd{median} function with additional argument \Rarg{na.rm = TRUE}. The latter one is necessary because \Robject{profits} contains missing values which would lead to a non-sensible result of the \Rcmd{median} function <>= median(Forbes2000$profits) @ The three categories with highest median profit are computed from the vector of sorted median profits <>= rev(sort(mprofits))[1:3] @ where \Rcmd{rev} rearranges the vector of median profits \Rcmd{sort}ed from smallest to largest. Of course, we can replace the \Rcmd{median} function with \Rcmd{mean} or whatever is appropriate in the call to \Rcmd{tapply}. In our situation, \Rcmd{mean} is not a good choice, because the distributions of profits or sales are naturally skewed. Simple graphical tools for the inspection of the empirical distributions are introduced later on and in \Sexpr{ch("DAGD")}. \subsection{Customizing Analyses} \index{Functions|(} In the preceding sections we have done quite complex analyses on our data using functions available from \R{}. However, the real power of the system comes to light when writing our own functions for our own analysis tasks. Although \R{} is a full-featured programming language, writing small helper functions for our daily work is not too complicated. We'll study two example cases. At first, we want to add a robust measure of variability to the location measures computed in the previous subsection. In addition to the median profit, computed via <>= median(Forbes2000$profits, na.rm = TRUE) @ we want to compute the inter-quartile range, i.e., the difference between the 3rd and 1st quartile. Although a quick search in the manual pages (via \texttt{help("interquartile")}) brings function \Rcmd{IQR} to our attention, we will approach this task without making use of this tool, but using function \Rcmd{quantile} for computing sample quantiles only. A function in \R{} is nothing but an object, and all objects are created equal. Thus, we `just' have to assign a \Rclass{function} object to a variable. A \Rclass{function} object consists of an argument list, defining arguments and possibly default values, and a body defining the computations. The body starts and ends with braces. Of course, the body is assumed to be valid \R{} code. In most cases we expect a function to return an object, therefore, the body will contain one or more \Rcmd{return} statements the arguments of which define the return values. Returning to our example, we'll name our function \Rcmd{iqr}. The \Rcmd{iqr} function should operate on numeric vectors, therefore it should have an argument \Robject{x}. This numeric vector will be passed on to the \Rcmd{quantile} function for computing the sample quartiles. The required difference between the $3^\text{rd}$ and $1^\text{st}$ quartile can then be computed using \Rcmd{diff}. The definition of our function reads as follows <>= iqr <- function(x) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE) return(diff(q)) } @ A simple test on simulated data from a standard normal distribution shows that our first function actually works, a comparison with the \Rcmd{IQR} function shows that the result is correct: <>= xdata <- rnorm(100) iqr(xdata) IQR(xdata) @ However, when the numeric vector contains missing values, our function fails as the following example shows: <>= xdata[1] <- NA iqr(xdata) @ <>= xdata[1] <- NA cat(try(iqr(xdata))) @ In order to make our little function more flexible it would be helpful to add all arguments of \Rcmd{quantile} to the argument list of \Rcmd{iqr}. The copy-and-paste approach that first comes to mind is likely to lead to inconsistencies and errors, for example when the argument list of \Rcmd{quantile} changes. Instead, the dot argument, a wildcard for any argument, is more appropriate and we redefine our function accordingly: <>= iqr <- function(x, ...) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE, ...) return(diff(q)) } iqr(xdata, na.rm = TRUE) IQR(xdata, na.rm = TRUE) @ Now, we can assess the variability of the profits using our new \Rcmd{iqr} tool: <>= iqr(Forbes2000$profits, na.rm = TRUE) @ Since there is no difference between functions that have been written by one of the \R{} developers and user-created functions, we can compute the inter-quartile range of profits for each of the business categories by using our \Rcmd{iqr} function inside a \Rcmd{tapply} statement; <>= iqr_profits <- tapply(Forbes2000$profits, Forbes2000$category, iqr, na.rm = TRUE) @ and extract the categories with the smallest and greatest variability <>= levels(Forbes2000$category)[which.min(iqr_profits)] levels(Forbes2000$category)[which.max(iqr_profits)] @ We observe less variable profits in tourism enterprises compared with profits in the pharmaceutical industry. As other members of the \Rcmd{apply} family, \Rcmd{tapply} is very helpful when the same task is to be done more than one time. Moreover, its use is more convenient compared to the usage of \Rcmd{for} loops. For the sake of completeness, we will compute the category-wise inter-quartile range of the profits using a \Rcmd{for} loop. \index{Functions|)} \index{Loops|(} Like a \Rclass{function}, a \Rcmd{for} loop consists of a body, i.e., a chain of \R{} commands to be executed. In addition, we need a set of values and a variable that iterates over this set. Here, the set we are interested in is the business categories: <>= bcat <- Forbes2000$category iqr_profits2 <- numeric(nlevels(bcat)) names(iqr_profits2) <- levels(bcat) for (cat in levels(bcat)) { catprofit <- subset(Forbes2000, category == cat)$profit this_iqr <- iqr(catprofit, na.rm = TRUE) iqr_profits2[levels(bcat) == cat] <- this_iqr } @ Compared to the usage of \Rcmd{tapply}, the above code is rather complicated. At first, we have to set up a vector for storing the results and assign the appropriate names to it. Next, inside the body of the \Rcmd{for} loop, the \Rcmd{iqr} function has to be called on the appropriate subset of all companies of the current business category \Robject{cat}. The corresponding inter-quartile range must then be assigned to the correct vector element in the result vector. Luckily, such complicated constructs will be used in only one of the remaining chapters of the book and are almost always avoidable in practical data analyses. \index{Loops|)} \subsection{Simple Graphics} The degree of skewness of a distribution can be investigated by constructing histograms using the \Rcmd{hist} function. (More sophisticated alternatives such as smooth density estimates will be considered in \Sexpr{ch("DE")}.) \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 2)) hist(Forbes2000$marketvalue) hist(log(Forbes2000$marketvalue)) @ \caption{Histograms of the market value and the logarithm of the market value for the companies contained in the Forbes 2000 list. \label{AItR:densplot}} \end{center} \end{figure} For example, the code for producing Figure~\ref{AItR:densplot} first divides the plot region into two equally spaced rows (the \Rcmd{layout} function) and then plots the histograms of the raw market values in the upper part using the \Rcmd{hist} function. The lower part of the figure depicts the histogram for the log-transformed market values which appear to be more symmetric. Bivariate relationships of two continuous variables are usually depicted as scatterplots. In \R, regression relationships are specified by so-called \stress{model formulae} which, in a simple bivariate case, may look like <>= fm <- marketvalue ~ sales class(fm) @ with the dependent variable on the left-hand side and the independent variable on the right-hand side. The tilde separates left- and right-hand sides. Such a model formula can be passed to a model function (for example to the linear model function as explained in \Sexpr{ch("MLR")}). The \Rcmd{plot} generic function implements a \Rclass{formula} method as well. Because the distributions of both market value and sales are skewed we choose to depict their logarithms. A raw scatterplot of $2000$ data points (Figure~\ref{AItR:scatter-raw}) is rather uninformative due to areas with very high density. This problem can be avoided by choosing a transparent color for the dots as shown in Figure~\ref{AItR:scatter}. \begin{figure} \begin{center} <>= plot(log(marketvalue) ~ log(sales), data = Forbes2000, pch = ".") @ \caption{Raw scatterplot of the logarithms of market value and sales. \label{AItR:scatter-raw}} \end{center} \end{figure} \begin{figure} \begin{center} <>= plot(log(marketvalue) ~ log(sales), data = Forbes2000, col = rgb(0,0,0,0.1), pch = 16) @ \caption{Scatterplot with transparent shading of points of the logarithms of market value and sales. \label{AItR:scatter}} \end{center} \end{figure} If the independent variable is a factor, a boxplot representation is a natural choice. For four selected countries, the distributions of the logarithms of the market value may be visually compared in Figure~\ref{AItR:box}. Prior to calling the \Rcmd{plot} function on our data, we have to remove empty levels from the \Robject{country} variable, because otherwise the $x$-axis would show all and not only the selected countries. This task is most easily performed by subsetting the corresponding factor with additional argument \Rcmd{drop = TRUE}. \index{Boxplot} \begin{figure} \begin{center} <>= tmp <- subset(Forbes2000, country %in% c("United Kingdom", "Germany", "India", "Turkey")) tmp$country <- tmp$country[,drop = TRUE] plot(log(marketvalue) ~ country, data = tmp, ylab = "log(marketvalue)", varwidth = TRUE) @ \caption{Boxplots of the logarithms of the market value for four selected countries, the width of the boxes is proportional to the square roots of the number of companies. \label{AItR:box}} \end{center} \end{figure} Here, the width of the boxes are proportional to the square root of the number of companies for each country and extremely large or small market values are depicted by single points. More elaborate graphical methods will be discussed in \Sexpr{ch("DAGD")}. \index{Forbes 2000 ranking|)} \section{Organizing an Analysis} <>= file.create("analysis.R") @ Although it is possible to perform an analysis typing all commands directly on the \R{} prompt it is much more comfortable to maintain a separate text file collecting all steps necessary to perform a certain data analysis task. Such an \R{} transcript file, for example called \file{analysis.R} created with your favorite text editor, can be sourced into \R{} using the \Rcmd{source} command <>= source("analysis.R", echo = TRUE) @ When all steps of a data analysis, i.e., data preprocessing, transformations, simple summary statistics and plots, model building and inference as well as reporting, are collected in such an \R{} transcript file, the analysis can be reproduced at any time, maybe with corrected or updated data as it frequently happens in our consulting practice. <>= file.remove("analysis.R") @ \section{Summary of Findings} Data manipulation precedes every statistical analysis and is often more complex than the final model fitting and display. The \R{} language in itself is very powerful and allows efficient data manipulation. For really large data sets that do not fit into the random access memory of the computer, we have to store the data elsewhere, for example in database systems or flat files. Packages for accessing the data from these sources are described in the `Large memory and out-of-memory data' section of the `High-performance and parallel computing' task view. \section{Final Comments} Reading data into \R{} is possible in many different ways, including direct connections to data base engines. Tabular data are handled by \Rclass{data.frame}s in \R{}, and the usual data manipulation techniques such as sorting, ordering or subsetting can be performed by simple \R{} statements. An overview on data stored in a \Rclass{data.frame} is given mainly by two functions: \Rcmd{summary} and \Rcmd{str}. Simple graphics such as histograms and scatterplots can be constructed by applying the appropriate \R{} functions (\Rcmd{hist} and \Rcmd{plot}) and we shall give many more examples of these functions and those that produce more interesting graphics in later chapters. \section*{Exercises} \begin{description} \exercise Calculate the median profit for the companies in the US and the median profit for the companies in the UK, France, and Germany. \exercise Find all German companies with negative profit. \exercise To which business category do most of the Bermuda island companies belong? \exercise For the $50$ companies in the Forbes data set with the highest profits, plot sales against assets (or some suitable transformation of each variable), labeling each point with the appropriate country name which may need to be abbreviated (using \Rcmd{abbreviate}) to avoid making the plot look too `messy'. %%' \exercise Find the average value of sales for the companies in each country in the Forbes data set, and find the number of companies in each country with profits above $5$ billion US dollars. \exercise List all the products made by companies in the UK. \exercise Plot sales against market value for companies in the UK and in Germany using different plotting symbols for the two countries. \exercise For the ten companies in the UK with the greatest profits construct a bar chart of profits labeled with the companies' name. \exercise How many of the $20$ companies with the greatest market value are from the US and how many are from the UK? \exercise Construct a histogram of profits for all companies in Germany with assets above three billion dollars; how many such companies are there? And which product does the company with the greatest profit make? \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/LaTeXBibTeX/0000755000175000017500000000000014133304614015373 5ustar nileshnileshHSAUR3/vignettes/LaTeXBibTeX/refstyle.bst0000755000175000017500000006715712357775377020015 0ustar nileshnilesh%% %% This is file `refstyle.bst', %% generated with the docstrip utility. %% %% The original source files were: %% %% merlin.mbs (with options: `,ay,nat,nm-rev,keyxyr,dt-beg,yr-par,note-yr,tit-qq,vnum-x,volp-com,add-pub,pre-pub,isbn,issn,url,url-blk,edby,edbyx,blk-com,pp,ed,xedn') %% ---------------------------------------- %% %% Copyright 1994-1999 Patrick W Daly % =============================================================== % IMPORTANT NOTICE: % This bibliographic style (bst) file has been generated from one or % more master bibliographic style (mbs) files, listed above. % % This generated file can be redistributed and/or modified under the terms % of the LaTeX Project Public License Distributed from CTAN % archives in directory macros/latex/base/lppl.txt; either % version 1 of the License, or any later version. % =============================================================== % Name and version information of the main mbs file: % \ProvidesFile{merlin.mbs}[1999/05/28 3.89 (PWD)] % For use with BibTeX version 0.99a or later %------------------------------------------------------------------- % This bibliography style file is intended for texts in ENGLISH % This is an author-year citation style bibliography. As such, it is % non-standard LaTeX, and requires a special package file to function properly. % Such a package is natbib.sty by Patrick W. Daly % The form of the \bibitem entries is % \bibitem[Jones et al.(1990)]{key}... % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}... % The essential feature is that the label (the part in brackets) consists % of the author names, as they should appear in the citation, with the year % in parentheses following. There must be no space before the opening % parenthesis! % With natbib v5.3, a full list of authors may also follow the year. % In natbib.sty, it is possible to define the type of enclosures that is % really wanted (brackets or parentheses), but in either case, there must % be parentheses in the label. % The \cite command functions as follows: % \citet{key} ==>> Jones et al. (1990) % \citet*{key} ==>> Jones, Baker, and Smith (1990) % \citep{key} ==>> (Jones et al., 1990) % \citep*{key} ==>> (Jones, Baker, and Smith, 1990) % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990) % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32) % \citeauthor{key} ==>> Jones et al. % \citeauthor*{key} ==>> Jones, Baker, and Smith % \citeyear{key} ==>> 1990 %--------------------------------------------------------------------- ENTRY { address author booktitle chapter edition editor howpublished institution isbn issn journal key month note number organization pages publisher school series title type url volume year } {} { label extra.label sort.label short.list } INTEGERS { output.state before.all mid.sentence after.sentence after.block } FUNCTION {init.state.consts} { #0 'before.all := #1 'mid.sentence := #2 'after.sentence := #3 'after.block := } STRINGS { s t } FUNCTION {output.nonnull} { 's := output.state mid.sentence = { ", " * write$ } { output.state after.block = { add.period$ write$ newline$ "\newblock " write$ } { output.state before.all = 'write$ { add.period$ " " * write$ } if$ } if$ mid.sentence 'output.state := } if$ s } FUNCTION {output} { duplicate$ empty$ 'pop$ 'output.nonnull if$ } FUNCTION {output.check} { 't := duplicate$ empty$ { pop$ "empty " t * " in " * cite$ * warning$ } 'output.nonnull if$ } FUNCTION {fin.entry} { add.period$ write$ newline$ } FUNCTION {new.block} { output.state before.all = 'skip$ { after.block 'output.state := } if$ } FUNCTION {new.sentence} { output.state after.block = 'skip$ { output.state before.all = 'skip$ { after.sentence 'output.state := } if$ } if$ } FUNCTION {add.blank} { " " * before.all 'output.state := } FUNCTION {date.block} { skip$ } FUNCTION {not} { { #0 } { #1 } if$ } FUNCTION {and} { 'skip$ { pop$ #0 } if$ } FUNCTION {or} { { pop$ #1 } 'skip$ if$ } FUNCTION {non.stop} { duplicate$ "}" * add.period$ #-1 #1 substring$ "." = } 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Journal on Computing"} MACRO {tocs} {"ACM Transactions on Computer Systems"} MACRO {tods} {"ACM Transactions on Database Systems"} MACRO {tog} {"ACM Transactions on Graphics"} MACRO {toms} {"ACM Transactions on Mathematical Software"} MACRO {toois} {"ACM Transactions on Office Information Systems"} MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} MACRO {tcs} {"Theoretical Computer Science"} FUNCTION {format.url} { url empty$ { "" } { "\urlprefix\url{" url * "}" * } if$ } INTEGERS { nameptr namesleft numnames } FUNCTION {format.names} { 's := "" 't := #1 'nameptr := s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ s nameptr "{ll}" format.name$ duplicate$ "others" = { 't := } { pop$ } if$ t "others" = { " " * bbl.etal * } { bbl.and space.word * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := namesleft #1 - 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{ bbl.chapter } { type "l" change.case$ } if$ chapter tie.or.space.connect pages empty$ 'skip$ { ", " * format.pages * } if$ } if$ } FUNCTION {format.in.ed.booktitle} { booktitle empty$ { "" } { editor empty$ { word.in booktitle emphasize * } { word.in booktitle emphasize * ", " * editor num.names$ #1 > { bbl.editors } { bbl.editor } if$ * " " * format.in.editors * } if$ } if$ } FUNCTION {format.thesis.type} { type empty$ 'skip$ { pop$ type "t" change.case$ } if$ } FUNCTION {format.tr.number} { type empty$ { bbl.techrep } 'type if$ number empty$ { "t" change.case$ } { number tie.or.space.connect } if$ } FUNCTION {format.article.crossref} { word.in " \cite{" * crossref * "}" * } FUNCTION {format.book.crossref} { volume empty$ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ word.in } { bbl.volume volume tie.or.space.connect bbl.of space.word * } if$ " \cite{" * crossref * "}" * } FUNCTION {format.incoll.inproc.crossref} { word.in " \cite{" * crossref * "}" * } FUNCTION {format.org.or.pub} { 't := "" address empty$ t empty$ and 'skip$ { address empty$ 'skip$ { address * } if$ t empty$ 'skip$ { address empty$ 'skip$ { ": " * } if$ t * } if$ } if$ } FUNCTION {format.publisher.address} { publisher empty$ { "empty publisher in " cite$ * warning$ "" } { publisher } if$ format.org.or.pub } FUNCTION {format.organization.address} { organization empty$ { "" } { organization } if$ format.org.or.pub } FUNCTION {article} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { journal emphasize "journal" output.check format.vol.num.pages output } { format.article.crossref output.nonnull format.pages output } if$ format.issn output format.url output format.note output fin.entry } FUNCTION {book} { output.bibitem author empty$ { format.editors "author and editor" output.check editor format.key output } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ format.date "year" output.check date.block format.btitle "title" output.check crossref missing$ { format.bvolume output format.number.series output format.publisher.address output } { format.book.crossref output.nonnull } if$ format.edition output format.isbn output format.url output format.note output fin.entry } FUNCTION {booklet} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title howpublished output address output format.isbn output format.url output format.note output fin.entry } FUNCTION {inbook} { output.bibitem author empty$ { format.editors "author and editor" output.check editor format.key output } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ format.date "year" output.check date.block format.btitle "title" output.check crossref missing$ { format.publisher.address output format.bvolume output format.chapter.pages "chapter and pages" output.check format.number.series output } { format.chapter.pages "chapter and pages" output.check format.book.crossref output.nonnull } if$ format.edition output crossref missing$ { format.isbn output } 'skip$ if$ format.url output format.note output fin.entry } FUNCTION {incollection} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { format.in.ed.booktitle "booktitle" output.check format.publisher.address output format.bvolume output format.number.series output format.chapter.pages output format.edition output format.isbn output } { format.incoll.inproc.crossref output.nonnull format.chapter.pages output } if$ format.url output format.note output fin.entry } FUNCTION {inproceedings} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { format.in.ed.booktitle "booktitle" output.check publisher empty$ { format.organization.address output } { organization output format.publisher.address output } if$ format.bvolume output format.number.series output format.pages output format.isbn output format.issn output } { format.incoll.inproc.crossref output.nonnull format.pages output } if$ format.url output format.note output fin.entry } FUNCTION {conference} { inproceedings } FUNCTION {manual} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.btitle "title" output.check organization output address output format.edition output format.url output format.note output fin.entry } FUNCTION {mastersthesis} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.btitle "title" output.check bbl.mthesis format.thesis.type output.nonnull school "school" output.check address output format.url output format.note output fin.entry } FUNCTION {misc} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.title output end.quote.title howpublished output format.url output format.note output fin.entry } FUNCTION {phdthesis} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.btitle "title" output.check bbl.phdthesis format.thesis.type output.nonnull school "school" output.check address output format.url output format.note output fin.entry } FUNCTION {proceedings} { output.bibitem format.editors output editor format.key output format.date "year" output.check date.block format.btitle "title" output.check format.bvolume output format.number.series output publisher empty$ { format.organization.address output } { organization output format.publisher.address output } if$ format.isbn output format.issn output format.url output format.note output fin.entry } FUNCTION {techreport} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title format.tr.number output.nonnull institution "institution" output.check address output format.url output format.note output fin.entry } FUNCTION {unpublished} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title format.url output format.note "note" output.check fin.entry } FUNCTION {default.type} { misc } READ FUNCTION {sortify} { purify$ "l" change.case$ } INTEGERS { len } FUNCTION {chop.word} { 's := 'len := s #1 len substring$ = { s len #1 + global.max$ substring$ } 's if$ } FUNCTION {format.lab.names} { 's := "" 't := s #1 "{vv~}{ll}" format.name$ s num.names$ duplicate$ #2 > { pop$ " " * bbl.etal * } { #2 < 'skip$ { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = { " " * bbl.etal * } { bbl.and space.word * s #2 "{vv~}{ll}" format.name$ * } if$ } if$ } if$ } FUNCTION {author.key.label} { author empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { author format.lab.names } if$ } FUNCTION {author.editor.key.label} { author empty$ { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } { author format.lab.names } if$ } FUNCTION {editor.key.label} { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } FUNCTION {calc.short.authors} { type$ "book" = type$ "inbook" = or 'author.editor.key.label { type$ "proceedings" = 'editor.key.label 'author.key.label if$ } if$ 'short.list := } FUNCTION {calc.label} { calc.short.authors short.list "(" * year duplicate$ empty$ short.list key field.or.null = or { pop$ "????" } 'skip$ if$ * 'label := } FUNCTION {sort.format.names} { 's := #1 'nameptr := "" s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" format.name$ 't := nameptr #1 > { " " * namesleft #1 = t "others" = and { "zzzzz" * } { t sortify * } if$ } { t sortify * } if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {sort.format.title} { 't := "A " #2 "An " #3 "The " #4 t chop.word chop.word chop.word sortify #1 global.max$ substring$ } FUNCTION {author.sort} { author empty$ { key empty$ { "to sort, need author or key in " cite$ * warning$ "" } { key sortify } if$ } { author sort.format.names } if$ } FUNCTION {author.editor.sort} { author empty$ { editor empty$ { key empty$ { "to sort, need author, editor, or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } { author sort.format.names } if$ } FUNCTION {editor.sort} { editor empty$ { key empty$ { "to sort, need editor or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } FUNCTION {presort} { calc.label label sortify " " * type$ "book" = type$ "inbook" = or 'author.editor.sort { type$ "proceedings" = 'editor.sort 'author.sort if$ } if$ #1 entry.max$ substring$ 'sort.label := sort.label * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {presort} SORT STRINGS { last.label next.extra } INTEGERS { last.extra.num number.label } FUNCTION {initialize.extra.label.stuff} { #0 int.to.chr$ 'last.label := "" 'next.extra := #0 'last.extra.num := #0 'number.label := } FUNCTION {forward.pass} { last.label label = { last.extra.num #1 + 'last.extra.num := last.extra.num int.to.chr$ 'extra.label := } { "a" chr.to.int$ 'last.extra.num := "" 'extra.label := label 'last.label := } if$ number.label #1 + 'number.label := } FUNCTION {reverse.pass} { next.extra "b" = { "a" 'extra.label := } 'skip$ if$ extra.label 'next.extra := extra.label duplicate$ empty$ 'skip$ { "{\natexlab{" swap$ * "}}" * } if$ 'extra.label := label extra.label * 'label := } EXECUTE {initialize.extra.label.stuff} ITERATE {forward.pass} REVERSE {reverse.pass} FUNCTION {bib.sort.order} { sort.label " " * year field.or.null sortify * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {bib.sort.order} SORT FUNCTION {begin.bib} { preamble$ empty$ 'skip$ { preamble$ write$ newline$ } if$ "\begin{thebibliography}{" number.label int.to.str$ * "}" * write$ newline$ "\newcommand{\enquote}[1]{``#1''}" write$ newline$ "\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi" write$ newline$ "\expandafter\ifx\csname url\endcsname\relax" write$ newline$ " \def\url#1{{\tt #1}}\fi" write$ newline$ "\expandafter\ifx\csname urlprefix\endcsname\relax\def\urlprefix{URL }\fi" write$ newline$ } EXECUTE {begin.bib} EXECUTE {init.state.consts} ITERATE {call.type$} FUNCTION {end.bib} { newline$ "\end{thebibliography}" write$ newline$ } EXECUTE {end.bib} %% End of customized bst file %% %% End of file `jasa.bst'. HSAUR3/vignettes/LaTeXBibTeX/setup.Rnw0000644000175000017500000000316212627003544017231 0ustar nileshnilesh \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} HSAUR3/vignettes/LaTeXBibTeX/HSAUR.bib0000644000175000017500000023027112357775377016770 0ustar nileshnilesh> library(utils); library(HSAUR2); HSAUR2:::pkgyears("tmp") > library(utils); library(HSAUR2); HSAUR2:::pkgversions("HSAUR.in") @manual{HSAUR:R, title = {R: A Language and Environment for Statistical Computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:AItR, title = {An Introduction to R}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:RDIE, title = {R Data Import/Export}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:RIA, title = {R Installation and Administration}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:WRE, title = {Writing R Extensions}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @book{HSAUR:Ripley1996, key = {216}, author = {Ripley, Brian D.}, title = {{Pattern} Recognition and Neural Networks}, year = {1996}, publisher = {Cambridge University Press}, address = {Cambridge, UK}, url = {http://www.stats.ox.ac.uk/pub/PRNN/}, pages = 403 } %% Chapter: Analysing Longitudinal Data @article{HSAUR:WatkinsWilliams1998, author = {E. Watkins and R. Williams}, title = {The efficacy of cognitive behavioural therapy}, journal = {Journal of Counseling and Clinical Psychology}, year = 1998, volume = 27, pages = {31-39} } %% et al? @article{HSAUR:Proudfootetal2003, author = {J. Proudfoot and D. Goldberg and A. Mann and B. S. Everitt and I. Marks and J. A. Gray}, title = {Computerized, interactive, multimedia cognitive-behavioural program for anxiety and depression in general practice}, journal = {Psychological Medicine}, year = 2003, volume = 33, number = 2, pages = {217-227} } %% edition? @manual{HSAUR:Becketal1996, author = {A. Beck and R. Steer and G. Brown}, title = {BDI-II Manual}, year = 1996, edition = {2nd}, organization = {The Psychological Corporation, San Antonio} } @book{HSAUR:Diggleetal2003, author = {P. J. Diggle and P. J. Heagerty and K. Y. Liang and S. L. Zeger}, title = {Analysis of Longitudinal Data}, year = {2003}, publisher = {Oxford University Press}, address = {Oxford, UK} } @book{HSAUR:Longford1993, author = {N. T. Longford}, title = {Random Coefficient Models}, year = {1993}, publisher = {Oxford University Press}, address = {Oxford, UK} } @article{HSAUR:Rubin1976, author = {D. Rubin}, title = {Inference and missing data}, journal = {Biometrika}, year = 1976, volume = 63, pages = {581-592} } @article{HSAUR:MurrayFindlay1988, author = {G. D. Murray and J. G. Findlay}, title = {Correcting for bias caused by dropouts in hypertension trials}, journal = {Statistics in Medicine}, year = 1988, volume = 7, pages = {941-946} } @article{HSAUR:DiggleKenward1994, author = {P. J. Diggle and M. G. Kenward}, title = {Informative dropout in longitudinal data analysis}, journal = {Journal of the Royal Statistical Society, Series C}, year = 1994, volume = 43, pages = {49-93} } @article{HSAUR:Carpenteretal2002, author = {J. Carpenter and S. Pocock and C. J. Lamm}, title = {Coping with missing data in clinical trials: {A} model-based approach applied to asthma trials}, journal = {Statistics in Medicine}, year = 2002, volume = {21}, pages = {1043-1066} } @incollection{HSAUR:Diggle1998, author = {P. J. Diggle}, title = {Dealing with missing values in longitudinal studies}, year = 1998, booktitle = {Statistical Analysis of Medical Data}, editor = {B. S. Everitt and G. Dunn}, publisher = {Arnold}, address = {London, UK} } @book{HSAUR:Everitt2002, author = {B. S. Everitt}, title = {Modern Medical Statistics}, year = 2002, publisher = {Arnold}, address = {London, UK} } @article{HSAUR:Heitjan1997, author = {D. F. Heitjan}, title = {Annotation: {W}hat can be done about missing data? {A}pproaches to imputation}, journal = {American Journal of Public Health}, year = 1997, volume = 87, pages = {548-550} } @book{HSAUR:MayorFrei2003, author = {M. Mayor and P. Frei}, title = {New Worlds in the Cosmos: {T}he Discovery of Exoplanets}, publisher = {Cambridge University Press}, year = 2003, address = {Cambridge, UK} } %%% check volume and pages @article{HSAUR:MayorQueloz1995, author = {M. Mayor and D. Queloz}, title = {A {J}upiter-mass companion to a solar-type star}, journal = {Nature}, year = 1995, volume = {378}, pages = {355} } @article{HSAUR:EverittBullmore1999, author = {B. S. Everitt and E. T. Bullmore}, title = {Mixture model mapping of brain activation in functional magnetic resonance images}, journal = {Human Brain Mapping}, year = 1999, volume = 7, pages = {1-14} } @book{HSAUR:Everittetal2001, author = {B. S. Everitt and S. Landau and M. Leese}, title = {Cluster Analysis}, publisher = {Arnold}, year = 2001, edition = {4th}, address = {London, UK} } @book{HSAUR:Gordon1999, author = {A. Gordon}, title = {Classification}, year = 1999, edition = {2nd}, publisher = {Chapman \& Hall/CRC}, address = {Boca Raton, Florida, USA} } @article{HSAUR:ScottSymons1971, author = {A. J. Scott and M. J. Symons}, title = {Clustering methods based on likelihood ratio criteria}, journal = {Biometrics}, year = 1971, volume = 27, pages = {387-398} } @article{HSAUR:BanfieldRaftery1993, author = {J. D. Banfield and A. E. Raftery}, title = {Model-based {G}aussian and non-{G}aussian clustering}, year = 1993, journal = {Biometrics}, volume = 49, pages = {803-821} } @article{HSAUR:FraleyRaftery1999, author = {G. Fraley and A. E. Raftery}, title = {{MCLUST: S}oftware for model-based cluster analysis}, journal = {Journal of Classification}, year = 1999, volume = 16, pages = {297-306} } @article{HSAUR:FriedmanRubin1967, author = {H. P. Friedman and J. Rubin}, title = {On some invariant criteria for grouping data}, journal = {Journal of the American Statistical Association}, year = 1967, volume = 62, pages = {1159-1178} } @article{HSAUR:Marriott1982, author = {F. H. C. Marriott}, title = {Optimization methods of cluster analysis}, journal = {Biometrika}, year = 1982, volume = 69, pages = {417-421} } @article{HSAUR:Dempsteretal1977, author = {A. P. Dempster and N. M. Laird and D. B. Rubin}, title = {Maximum likelihood from incomplete data via the {EM} algorithm {(C/R: p22-37)}}, journal = {Journal of the Royal Statistical Society, Series B}, year = 1977, volume = 39, pages = {1-22} } @article{HSAUR:DubesJain1979, author = {R. Dubes and A. K. Jain}, title = {Validity studies in clustering methodologies}, journal = {Pattern Recognition}, year = 1979, volume = 8, pages = {247-260} } @article{HSAUR:Tubbetal1980, author = {A. Tubb and N. J. Parker and G. Nickless}, title = {The analysis of {Romano-British} pottery by atomic absorption spectrophotometry}, journal = {Archaeometry}, year = 1980, volume = 22, pages = {153-171} } @article{HSAUR:Alonetal1999, author = {U. Alon and N. Barkai and D. A. Notternam and K. Gish and S. Ybarra and D. Mack and A. J. Levine}, title = {Broad patterns of gene expressions revealed by clustering analysis of tumour and normal colon tissues probed by oligonucleotide arrays}, journal = {Cell Biology}, year = 1999, volume = 99, pages = {6754-6760} } @article{HSAUR:Woodleyetal1977, author = {W. L. Woodley and J. Simpson and R. Biondini and J. Berkeley}, title = {Rainfall results 1970-75: {F}lorida area cumulus experiment}, year = {1977}, journal = {Science}, volume = {195}, pages = {735-742} } @book{HSAUR:EfronTibshirani1993, author = {B. Efron and R. J. Tibshirani}, title = {An Introduction to the Bootstrap}, year = {1993}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:CookWeisberg1982, author = {R. D. Cook and S. Weisberg}, title = {Residuals and Influence in Regression}, year = {1982}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:VenablesRipley2002, author = {William N. Venables and Brian D. Ripley}, title = {Modern Applied Statistics with {S}}, edition = {4th}, publisher = {Springer-Verlag}, address = {New York, USA}, year = 2002, note = {{ISBN} 0-387-95457-0}, url = {http://www.stats.ox.ac.uk/pub/MASS4/} } @book{HSAUR:McLachlanPeel2000, author = {G. McLachlan and D. Peel}, title = {Finite Mixture Models}, year = 2000, publisher = {John Wiley \& Sons}, address = {New York, USA} } @article{HSAUR:Pearson1894, author = {Karl Pearson}, title = {Contributions to the mathematical theory of evolution}, year = 1894, journal = {Philosophical Transactions A}, volume = 185, pages = {71-110} } @book{HSAUR:Scott1992, author = {D. W. Scott}, title = {Multivariate Density Estimation}, year = 1992, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Silverman1986, author = {B. Silverman}, title = {Density Estimation}, year = 1986, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:Simonoff1996, author = {J. S. Simonoff}, title = {Smoothing Methods in Statistics}, year = 1996, publisher = {Springer-Verlag}, address = {New York, USA} } @article{HSAUR:VanismaGreve1972, author = {F. Vanisma and J. P. {De Greve}}, title = {Close binary systems before and after mass transfer}, journal = {Astrophysics and Space Science}, year = 1972, volume = 87, pages = {377-401} } @book{HSAUR:WandJones1995, author = {M. P. Wand and M. C. Jones}, title = {Kernel Smoothing}, year = 1995, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Wilkinson1992, author = {L. Wilkinson}, title = {Graphical displays}, journal = {Statistical Methods in Medical Research}, year = 1992, volume = 1, pages = {3-25} } %% An Introduction to R @book{HSAUR:Becker+Chambers+Wilks:1988, author = {Richard A. Becker and John M. Chambers and Allan R. Wilks}, title = {The New {S} Language}, publisher = {Chapman \& Hall}, year = 1988, address = {London, UK}, } @book{HSAUR:Chambers+Hastie:1992, author = {John M. Chambers and Trevor J. Hastie}, title = {Statistical Models in {S}}, publisher = {Chapman \& Hall}, year = 1992, address = {London, UK}, } @book{HSAUR:Chambers:1998, author = {John M. Chambers}, title = {Programming with Data}, publisher = {Springer-Verlag}, year = 1998, address = {New York, USA}, } %% Simple Inference @book{HSAUR:Agresti1996, author = {A. Agresti}, title = {An Introduction to Categorical Data Analysis}, year = 1996, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Everitt1992, author = {Brian S. Everitt}, title = {The Analysis of Contingency Tables}, year = 1992, edition = {2nd}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Haberman1973, author = {S. J. Haberman}, title = {The analysis of residuals in cross-classified tables}, journal = {Biometrics}, year = 1973, volume = 29, pages = {205-220} } @book{HSAUR:Handetal1994, author = {D. J. Hand and F. Daly and A. D. Lunn and K. J. McConway and E. Ostrowski}, title = {A Handbook of Small Datasets}, year = 1994, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Mann1981, author = {L. Mann}, title = {The baiting crowd in episodes of threatened suicide}, journal = {Journal of Personality and Social Psychology}, year = 1981, volume = 41, pages = {703-709} } @article{HSAUR:MehtaPatel1983, author = {Cyrus R. Mehta and Nitin R. Patel}, title = {A Network Algorithm for Performing {F}isher's Exact Test in $r \times c $ Contingency Tables}, journal = {Journal of the American Statistical Association}, pages = {427-434}, year = {1983}, month = {June}, volume = {78}, number = {382} } @book{HSAUR:Fisher1935, author = {R. A. Fisher}, title = {The Design of Experiments}, year = 1935, publisher = {Oliver and Boyd}, address = {Edinburgh, UK} } @article{HSAUR:Pitman1937, author = {E. J. G. Pitman}, title = {Significance tests which may be applied to samples from any populations}, journal = {Biometrika}, year = 1937, volume = 29, pages = {322-335} } @book{HSAUR:Barlowetal1972, author = {R. E. Barlow and D. J. Bartholomew and J. M. Bremner and H. D. Brunk}, title = {Statistical Inference under Order Restrictions}, year = 1972, publisher = {John Wiley \& Sons}, address = {New York, USA} } @article{HSAUR:Corbetetal1970, author = {G. B. Corbet and J. Cummins and S. R. Hedges and W. J. Krzanowski}, title = {The taxonomic structure of {B}ritish water voles, genus \textit{Arvicola}}, year = 1970, journal = {Journal of Zoology}, volume = 61, pages = {301-316} } @book{HSAUR:EverittRabeHesketh1997, author = {B. S. Everitt and S. Rabe-Hesketh}, title = {The Analysis of Proximity Data}, year = 1997, publisher = {Arnold}, address = {London, UK} } @book{HSAUR:EverittRabeHesketh2001, author = {B. S. Everitt and S. Rabe-Hesketh}, title = {Analysing Medical Data Using {S-Plus}}, year = 2001, publisher = {Springer-Verlag}, address = {New York, USA} } @book{HSAUR:SkrondalRabeHesketh2004, author = {A. Skrondal and S. 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Walter}, title = {Secondary prevention of myocardial infarction. {C}omparison of acetylsalicylic acid, phenprocoumon and placebo. {A} multicenter two-year prospective study}, journal = {Thrombosis and Haemostasis}, year = 1979, volume = 41, number = 1, pages = {225-236} } @article{HSAUR:Aspirin1980, author = {{Aspirin Myocardial Infarction Study Research Group}}, title = {A randomized, controlled trial of aspirin in persons recovered from myocardial infarction}, year = 1980, journal = {Journal of the American Medical Association}, volume = 243, number = 7, pages = {661-669} } @article{HSAUR:Persantine1980, author = {{Persantine-Aspirin Reinfarction Study Research Group}}, title = {Persantine and {A}spirin in coronary heart disease}, journal = {Circulation}, year = 1980, volume = 62, number = 3, pages = {449-461} } @article{HSAUR:ISIS21988, author = {{ISIS-2 (Second International Study of Infarct Survival) Collaborative Group}}, title = {Randomised trial of intravenous streptokinase, oral aspirin, both, or neither among 17,187 cases of suspected acute myocardial infarction: {ISIS-2}}, year = 1988, journal = {Lancet}, volume = 13, pages = {349-360} } @article{HSAUR:Mazess1984, author = {R. B. Mazess and W. W. Peppler and M. Gibbons}, title = {Total body composition by dual-photon {(153Gd)} absorptiometry}, year = 1984, journal = {American Journal of Clinical Nutrition}, volume = 40, pages = {834-839} } @book{HSAUR:Goldberg1972, author = {D. Goldberg}, year = 1972, title = {The Detection of Psychiatric Illness by Questionnaire}, publisher = {Oxford University Press}, address = {Oxford, UK} } %% PACKAGES @article{PKG:sandwich, title = {Econometric Computing with {HC} and {HAC} Covariance Matrix Estimators}, author = {Achim Zeileis}, journal = {Journal of Statistical Software}, year = {2004}, volume = {11}, number = {10}, pages = {1--17}, url = {http://www.jstatsoft.org/v11/i10/}, } @Manual{PKG:coin, title = {\Rpackage{coin}: Conditional Inference Procedures in a Permutation Test Framework}, author = {Torsten Hothorn and Kurt Hornik and Mark van de Wiel and Achim Zeileis}, year = {2013}, url = {http://CRAN.R-project.org/package=coin}, note = {\rR{} package version 1.0-23} } @Manual{PKG:KernSmooth, title = {\Rpackage{KernSmooth}: Functions for Kernel Smoothing for Wand \& Jones (1995)}, author = {Matt P. Wand and Brian D. Ripley}, year = {2014}, note = {\rR{} package version 2.23-10}, url = {http://CRAN.R-project.org/package=KernSmooth}, } @Manual{PKG:boot, title = {\Rpackage{boot}: Bootstrap \rR{} (\rSPLUS) Functions}, author = {Angelo Canty and Brian D. Ripley}, year = {2014}, url = {http://CRAN.R-project.org/package=boot}, note = {\rR{} package version 1.3-9}, } @Manual{PKG:mclust, title = {\Rpackage{mclust}: Model-based Cluster Analysis}, author = {C. Fraley and A. E. Raftery and Ron Wehrens}, year = {2014}, note = {\rR{} package version 4.3}, url = {http://www.stat.washington.edu/mclust}, } @Manual{PKG:randomForest, title = {\Rpackage{randomForest}: {B}reiman and {C}utler's Random Forests for Classification and Regression}, author = {Leo Breiman and Adele Cutler and Andy Liaw and Matthew Wiener}, year = {2013}, note = {\rR{} package version 4.6-7}, url = {http://stat-www.berkeley.edu/users/breiman/RandomForests}, } @Manual{PKG:rpart, title = {\Rpackage{rpart}: Recursive Partitioning}, author = {Terry M. Therneau and Beth Atkinson and Brian D. Ripley}, year = {2014}, note = {\rR{} package version 4.1-8}, url = {http://mayoresearch.mayo.edu/mayo/research/biostat/splusfunctions.cfm}, } @Manual{PKG:mlbench, title = {\Rpackage{mlbench}: Machine Learning Benchmark Problems}, author = {Friedrich Leisch and Evgenia Dimitriadou}, year = {2013}, url = {http://CRAN.R-project.org/package=mlbench}, note = {\rR{} package version 2.1-1}, } @Manual{PKG:nlme, title = {\Rpackage{nlme}: Linear and Nonlinear Mixed Effects Models}, author = {Jos\'{e} C. Pinheiro and Douglas M. Bates and Saikat DebRoy and Deepayan Sarkar}, year = {2014}, url = {http://CRAN.R-project.org/package=nlme}, note = {\rR{} package version 3.1-113}, } @Manual{PKG:lme4, title = {\Rpackage{lme4}: Linear Mixed-Effects Models Using S4 Classes}, author = {Douglas Bates and Deepayan Sarkar}, year = {2014}, url = {http://CRAN.R-project.org/package=lme4}, note = {\rR{} package version 1.1-5}, } @Manual{PKG:gee, title = {\Rpackage{gee}: Generalized Estimation Equation Solver}, author = {Vincent J. Carey and Thomas Lumley and Brian D. Ripley}, year = {2013}, url = {http://CRAN.R-project.org/package=gee}, note = {\rR{} package version 4.13-18}, } @Manual{PKG:rmeta, title = {\Rpackage{rmeta}: {M}eta-Analysis}, author = {Thomas Lumley}, year = {2013}, url = {http://CRAN.R-project.org/package=rmeta}, note = {\rR{} package version 2.16}, } @Manual{PKG:ape, title = {\Rpackage{ape}: {A}nalyses of Phylogenetics and Evolution}, author = {Emmanuel Paradis and Korbinian Strimmer and Julien Claude and Gangolf Jobb and Rainer Opgen-Rhein and Julien Dutheil and Yvonnick Noel and Ben Bolker}, year = {2014}, url = {http://CRAN.R-project.org/package=ape}, note = {\rR{} package version 3.1-1}, } @Manual{PKG:survival, title = {\Rpackage{survival}: {S}urvival Analysis, Including Penalised Likelihood}, author = {Terry M. Therneau and Thomas Lumley}, year = {2014}, url = {http://CRAN.R-project.org/package=survival}, note = {\rR{} package version 2.37-7}, } @Manual{PKG:mfp, title = {\Rpackage{mfp}: {M}ultivariable Fractional Polynomials}, author = {Gareth Ambler and Axel Benner}, year = {2013}, url = {http://CRAN.R-project.org/package=mfp}, note = {\rR{} package version 1.4.9}, } @Manual{PKG:vcd, title = {\Rpackage{vcd}: {V}isualizing Categorical Data}, author = {David Meyer and Achim Zeileis and Alexandros Karatzoglou and Kurt Hornik}, year = {2013}, url = {http://CRAN.R-project.org/package=vcd}, note = {\rR{} package version 1.3-1}, } @Manual{PKG:leaps, title = {\Rpackage{leaps}: {R}egression Subset Selection}, author = {Thomas Lumley and Alan Miller}, year = {2013}, url = {http://CRAN.R-project.org/package=leaps}, note = {\rR{} package version 2.9}, } @Manual{PKG:party, title = {\Rpackage{party}: {A} Laboratory for Recursive Partytioning}, author = {Torsten Hothorn and Kurt Hornik and Carolin Strobl and Achim Zeileis}, year = {2014}, url = {http://CRAN.R-project.org/package=party}, note = {\rR{} package version 1.0-13} } @Manual{PKG:multcomp, title = {\Rpackage{multcomp}: Simultaneous Inference for General Linear Hypotheses}, author = {Torsten Hothorn and Frank Bretz and Peter Westfall}, year = {2014}, note = {\rR{} package version 1.3-2}, url = {http://CRAN.R-project.org/package=multcomp} } @Manual{PKG:lattice, title = {\Rpackage{lattice}: Lattice Graphics}, author = {Deepayan Sarkar}, year = {2014}, note = {\rR{} package version 0.20-27}, url = {http://CRAN.R-project.org/package=lattice} } @Manual{PKG:partykit, title = {\Rpackage{partykit}: A Toolkit for Recursive Partytioning}, author = {Torsten Hothorn and Achim Zeileis}, year = {2014}, note = {\rR{} package version 0.8-0}, url = {http://R-forge.R-project.org/projects/partykit/} } @Manual{PKG:alr3, title = {\Rpackage{alr3}: Methods and Data to Accompany {Applied Linear Regression 3rd edition}}, author = {Sanford Weisberg}, year = {2013}, note = {\rR{} package version 2.0.5}, url = {http://www.stat.umn.edu/alr}, } @Manual{PKG:mboost, title = {\Rpackage{mboost}: Model-Based Boosting}, author = {Torsten Hothorn and Peter B\"uhlmann and Thomas Kneib and Matthias Schmid and Benjamin Hofner}, year = {2013}, note = {\rR{} package version 2.2-3}, url = {http://CRAN.R-project.org/package=mboost} } @Manual{PKG:meta, title = {\Rpackage{meta}: {M}eta-Analysis}, author = {Guido Schwarzer}, year = {2014}, note = {\rR{} package version 3.2-1}, url = {http://CRAN.R-project.org/package=meta} } @Manual{PKG:rgl, title = {\Rpackage{rgl}: 3D Visualization Device System (OpenGL)}, author = {Daniel Adler and Duncan Murdoch}, year = {2014}, note = {\rR{} package version 0.93.996}, url = {http://rgl.neoscientists.org}, } @Manual{PKG:wordcloud, title = {\Rpackage{wordcloud}: Word Clouds}, author = {Ian Fellows}, year = {2014}, note = {\rR{} package version 2.4}, url = {http://CRAN.R-project.org/package=wordcloud} } @Manual{PKG:quantreg, title = {\Rpackage{quantreg}: {Quantile} Regression}, author = {Roger Koenker}, year = {2013}, url = {http://CRAN.R-project.org/package=quantreg}, note = {\rR{} package version 5.05} } @Manual{PKG:MASS, title = {\Rpackage{MASS}: Support Functions and Datasets for Venables and Ripley's MASS}, author = {Brian D. Ripley}, year = {2014}, url = {http://CRAN.R-project.org/package=MASS}, note = {\rR{} package version 7.3-29} } @Manual{PKG:INLA, title = {\Rpackage{INLA}: Functions Which Allow to Perform Full Bayesian Analysis of Latent Gaussian Models Using Integrated Nested Laplace Approximaxion}, author = {Havard Rue and Sara Martino and Finn Lindgren and Daniel Simpson and Andrea Riebler}, year = {2013}, url = {http://www.r-inla.org/download}, note = {\rR{} package version 0.0-1379661604} } @Manual{PKG:rjags, title = {\Rpackage{rjags}: Bayesian Graphical Models Using {MCMC}}, author = {Martyn Plummer and Alexey Stukalov}, year = {2014}, url = {http://CRAN.R-project.org/package=rjags}, note = {\rR{} package version 3-13} } @Manual{PKG:sp, title = {\Rpackage{sp}: Classes and Methods for Spatial Data}, author = {Edzer Pebesma and Roger Bivand}, year = {2013}, url = {http://CRAN.R-project.org/package=sp}, note = {\rR{} package version 1.0-14} } @Manual{PKG:mice, title = {\Rpackage{mice}: Multivariate Imputation by Chained Equations}, author = {Stef van Buuren and Karin Groothuis-Oudshoorn}, year = {2014}, url = {http://CRAN.R-project.org/package=mice}, note = {\rR{} package version 2.21} } @book{HSAUR:Sarkar2008, title = {Lattice: {M}ultivariate Data Visualization with \rR{}}, author = {Deepayan Sarkar}, year = 2008, publisher = {Springer-Verlag}, address = {New York, USA} } @article{HSAUR:Mazessetal1984, author = {R. 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The} Northern {Andes} of {South America}}, journal = {The American Naturalist}, volume = 104, pages = {373--388} } @book{HSAUR:Aitkin1989, author = {M. Aitkin and D. Anderson and B. Francis and J. Hinde}, title = {Statistical Modelling in {GLIM}}, year = 1989, publisher = {Oxford University Press}, address = {New York, USA}, } @incollection{HSAUR:Morabia2013, author = {Alfredo Morabia}, editor = {Wolfgang Ahrens and Iris Pigeot}, booktitle = {Handbook of Epidemiology}, title = {History of Epidemiological Methods and Concepts}, pages = {43--74}, year = {2013}, edition = {2nd}, publisher = {Springer-Verlag}, address = {New York, USA}, } @Article{HSAUR:ZeileisHothornHornik2008, author = {Achim Zeileis and Torsten Hothorn and Kurt Hornik}, title = {Model-based Recursive Partitioning}, journal = {Journal of Computational and Graphical Statistics}, year = {2008}, volume = 17, number = 2, pages = {492--514}, doi = {10.1198/106186008X319331}, } > > HSAUR3/vignettes/Ch_analysing_longitudinal_dataII.Rnw0000644000175000017500000005336314133304452022445 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analyzing Longitudinal Data II} %%\VignetteDepends{gee,lme4} \setcounter{chapter}{13} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= options(digits = 3) if (!interactive()) { print.summary.gee <- function (x, digits = NULL, quote = FALSE, prefix = "", ...) { if (is.null(digits)) digits <- options()$digits else options(digits = digits) cat("...") cat("\nModel:\n") cat(" Link: ", x$model$link, "\n") cat(" Variance to Mean Relation:", x$model$varfun, "\n") if (!is.null(x$model$M)) cat(" Correlation Structure: ", x$model$corstr, ", M =", x$model$M, "\n") else cat(" Correlation Structure: ", x$model$corstr, "\n") cat("\n...") nas <- x$nas if (!is.null(nas) && any(nas)) cat("\n\nCoefficients: (", sum(nas), " not defined because of singularities)\n", sep = "") else cat("\n\nCoefficients:\n") print(x$coefficients, digits = digits) cat("\nEstimated Scale Parameter: ", format(round(x$scale, digits))) cat("\n...\n") invisible(x) } } @ \chapter[Analyzing Longitudinal Data II]{ Analyzing Longitudinal Data II -- Generalized Estimation Equations and Linear Mixed Effect Models: Treating Respiratory Illness and Epileptic Seizures \label{ALDII}} \section{Introduction} \section{Methods for Non-normal Distributions} \section{Analysis Using \R{}: GEE} \subsection{Beat the Blues Revisited} To use the \Rcmd{gee} function, package \Rpackage{gee} \citep{PKG:gee} has to be installed and attached: <>= library("gee") @ The \Rcmd{gee} function is used in a similar way to the \Rcmd{lme} function met in \Sexpr{ch("ALDI")} with the addition of the features of the \Rcmd{glm} function that specify the appropriate error distribution for the response and the implied link function, and an argument to specify the structure of the working correlation matrix. Here we will fit an independence structure and then an exchangeable structure. The \R{} code for fitting generalized estimation equations to the \Robject{BtheB\_long} data (as constructed in \Sexpr{ch("ALDI")}) with identity working correlation matrix is as follows (note that the \Rcmd{gee} function assumes the rows of the \Rclass{data.frame} \Robject{BtheB\_long} to be ordered with respect to subjects): <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt" @ <>= osub <- order(as.integer(BtheB_long$subject)) BtheB_long <- BtheB_long[osub,] btb_gee <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "independence") @ and with exchangeable correlation matrix: <>= btb_gee1 <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "exchangeable") @ The \Rcmd{summary} method can be used to inspect the fitted models; the results are shown in Figures~\ref{ALDII-gee-summary} and \ref{ALDII-gee1-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{btb\_gee} model (slightly abbreviated). \label{ALDII-gee-summary}} \SchunkLabel <>= summary(btb_gee) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{btb\_gee1} model (slightly abbreviated). \label{ALDII-gee1-summary}} \SchunkLabel <>= summary(btb_gee1) @ \SchunkRaw \subsection{Respiratory Illness \label{ALDII:resp}} The baseline status, i.e., the status for \Robject{month == 0}, will enter the models as an explanatory variable and thus we have to rearrange the \Rclass{data.frame} \Robject{respiratory} in order to create a new variable \Robject{baseline}: <>= data("respiratory", package = "HSAUR3") resp <- subset(respiratory, month > "0") resp$baseline <- rep(subset(respiratory, month == "0")$status, rep(4, 111)) resp$nstat <- as.numeric(resp$status == "good") resp$month <- resp$month[, drop = TRUE] @ <>= names(resp)[names(resp) == "treatment"] <- "trt" levels(resp$trt)[2] <- "trt" @ The new variable \Robject{nstat} is simply a dummy coding for a poor respiratory status. Now we can use the data \Robject{resp} to fit a logistic regression model and GEE models with an independent and an exchangeable correlation structure as follows. <>= resp_glm <- glm(status ~ centre + trt + gender + baseline + age, data = resp, family = "binomial") resp_gee1 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) resp_gee2 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) @ \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_glm} model. \label{ALDII-resp-glm-summary}} \SchunkLabel <>= summary(resp_glm) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_gee1} model (slightly abbreviated). \label{ALDII-resp-gee1-summary}} \SchunkLabel <>= summary(resp_gee1) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_gee2} model (slightly abbreviated). \label{ALDII-resp-gee2-summary}} \SchunkLabel <>= summary(resp_gee2) @ \SchunkRaw The estimated treatment effect taken from the exchangeable structure GEE model is \Sexpr{round(coef(resp_gee2)["trttrt"], 3)} which, using the robust standard errors, has an associated $95\%$ confidence interval <>= se <- summary(resp_gee2)$coefficients["trttrt", "Robust S.E."] coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975) @ These values reflect effects on the log-odds scale. Interpretation becomes simpler if we exponentiate the values to get the effects in terms of odds. This gives a treatment effect of \Sexpr{round(exp(coef(resp_gee2)["trttrt"]), 3)} and a $95\%$ confidence interval of <>= exp(coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975)) @ The odds of achieving a `good' respiratory status with the active treatment is between %' about twice and seven times the corresponding odds for the placebo. \subsection{Epilepsy} Moving on to the count data in \Robject{epilepsy} from Table~\ref{ALDII-epilepsy-tab}, we begin by calculating the means and variances of the number of seizures for all interactions between treatment and period: <>= data("epilepsy", package = "HSAUR3") itp <- interaction(epilepsy$treatment, epilepsy$period) tapply(epilepsy$seizure.rate, itp, mean) tapply(epilepsy$seizure.rate, itp, var) @ Some of the variances are considerably larger than the corresponding means, which for a Poisson variable may suggest that overdispersion may be a problem, see \Sexpr{ch("GLM")}. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) ylim <- range(epilepsy$seizure.rate) placebo <- subset(epilepsy, treatment == "placebo") progabide <- subset(epilepsy, treatment == "Progabide") boxplot(seizure.rate ~ period, data = placebo, ylab = "Number of seizures", xlab = "Period", ylim = ylim, main = "Placebo") boxplot(seizure.rate ~ period, data = progabide, main = "Progabide", ylab = "Number of seizures", xlab = "Period", ylim = ylim) @ \caption{Boxplots of numbers of seizures in each two-week period post randomization for placebo and active treatments. \label{ALDII-plot1}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) ylim <- range(log(epilepsy$seizure.rate + 1)) boxplot(log(seizure.rate + 1) ~ period, data = placebo, main = "Placebo", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) boxplot(log(seizure.rate + 1) ~ period, data = progabide, main = "Progabide", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) @ \caption{Boxplots of log of numbers of seizures in each two-week period post randomization for placebo and active treatments. \label{ALDII-plot2}} \end{center} \end{figure} We can now fit a Poisson regression model to the data assuming independence using the \Rcmd{glm} function. We also use the GEE approach to fit an independence structure, followed by an exchangeable structure using the following \R{} code: <>= per <- rep(log(2),nrow(epilepsy)) epilepsy$period <- as.numeric(epilepsy$period) names(epilepsy)[names(epilepsy) == "treatment"] <- "trt" fm <- seizure.rate ~ base + age + trt + offset(per) epilepsy_glm <- glm(fm, data = epilepsy, family = "poisson") epilepsy_gee1 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) epilepsy_gee2 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) epilepsy_gee3 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = FALSE, scale.value = 1) @ As usual we inspect the fitted models using the \Rcmd{summary} method, the results are given in Figures~\ref{ALDII-epilepsy-glm-summary}, \ref{ALDII-epilepsy-gee1-summary}, \ref{ALDII-epilepsy-gee2-summary}, and \ref{ALDII-epilepsy-gee3-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_glm} model. \label{ALDII-epilepsy-glm-summary}} \SchunkLabel <>= summary(epilepsy_glm) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee1} model (slightly abbreviated). \label{ALDII-epilepsy-gee1-summary}} \SchunkLabel <>= summary(epilepsy_gee1) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee2} model (slightly abbreviated). \label{ALDII-epilepsy-gee2-summary}} \SchunkLabel <>= summary(epilepsy_gee2) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee3} model (slightly abbreviated). \label{ALDII-epilepsy-gee3-summary}} \SchunkLabel <>= summary(epilepsy_gee3) @ \SchunkRaw \section{Analysis Using \R{}: Random Effects} As an example of using generalized mixed models for the analysis of longitudinal data with a non-normal response, the following logistic model will be fitted to the respiratory illness data \begin{eqnarray*} \text{logit}(\P(\text{status} = \text{good})) & = & \beta_0 + \beta_1 \text{treatment} + \beta_2 \text{time} + \beta_3 \text{gender} \\% & & + \beta_4 \text{age} + \beta_5 \text{centre} + \beta_6 \text{baseline} + u \end{eqnarray*} where $u$ is a subject-specific random effect. The necessary \R{} code for fitting the model using the \Rcmd{glmer} function from package \Rpackage{lme4} \citep{PKG:lme4,HSAUR:Bates2005} is: <>= library("lme4") resp_lmer <- glmer(status ~ baseline + month + trt + gender + age + centre + (1 | subject), family = binomial(), data = resp) exp(fixef(resp_lmer)) @ The significance of the effects as estimated by this random effects model and by the GEE model described in Section~\ref{ALDII:resp} is generally similar. But as expected from our previous discussion the estimated coefficients are substantially larger. While the estimated effect of treatment on a randomly sampled individual, given the set of observed covariates, is estimated by the marginal model using GEE to increase the log-odds of being disease free by $\Sexpr{round(coef(resp_gee2)["trttrt"], 3)}$, the corresponding estimate from the random effects model is $\Sexpr{round(fixef(resp_lmer)["trttrt"], 3)}$. These are not inconsistent results but reflect the fact that the models are estimating different parameters. The random effects estimate is conditional upon the patient's random effect, a quantity that is rarely known in practice. Were we to examine the log-odds of the average predicted probabilities with and without treatment (averaged over the random effects) this would give an estimate comparable to that estimated within the marginal model. <>= su <- summary(resp_lmer) if (!interactive()) { summary <- function(x) { cat("\n...\n") cat("Fixed effects:\n") lme4V <- packageDescription("lme4")$Version if (compareVersion("0.999999-2", lme4V) >= 0) { printCoefmat(su@coefs) } else { printCoefmat(su$coefficients) } cat("\n...\n") } } @ \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_lmer} model (abbreviated). \label{ALDII-resp-lmer-summary}} \SchunkLabel <>= summary(resp_lmer) @ \SchunkRaw \clearpage \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_multiple_linear_regression.Rnw0000644000175000017500000005606514133304452022123 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Multiple Linear Regression} %%\VignetteDepends{wordcloud} \setcounter{chapter}{5} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("wordcloud") @ \chapter[Simple and Multiple Linear Regression]{Simple and Multiple Linear Regression: \\ How Old is the Universe and Cloud Seeding \label{MLR}} \section{Introduction} \index{Age of the Universe} \cite{HSAUR:Freedmanetal2001} give the relative velocity and the distance of $24$ galaxies, according to measurements made using the Hubble Space Telescope -- the data are contained in the \Rpackage{gamair} package accompanying \cite{HSAUR:Wood2006}, see Table~\ref{MLR-hubble-tab}. Velocities are assessed by measuring the Doppler red shift in the spectrum of light observed from the galaxies concerned, although some correction for `local' velocity components is required. Distances are measured using the known relationship between the period of Cepheid variable stars and their luminosity. How can these data be used to estimate the age of the universe? Here we shall show how this can be done using simple linear regression. <>= data("hubble", package = "gamair") names(hubble) <- c("galaxy", "velocity", "distance") toLatex(HSAURtable(hubble, package = "gamair"), pcol = 2, caption = paste("Distance and velocity for 24 galaxies."), label = "MLR-hubble-tab") @ \vspace*{-1cm} \textit{Source}: From Freedman W. L., et al., \textit{The Astrophysical Journal}, 553, 47--72, 2001. With permission. \vspace*{1cm} \index{Cloud seeding} {\tabcolsep3.5pt <>= data("clouds", package = "HSAUR3") names(clouds) <- c("seeding", "time", "sne", "cloudc", "prewet", "EM", "rain") toLatex(HSAURtable(clouds), pcol = 1, caption = paste("Cloud seeding experiments in Florida -- see text for", "explanations of the variables. Note that the \\Robject{clouds} data set has slightly different variable names."), label = "MLR-clouds-tab") @ } Weather modification, or cloud seeding, is the treatment of individual clouds or storm systems with various inorganic and organic materials in the hope of achieving an increase in rainfall. Introduction of such material into a cloud that contains supercooled water, that is, liquid water colder than zero degrees Celsius, has the aim of inducing freezing, with the consequent ice particles growing at the expense of liquid droplets and becoming heavy enough to fall as rain from clouds that otherwise would produce none. The data shown in Table~\ref{MLR-clouds-tab} were collected in the summer of 1975 from an experiment to investigate the use of massive amounts of silver iodide ($100$ to $1000$ grams per cloud) in cloud seeding to increase rainfall \citep{HSAUR:Woodleyetal1977}. In the experiment, which was conducted in an area of Florida, 24 days were judged suitable for seeding on the basis that a measured suitability criterion, denoted \stress{S-Ne}, was not less than $1.5$. Here \stress{S} is the `seedability', %' the difference between the maximum height of a cloud if seeded and the same cloud if not seeded predicted by a suitable cloud model, and \stress{Ne} is the number of hours between $1300$ and $1600$ G.M.T. with $10$ centimeter echoes in the target; this quantity biases the decision for experimentation against naturally rainy days. Consequently, optimal days for seeding are those on which seedability is large and the natural rainfall early in the day is small. On suitable days, a decision was taken at random as to whether to seed or not. For each day the following variables were measured: \begin{description} \item[\Robject{seeding}] a factor indicating whether seeding action occurred (yes or no), \item[\Robject{time}] number of days after the first day of the experiment, \item[\Robject{cloudc}] the percentage cloud cover in the experimental area, measured using radar, \item[\Robject{prewet}] the total rainfall in the target area one hour before seeding (in cubic meters $\times 10^{7}$), \item[\Robject{EM}] a factor showing whether the radar echo was moving or stationary, \item[\Robject{rain}] the amount of rain in cubic meters $\times 10^{7}$, \item[\Robject{sne}] suitability criterion, see above. \end{description} The objective in analyzing these data is to see how rainfall is related to the explanatory variables and, in particular, to determine the effectiveness of seeding. The method to be used is \stress{multiple linear regression}. \section{Simple Linear Regression} \section{Multiple Linear Regression \label{MLR-MLR}} \subsection{Regression Diagnostics} \section{Analysis Using \R{}} \subsection{Estimating the Age of the Universe} Prior to applying a simple regression to the data it will be useful to look at a plot to assess their major features. The \R{} code given in Figure~\ref{MLR-hubble-plot} produces a scatterplot of velocity and distance. \begin{figure} \begin{center} <>= plot(velocity ~ distance, data = hubble) @ \caption{Scatterplot of velocity and distance. \label{MLR-hubble-plot}} \end{center} \end{figure} The diagram shows a clear, strong relationship between velocity and distance. The next step is to fit a simple linear regression model to the data, but in this case the nature of the data requires a model without intercept because if distance is zero so is relative speed. So the model to be fitted to these data is \begin{eqnarray*} \text{velocity} = \beta_1 \text{distance} + \varepsilon. \end{eqnarray*} This is essentially what astronomers call Hubble's Law and $\beta_1$ is known as Hubble's constant; $\beta_1^{-1}$ gives an approximate age of the universe. To fit this model we are estimating $\beta_1$ using formula (\ref{MLR:beta1}). Although this operation is rather easy <>= sum(hubble$distance * hubble$velocity) / sum(hubble$distance^2) @ it is more convenient to apply \R's linear modeling function <>= hmod <- lm(velocity ~ distance - 1, data = hubble) @ Note that the model formula specifies a model without intercept. We can now extract the estimated model coefficients via <>= coef(hmod) @ and add this estimated regression line to the scatterplot; the result is shown in Figure~\ref{MLR-hubble-lmplot}. In addition, we produce a scatterplot of the residuals $y_i - \hat{y}_i$ against fitted values $\hat{y}_i$ to assess the quality of the model fit. It seems that for higher distance values the variance of velocity increases; however, we are interested in only the estimated parameter $\hat{\beta}_1$ which remains valid under variance heterogeneity (in contrast to $t$-tests and associated $p$-values). Now we can use the estimated value of $\beta_1$ to find an approximate value for the age of the universe. The Hubble constant itself has units of $\text{km} \times \text{sec}^{-1} \times \text{Mpc}^{-1}$. A mega-parsec (Mpc) is $3.09 \times 10^{19}$km, so we need to divide the estimated value of $\beta_1$ by this amount in order to obtain Hubble's constant with units of $\text{sec}^{-1}$. The approximate age of the universe in seconds will then be the inverse of this calculation. Carrying out the necessary computations <>= Mpc <- 3.09 * 10^19 ysec <- 60^2 * 24 * 365.25 Mpcyear <- Mpc / ysec 1 / (coef(hmod) / Mpcyear) @ gives an estimated age of roughly $12.8$ billion years. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) plot(velocity ~ distance, data = hubble) abline(hmod) plot(hmod, which = 1) @ \caption{Scatterplot of velocity and distance with estimated regression line (left) and plot of residuals against fitted values (right). \label{MLR-hubble-lmplot}} \end{center} \end{figure} \subsection{Cloud Seeding} Again, a graphical display highlighting the most important aspects of the data will be helpful. Here we will construct boxplots of the rainfall in each category of the dichotomous explanatory variables and scatterplots of rainfall against each of the continuous explanatory variables. \begin{figure} \begin{center} <>= data("clouds", package = "HSAUR3") layout(matrix(1:2, nrow = 2)) bxpseeding <- boxplot(rain ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rain ~ EM, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") @ <>= layout(matrix(1:2, nrow = 2)) bxpseeding <- boxplot(rain ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rain ~ EM, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") @ \caption{Boxplots of \Robject{rain}. \label{MLR-rainfall-boxplot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:4, nrow = 2)) plot(rain ~ time, data = clouds) plot(rain ~ cloudc, data = clouds) plot(rain ~ sne, data = clouds, xlab="S-Ne criterion") plot(rain ~ prewet, data = clouds) @ \caption{Scatterplots of \Robject{rain} against the continuous covariates. \label{MLR-rainfall-scplot}} \end{center} \end{figure} Both the boxplots (Figure~\ref{MLR-rainfall-boxplot}) and the scatterplots (Figure~\ref{MLR-rainfall-scplot}) show some evidence of outliers. The row names of the extreme observations in the \Robject{clouds} \Rclass{data.frame} can be identified via <>= rownames(clouds)[clouds$rain %in% c(bxpseeding$out, bxpecho$out)] @ where \Robject{bxpseeding} and \Robject{bxpecho} are variables created by \Rcmd{boxplot} in Figure~\ref{MLR-rainfall-boxplot}. Now we shall not remove these observations but bear in mind during the modeling process that they may cause problems. In this example it is sensible to assume that the effect of some of the other explanatory variables is modified by seeding and therefore consider a model that includes seeding as covariate and, furthermore, allows interaction terms \index{Interaction} for \Robject{seeding} with each of the covariates except \Robject{time}. This model can be described by the \Rclass{formula} <>= clouds_formula <- rain ~ seeding + seeding:(sne + cloudc + prewet + EM) + time @ and the design matrix $\X^\star$ can be computed via <>= Xstar <- model.matrix(clouds_formula, data = clouds) @ By default, treatment contrasts have been applied to the dummy codings of the factors \Robject{seeding} and \Robject{EM} as can be seen from the inspection of the \Robject{contrasts} attribute of the model matrix <>= attr(Xstar, "contrasts") @ The default contrasts can be changed via the \Rarg{contrasts.arg} argument to \Rcmd{model.matrix} or the \Robject{contrasts} argument to the fitting function, for example \Rcmd{lm} or \Rcmd{aov} as shown in \Sexpr{ch("ANOVA")}. However, such internals are hidden and performed by high-level model-fitting functions such as \Rcmd{lm} which will be used to fit the linear model defined by the \Rclass{formula} \Robject{clouds\_formula}: <>= clouds_lm <- lm(clouds_formula, data = clouds) class(clouds_lm) @ The result of the model fitting is an object of class \Rclass{lm} for which a \Rcmd{summary} method showing the conventional regression analysis output is available. The output in Figure~\ref{MLR-clouds-summary} shows the estimates $\hat{\beta}^\star$ with corresponding standard errors and $t$-statistics as well as the $F$-statistic with associated $p$-value. \renewcommand{\nextcaption}{\R{} output of the linear model fit for the \Robject{clouds} data. \label{MLR-clouds-summary}} \SchunkLabel <>= summary(clouds_lm) @ \SchunkRaw Many methods are available for extracting components of the fitted model. The estimates $\hat{\beta}^\star$ can be assessed via \newpage <>= betastar <- coef(clouds_lm) betastar @ and the corresponding covariance matrix $\Cov(\hat{\beta}^\star)$ is available from the \Rcmd{vcov} method <>= Vbetastar <- vcov(clouds_lm) @ where the square roots of the diagonal elements are the standard errors as shown in Figure~\ref{MLR-clouds-summary} <>= sqrt(diag(Vbetastar)) @ \begin{figure} \begin{center} <>= psymb <- as.numeric(clouds$seeding) plot(rain ~ sne, data = clouds, pch = psymb, xlab = "S-Ne criterion") abline(lm(rain ~ sne, data = clouds, subset = seeding == "no")) abline(lm(rain ~ sne, data = clouds, subset = seeding == "yes"), lty = 2) legend("topright", legend = c("No seeding", "Seeding"), pch = 1:2, lty = 1:2, bty = "n") @ \caption{Regression relationship between S-Ne criterion and rainfall with and without seeding. \label{MLR-clouds-lmplot}} \end{center} \end{figure} In order to investigate the quality of the model fit, we need access to the residuals and the fitted values. The residuals can be found by the \Rcmd{residuals} method and the fitted values of the response from the \Rcmd{fitted} (or \Rcmd{predict}) method <>= clouds_resid <- residuals(clouds_lm) clouds_fitted <- fitted(clouds_lm) @ Now the residuals and the fitted values can be used to construct diagnostic plots; for example the residual plot in Figure~\ref{MLR-resid} where each observation is labelled by its number (using \Rcmd{textplot} from package \Rpackage{wordclouds}). Observations $1$ and $15$ give rather large residual values and the data should perhaps be reanalysed after these two observations are removed. The normal probability plot of the residuals shown in Figure~\ref{MLR-qqplot} shows a reasonable agreement between theoretical and sample quantiles, however, observations $1$ and $15$ are extreme again. \begin{figure} \begin{center} <>= plot(clouds_fitted, clouds_resid, xlab = "Fitted values", ylab = "Residuals", type = "n", ylim = max(abs(clouds_resid)) * c(-1, 1)) abline(h = 0, lty = 2) textplot(clouds_fitted, clouds_resid, words = rownames(clouds), new = FALSE) @ \caption{Plot of residuals against fitted values for \Robject{clouds} seeding data. \label{MLR-resid}} \end{center} \end{figure} \begin{figure} \begin{center} <>= qqnorm(clouds_resid, ylab = "Residuals") qqline(clouds_resid) @ \caption{Normal probability plot of residuals from cloud seeding model \Robject{clouds\_lm}. \label{MLR-qqplot}} \end{center} \end{figure} An index plot of the Cook's distances for each observation %' (and many other plots including those constructed above from using the basic functions) can be found from applying the \Rcmd{plot} method to the object that results from the application of the \Rcmd{lm} function. \begin{figure} \begin{center} <>= plot(clouds_lm) @ <>= plot(clouds_lm, which = 4, sub.caption = NULL) @ \caption{Index plot of Cook's distances for cloud seeding data. %' \label{MLR-cook}} \end{center} \end{figure} Figure~\ref{MLR-cook} suggests that observations 2 and 18 have undue influence on the estimated regression coefficients, but the two outliers identified previously do not. Again it may be useful to look at the results after these two observations have been removed (see Exercise 6.2). %% \ref{MLR-ex2}) \index{Regression diagnostics|)} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_principal_components_analysis.Rnw0000644000175000017500000004132714133304452022622 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Principal Component Analysis} \setcounter{chapter}{18} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Principal Component Analysis]{Principal Component Analysis: The Olympic Heptathlon \label{PCA}} \section{Introduction} \section{Principal Component Analysis} \section{Analysis Using \R{}} To begin it will help to score all seven events in the same direction, so that `large' values are `good'. We will recode the running events to achieve this; <>=a data("heptathlon", package = "HSAUR3") heptathlon$hurdles <- max(heptathlon$hurdles) - heptathlon$hurdles heptathlon$run200m <- max(heptathlon$run200m) - heptathlon$run200m heptathlon$run800m <- max(heptathlon$run800m) - heptathlon$run800m @ \begin{figure} \begin{center} <>= score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) @ \caption{Scatterplot matrix for the \Robject{heptathlon} data (all countries). \label{PCA-heptathlon-scatter}} \end{center} \end{figure} Figure~\ref{PCA-heptathlon-scatter} shows a scatterplot matrix of the results from all $25$ competitors for the seven events. Most of the scatterplots in the diagram suggest that there is a positive relationship between the results for each pairs of events. The exception are the plots involving the javelin event which give little evidence of any relationship between the result for this event and the results from the other six events; we will suggest possible reasons for this below, but first we will examine the numerical values of the between pairs events correlations by applying the \Rcmd{cor} function <>= w <- options("width") options(width = 65) @ <>= round(cor(heptathlon[,-score]), 2) @ <>= options(width = w$width) @ Examination of these numerical values confirms that most pairs of events are positively correlated, some moderately (for example, high jump and shot) and others relatively highly (for example, high jump and hurdles). And we see that the correlations involving the javelin event are all close to zero. One possible explanation for the latter finding is perhaps that training for the other six events does not help much in the javelin because it is essentially a `technical' event. An alternative explanation is found if we examine the scatterplot matrix in Figure~\ref{PCA-heptathlon-scatter} a little more closely. It is very clear in this diagram that for all events except the javelin there is an outlier, the competitor from Papua New Guinea (PNG), who is much poorer than the other athletes at these six events and who finished last in the competition in terms of points scored. But surprisingly in the scatterplots involving the javelin it is this competitor who again stands out but because she has the third highest value for the event. It might be sensible to look again at both the correlation matrix and the scatterplot matrix after removing the competitor from PNG; the relevant \R{} code is <>= heptathlon <- heptathlon[-grep("PNG", rownames(heptathlon)),] @ Now, we again look at the scatterplot and correlation matrix; \begin{figure} \begin{center} <>= score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) @ \caption{Scatterplot matrix for the \Robject{heptathlon} data after removing observations of the PNG competitor. \label{PCA-heptathlon-scatter2}} \end{center} \end{figure} <>= w <- options("width") options(width = 65) @ <>= round(cor(heptathlon[,-score]), 2) @ <>= options(width = w$width) @ The correlations change quite substantially and the new scatterplot matrix in Figure~\ref{PCA-heptathlon-scatter2} does not point us to any further extreme observations. In the remainder of this chapter we analyze the \Robject{heptathlon} data with the observations of the competitor from Papua New Guinea removed. <>= w <- options("digits") options(digits = 4) @ Because the results for the seven heptathlon events are on different scales we shall extract the principal components from the correlation matrix. A principal component analysis of the data can be applied using the \Rcmd{prcomp} function with the \Rcmd{scale} argument set to \Robject{TRUE} to ensure the analysis is carried out on the correlation matrix. The result is a list containing the coefficients defining each component (sometimes referred to as \stress{loadings}), \index{Loadings} the principal component scores, etc. The required code is (omitting the \Robject{score} variable) <>= heptathlon_pca <- prcomp(heptathlon[, -score], scale = TRUE) print(heptathlon_pca) @ The \Rcmd{summary} method can be used for further inspection of the details: <>= summary(heptathlon_pca) @ <>= options(digits = w$digits) @ The linear combination for the first principal component is <>= a1 <- heptathlon_pca$rotation[,1] a1 @ We see that the hurdles and long jump competitions receive the highest weight but the javelin result is less important. For computing the first principal component, the data need to be rescaled appropriately. The center and the scaling used by \Rcmd{prcomp} internally can be extracted from the \Robject{heptathlon\_pca} via <>= center <- heptathlon_pca$center scale <- heptathlon_pca$scale @ Now, we can apply the \Rcmd{scale} function to the data and multiply with the loadings matrix in order to compute the first principal component score for each competitor <>= hm <- as.matrix(heptathlon[,-score]) drop(scale(hm, center = center, scale = scale) %*% heptathlon_pca$rotation[,1]) @ or, more conveniently, by extracting the first from all precomputed principal components <>= predict(heptathlon_pca)[,1] @ \begin{figure} \begin{center} <>= plot(heptathlon_pca) @ \caption{Barplot of the variances explained by the principal components (with observations for PNG removed). \label{PCA-heptathlon-pca-plot}} \end{center} \end{figure} <>= sdev <- heptathlon_pca$sdev prop12 <- round(sum(sdev[1:2]^2)/sum(sdev^2)*100, 0) @ The first two components account for $\Sexpr{prop12}\%$ of the variance. A barplot of each component's variance (see %%' Figure~\ref{PCA-heptathlon-pca-plot}) shows how the first two components dominate. A plot of the data in the space of the first two principal components, with the points labeled by the name of the corresponding competitor, can be produced as shown with Figure~\ref{PCA-heptathlon-biplot}. In addition, the first two loadings for the events are given in a second coordinate system, also illustrating the special role of the javelin event. This graphical representation is known as \stress{biplot} \citep{HSAUR:Gabriel1971}. \index{Biplot} A biplot is a graphical representation of the information in an $n \times p$ data matrix. The `bi' is a reflection that the technique produces a diagram that gives variance and covariance information about the variables and information about generalized distances between individuals. The coordinates used to produce the biplot can all be obtained directly from the principal components analysis of the covariance matrix of the data and so the plots can be viewed as an alternative representation of the results of such an analysis. Full details of the technical details of the biplot are given in \cite{HSAUR:Gabriel1981} and in \cite{HSAUR:GowerHand1996}. Here we simply construct the biplot for the heptathlon data (without PNG); the result is shown in Figure~\ref{PCA-heptathlon-biplot}. The plot clearly shows that the winner of the gold medal, Jackie Joyner-Kersee, accumulates the majority of her points from the three events long jump, hurdles, and 200m. \begin{figure} \begin{center} <>= biplot(heptathlon_pca, col = c("gray", "black")) @ <>= tmp <- heptathlon[, -score] rownames(tmp) <- abbreviate(gsub(" \\(.*", "", rownames(tmp))) biplot(prcomp(tmp, scale = TRUE), col = c("black", "lightgray"), xlim = c(-0.5, 0.7)) @ \caption{Biplot of the (scaled) first two principal components (with observations for PNG removed). \label{PCA-heptathlon-biplot}} \end{center} \end{figure} The correlation between the score given to each athlete by the standard scoring system used for the heptathlon and the first principal component score can be found from <>= cor(heptathlon$score, heptathlon_pca$x[,1]) @ This implies that the first principal component is in good agreement with the score assigned to the athletes by official Olympic rules; a scatterplot of the official score and the first principal component is given in Figure~\ref{PCA-heptathlonscore}. \begin{figure} \begin{center} <>= plot(heptathlon$score, heptathlon_pca$x[,1]) @ \caption{Scatterplot of the score assigned to each athlete in 1988 and the first principal component. \label{PCA-heptathlonscore}} \end{center} \end{figure} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_conditional_inference.Rnw0000644000175000017500000003731214133304452021011 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Conditional Inference} %%\VignetteDepends{coin} \setcounter{chapter}{3} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Conditional Inference]{Conditional Inference: Guessing Lengths, Suicides, Gastrointestinal Damage, and Newborn Infants \label{CI}} <>= data("roomwidth", package = "HSAUR3") nobs <- table(roomwidth$unit) ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - length(unique(x))) library("coin") @ \section{Introduction} \section{Conditional Test Procedures} \section{Analysis Using \R{}} \subsection{Estimating the Width of a Room Revised} The unconditional analysis of the room width estimated by two groups of students in \Sexpr{ch("SI")} led to the conclusion that the estimates in meters are slightly larger than the estimates in feet. Here, we reanalyze these data in a conditional framework. First, we convert meters into feet and store the vector of observations in a variable \Robject{y}: <>= data("roomwidth", package = "HSAUR3") convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) feet <- roomwidth$unit == "feet" meter <- !feet y <- roomwidth$width * convert @ The test statistic is simply the difference in means <>= T <- mean(y[feet]) - mean(y[meter]) T @ In order to approximate the conditional distribution of the test statistic $T$ we compute $9999$ test statistics for shuffled $y$ values. A permutation of the $y$ vector can be obtained from the \Rcmd{sample} function. <>= meandiffs <- double(9999) for (i in 1:length(meandiffs)) { sy <- sample(y) meandiffs[i] <- mean(sy[feet]) - mean(sy[meter]) } @ \begin{figure} \begin{center} <>= hist(meandiffs) abline(v = T, lty = 2) abline(v = -T, lty = 2) @ \caption{An approximation for the conditional distribution of the difference of mean \Robject{roomwidth} estimates in the feet and meters group under the null hypothesis. The vertical lines show the negative and positive absolute value of the test statistic $T$ obtained from the original data. \label{CI:perm}} \end{center} \end{figure} The distribution of the test statistic $T$ under the null hypothesis of independence of room width estimates and groups is depicted in Figure~\ref{CI:perm}. Now, the value of the test statistic $T$ for the original unshuffled data can be compared with the distribution of $T$ under the null hypothesis (the vertical lines in Figure~\ref{CI:perm}). The $p$-value, i.e., the proportion of test statistics $T$ larger than \Sexpr{-round(T, 3)} or smaller than \Sexpr{round(T, 3)}, is <>= greater <- abs(meandiffs) > abs(T) mean(greater) @ with a confidence interval of <>= binom.test(sum(greater), length(greater))$conf.int @ Note that the approximated conditional $p$-value is roughly the same as the $p$-value reported by the $t$-test in \Sexpr{ch("SI")}. \renewcommand{\nextcaption}{\R{} output of the exact permutation test applied to the \Robject{roomwidth} data. \label{CI-roomwidth-p-fig}} \SchunkLabel <>= library("coin") independence_test(y ~ unit, data = roomwidth, distribution = exact()) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the exact conditional Wilcoxon rank sum test applied to the \Robject{roomwidth} data. \label{CI-roomwidth-w-fig}} \SchunkLabel <>= wilcox_test(y ~ unit, data = roomwidth, distribution = exact()) @ \SchunkRaw \subsection{Crowds and Threatened Suicide} \renewcommand{\nextcaption}{\R{} output of Fisher's exact test for the %' \Robject{suicides} data. \label{CI-suicides-fig}} \SchunkLabel <>= data("suicides", package = "HSAUR3") fisher.test(suicides) @ \SchunkRaw <>= ftp <- round(fisher.test(suicides)$p.value, 3) ctp <- round(chisq.test(suicides)$p.value, 3) @ \subsection{Gastrointestinal Damage} \label{CI:Lanza} Here we are interested in the comparison of two groups of patients, where one group received a placebo and the other one Misoprostol. In the trials shown here, the response variable is measured on an ordered scale -- see Table~\ref{CI:scores}. Data from four clinical studies are available and thus the observations are naturally grouped together. From the \Rclass{data.frame} \Robject{Lanza} we can construct a three-way table as follows: <>= data("Lanza", package = "HSAUR3") xtabs(~ treatment + classification + study, data = Lanza) @ <>= options(width = 65) @ For the first study, the null hypothesis of independence of treatment and gastrointestinal damage, i.e., of no treatment effect of Misoprostol, is tested by <>= library("coin") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "I") @ and, by default, the conditional distribution is approximated by the corresponding limiting distribution. The $p$-value indicates a strong treatment effect. For the second study, the asymptotic $p$-value is a little bit larger: <>= cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II") @ and we make sure that the implied decision is correct by calculating a confidence interval for the exact $p$-value: <>= p <- cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II", distribution = approximate(B = 19999)) pvalue(p) @ The third and fourth study indicate a strong treatment effect as well: <>= cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "III") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "IV") @ At the end, a separate analysis for each study is unsatisfactory. Because the design of the four studies is the same, we can use \Robject{study} as a block variable and perform a global linear-association test investigating the treatment effect of Misoprostol in all four studies. The block variable can be incorporated into the \Rclass{formula} by the \texttt{|} symbol. <>= cmh_test(classification ~ treatment | study, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30))) @ Based on this result, a strong treatment effect can be established. \subsection{Teratogenesis} \index{Teratogenesis} In this example, the medical doctor (MD) and the research assistant (RA) assessed the number of anomalies ($0, 1, 2$ or $3$) for each of $395$ babies: <>= anomalies <- c(235, 23, 3, 0, 41, 35, 8, 0, 20, 11, 11, 1, 2, 1, 3, 1) anomalies <- as.table(matrix(anomalies, ncol = 4, dimnames = list(MD = 0:3, RA = 0:3))) anomalies @ We are interested in testing whether the number of anomalies assessed by the medical doctor differs structurally from the number reported by the research assistant. Because we compare \stress{paired} observations, i.e., one pair of measurements for each newborn, a test of marginal homogeneity (a generalization of McNemar's test, \Sexpr{ch("SI")}) needs to be applied: %%' %\newpage <>= mh_test(anomalies) @ The $p$-value indicates a deviation from the null hypothesis. However, the levels of the response are not treated as ordered. Similar to the analysis of the gastrointestinal damage data above, we can take this information into account by the definition of an appropriate score. Here, the number of anomalies is a natural choice: <>= mh_test(anomalies, scores = list(response = c(0, 1, 2, 3))) @ In our case, one can conclude that the assessment of the number of anomalies differs between the medical doctor and the research assistant. %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_cluster_analysis.Rnw0000644000175000017500000004355014133304452020055 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Cluster Analysis} %%\VignetteDepends{scatterplot3d,mclust,mvtnorm,lattice} \setcounter{chapter}{20} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} <>= library("mclust") library("mvtnorm") mai <- par("mai") options(SweaveHooks = list(rmai = function() { par(mai = mai * c(1,1,1,2))})) data("pottery", package = "HSAUR3") @ \chapter[Cluster Analysis]{Cluster Analysis: Classifying Romano-British Pottery and Exoplanets \label{CA}} \section{Introduction} \section{Cluster Analysis} \section{Analysis Using \R{}} \subsection{Classifying Romano-British Pottery} We start our analysis with computing the dissimilarity matrix containing the Euclidean distance of the chemical measurements on all $\Sexpr{nrow(pottery)}$ pots. The resulting $\Sexpr{nrow(pottery)} \times \Sexpr{nrow(pottery)}$ matrix can be inspected by an \stress{image plot}, here obtained from \index{Image plot} function \Rcmd{levelplot} available in package \Rpackage{lattice} \citep{PKG:lattice, HSAUR:Sarkar2008}. Such a plot associates each cell of the dissimilarity matrix with a color or a gray value. We choose a very dark grey for cells with distance zero (i.e., the diagonal elements of the dissimilarity matrix) and pale values for cells with greater Euclidean distance. Figure~\ref{CA-pottery-distplot} leads to the impression that there are at least three distinct groups with small inter-cluster differences (the dark rectangles) whereas much larger distances can be observed for all other cells. \begin{figure} \begin{center} <>= pottery_dist <- dist(pottery[, colnames(pottery) != "kiln"]) library("lattice") levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number") @ <>= trellis.par.set(standard.theme(color = FALSE)) plot(levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number")) @ \caption{Image plot of the dissimilarity matrix of the \Robject{pottery} data. \label{CA-pottery-distplot}} \end{center} \end{figure} We now construct three series of partitions using single, complete, and average linkage hierarchical clustering as introduced in Subsections~\ref{CA:HC} and \ref{CA:diss}. The function \Rcmd{hclust} performs all three procedures based on the dissimilarity matrix of the data; its \Rcmd{method} argument is used to specify how the distance between two clusters is assessed. The corresponding \Rcmd{plot} method draws a dendrogram; the code and results are given in Figure~\ref{CA-pottery-hclust}. Again, all three dendrograms lead to the impression that three clusters fit the data best (although this judgement is very informal). \begin{figure} \begin{center} <>= pottery_single <- hclust(pottery_dist, method = "single") pottery_complete <- hclust(pottery_dist, method = "complete") pottery_average <- hclust(pottery_dist, method = "average") layout(matrix(1:3, ncol = 3)) plot(pottery_single, main = "Single Linkage", sub = "", xlab = "") plot(pottery_complete, main = "Complete Linkage", sub = "", xlab = "") plot(pottery_average, main = "Average Linkage", sub = "", xlab = "") @ \caption{Hierarchical clustering of \Robject{pottery} data and resulting dendrograms. \label{CA-pottery-hclust}} \end{center} \end{figure} From the \Robject{pottery\_average} object representing the average linkage hierarchical clustering, we derive the three-cluster solution by cutting the dendrogram at a height of four (which, based on the right display in Figure~\ref{CA-pottery-hclust} leads to a partition of the data into three groups). Our interest is now a comparison with the kiln sites at which the pottery was found. <>= pottery_cluster <- cutree(pottery_average, h = 4) xtabs(~ pottery_cluster + kiln, data = pottery) @ The contingency table shows that cluster 1 contains all pots found at kiln site number one, cluster 2 contains all pots from kiln sites number two and three, and cluster three collects the ten pots from kiln sites four and five. In fact, the five kiln sites are from three different regions defined by one, two and three, and four and five, so the clusters actually correspond to pots from three different regions. \subsection{Classifying Exoplanets} \begin{figure} \begin{center} <>= data("planets", package = "HSAUR3") library("scatterplot3d") scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, pch = 16, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, scale.y = 0.7, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") @ \caption{3D scatterplot of the logarithms of the three variables available for each of the exoplanets. \label{CA-planets-scatter}} \end{center} \end{figure} \begin{figure} \begin{center} <>= rge <- apply(planets, 2, max) - apply(planets, 2, min) planet.dat <- sweep(planets, 2, rge, FUN = "/") n <- nrow(planet.dat) wss <- rep(0, 10) wss[1] <- (n - 1) * sum(apply(planet.dat, 2, var)) for (i in 2:10) wss[i] <- sum(kmeans(planet.dat, centers = i)$withinss) plot(1:10, wss, type = "b", xlab = "Number of groups", ylab = "Within groups sum of squares") @ \caption{Within-cluster sum of squares for different numbers of clusters for the exoplanet data. \label{CA-planets-ss}} \end{center} \end{figure} Sadly Figure~\ref{CA-planets-ss} gives no completely convincing verdict on the number of groups we should consider, but using a little imagination `little elbows' can be spotted at the three and five group solutions. %%' We can find the number of planets in each group using <>= planet_kmeans3 <- kmeans(planet.dat, centers = 3) table(planet_kmeans3$cluster) @ The centers of the clusters for the untransformed data can be computed using a small convenience function <>= ccent <- function(cl) { f <- function(i) colMeans(planets[cl == i,]) x <- sapply(sort(unique(cl)), f) colnames(x) <- sort(unique(cl)) return(x) } @ which, applied to the three-cluster solution obtained by $k$-means gets <>= ccent(planet_kmeans3$cluster) @ @ for the three-cluster solution and, for the five cluster solution using <>= planet_kmeans5 <- kmeans(planet.dat, centers = 5) table(planet_kmeans5$cluster) ccent(planet_kmeans5$cluster) @ \subsection{Model-based Clustering in \R{}} We now proceed to apply model-based clustering to the \Robject{planets} data. \R{} functions for model-based clustering are available in package \Rpackage{mclust} \citep{PKG:mclust,HSAUR:FraleyRaftery2002}. Here we use the \Rcmd{Mclust} function since this selects both the most appropriate model for the data \stress{and} the optimal number of groups based on the values of the BIC computed over several models and a range of values for number of groups. The necessary code is: <>= library("mclust") planet_mclust <- Mclust(planet.dat) @ and we first examine a plot of BIC values using the \R{} code that is displayed on top of Figure~\ref{CA-mclust1}. In this diagram the different plotting symbols refer to different model assumptions about the shape of clusters: \begin{description} \item[EII] spherical, equal volume, \item[VII] spherical, unequal volume, \item[EEI] diagonal, equal volume and shape, \item[VEI] diagonal, varying volume, equal shape, \item[EVI] diagonal, equal volume, varying shape, \item[VVI] diagonal, varying volume and shape, \item[EEE] ellipsoidal, equal volume, shape, and orientation, \item[EEV] ellipsoidal, equal volume and equal shape, \item[VEV] ellipsoidal, equal shape, \item[VVV] ellipsoidal, varying volume, shape, and orientation \end{description} \begin{figure} \begin{center} <>= plot(planet_mclust, planet.dat, what = "BIC", col = "black", ylab = "-BIC", ylim = c(0, 350)) @ \caption{Plot of BIC values for a variety of models and a range of number of clusters. \label{CA-mclust1}} \end{center} \end{figure} The BIC selects model VVI (diagonal varying volume and varying shape) with three clusters as the best solution as can be seen from the \Rcmd{print} output: <>= print(planet_mclust) @ This solution can be shown graphically as a scatterplot matrix. The plot is shown in Figure~\ref{CA-planets-mclust-scatter}. Figure~\ref{CA-planets-mclust-scatterclust} depicts the clustering solution in the three-dimensional space. \begin{figure} \begin{center} <>= clPairs(planet.dat, classification = planet_mclust$classification, symbols = 1:3, col = "black") @ \caption{Scatterplot matrix of planets data showing a three-cluster solution from \Rcmd{Mclust}. \label{CA-planets-mclust-scatter}} \end{center} \end{figure} \begin{figure} \begin{center} <>= scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, scale.y = 0.7, pch = planet_mclust$classification, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") @ \caption{3D scatterplot of planets data showing a three-cluster solution from \Rcmd{Mclust}. \label{CA-planets-mclust-scatterclust}} \end{center} \end{figure} The number of planets in each cluster and the mean vectors of the three clusters for the untransformed data can now be inspected by using <>= table(planet_mclust$classification) ccent(planet_mclust$classification) @ Cluster 1 consists of planets about the same size as Jupiter with very short periods and eccentricities (similar to the first cluster of the $k$-means solution). Cluster 2 consists of slightly larger planets with moderate periods and large eccentricities, and cluster 3 contains the very large planets with very large periods. These two clusters do not match those found by the $k$-means approach. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_bayesian_inference.Rnw0000644000175000017500000007256114133304452020306 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Bayesian Inference} %%\VignetteDepends{rmeta,coin} \setcounter{chapter}{17} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Bayesian Inference]{Incorporating Prior Knowledge via Bayesian Inference: Smoking and Lung Cancer \label{BI}} \section{Introduction} \index{Smoking and lung cancer|(} At the beginning of the 20th century, the death toll due to lung cancer was on the rise and the search for possible causes began. For lung cancer in pit workers, animal experiments showed that the so-called `Schneeberg lung disease' was induced by radiation. But this could not explain the increasing incidence of lung cancer in the general population. The identification of possible risk factors was a challenge for epidemiology and statistics, both disciplines being still in their infancy in the 1920s and 1930s. The first modern controlled epidemiological study on the effect of smoking on lung cancer was performed by Franz Hermann M\"uller as part of his dissertation at the University of Cologne in 1939. The results were published a year later \citep{HSAUR:Mueller1940}. M\"uller sent out questionnaires to the relatives of people who had recently died of lung cancer, asking about the smoking behavior and its intensity of the deceased relative. He also sent the questionnaire to healthy controls to obtain information about the smoking behavior in a control group, although it is not clear how this control group was defined. The number of lung cancer patients and healthy controls in five different groups (nonsmokers to extreme smokers) are given in Table~\ref{BI-Smoking_Mueller1940-tab}. <>= data("Smoking_Mueller1940", package = "HSAUR3") toLatex(HSAURtable(Smoking_Mueller1940), caption = paste("Smoking and lung cancer case-control study by M\\\"uller (1940).", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-15 (moderate), 16-25 (heavy), 26-35 (very heavy),", "and more than 35 (extreme)."), label = "BI-Smoking_Mueller1940-tab") @ Four years later Erich Sch\"oninger also wrote his dissertation on the association between smoking and lung cancer and, together with his supervisor Eberhard Schairer at the University of Jena, published his results on a case-control study \citep{HSAUR:SchairerSchoeninger1944} where he assessed the smoking behavior of lung cancer patients, patients diagnosed with other forms of cancer, and also a healthy control group. The data are given in Table~\ref{BI-Smoking_SchairerSchoeniger1944-tab}. <>= x <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) toLatex(HSAURtable(x, xname = "Smoking_SchairerSchoeniger1944"), caption = paste("Smoking and lung cancer case-control study by Schairer and Sch\\\"oniger (1944). Cancer other than lung cancer omitted.", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-5 (moderate), 6-10 (medium), 11-20 (heavy),", "and more than 20 (very heavy)."), label = "BI-Smoking_SchairerSchoeniger1944-tab") @ Shortly after the war, a Dutch epidemiologist reported on a case-control study performed in Amsterdam \citep{HSAUR:Wassink1945} and found similar results as the two German studies; see Table~\ref{BI-Smoking_Wassink1945-tab}. <>= data("Smoking_Wassink1945", package = "HSAUR3") toLatex(HSAURtable(Smoking_Wassink1945), caption = paste("Smoking and lung cancer case-control study by Wassink (1945).", "Smoking categories correspond to the categories used by M\\\"uller (1940)."), label = "BI-Smoking_Wassink1945-tab") @ In 1950 perhaps the most important, but not the first, case-control study showing an increasing risk of developing lung cancer with the amount of tobacco smoked, was published in Great Britain by Richard Doll and Austin Bradford Hill \citep{HSAUR:DollHill1950}. We restrict discussion here to data obtained for males and the data shown in Table~\ref{BI-Smoking_DollHill1950-tab} corresponds to the most recent amount of tobacco consumed regularly by smokers before disease onset \citep[Table~V in][]{HSAUR:DollHill1950}. <>= data("Smoking_DollHill1950", package = "HSAUR3") x <- as.table(Smoking_DollHill1950[,,"Male", drop = FALSE]) toLatex(HSAURtable(x, xname = "Smoking_DollHill1950"), caption = paste("Smoking and lung cancer case-control study (only males) by Doll and Hill (1950).", "The labels for the smoking categories give the number of cigarettes smoked every day."), label = "BI-Smoking_DollHill1950-tab") @ Although the design of the studies by \cite{HSAUR:Mueller1940} and \cite{HSAUR:SchairerSchoeninger1944}, especially the selection of their control groups, can be criticized \citep[see][for a detailed discussion]{HSAUR:Morabia2013} and the study by \cite{HSAUR:DollHill1950} was larger than the older studies and more detailed information on the smoking behavior was obtained by direct patient interviews, the information provided by the earlier studies was not taken into account by \cite{HSAUR:DollHill1950}. They cite \cite{HSAUR:Mueller1940} in their introduction, but did not compare their findings with his results. It is remarkable to see that both \cite{HSAUR:SchairerSchoeninger1944} and \cite{HSAUR:Wassink1945} extensively made use of the report by \cite{HSAUR:Mueller1940} and go as far as analyzing the merged data \citep[Grafiek I, E, and F, in][]{HSAUR:Wassink1945}. In an informal way, these authors wanted to use the already available information, in today's terms called `prior knowledge', to make a stronger case with the new data. Formal statistical methods to incorporate prior knowledge into data analysis as part of the `Bayesian' way of doing statistical analyses were developed in the second half of the last century, and we will focus on them in the present chapter. \index{Smoking and lung cancer|)} \section{Bayesian Inference} \section{Analysis Using \R{}} \subsection{One-by-one Analysis} For the analysis of the four different case-control studies on smoking and lung cancer, we will (retrospectively, of course) update our knowledge with every new study. We begin with a re-analysis of the data described by \cite{HSAUR:Mueller1940}. Using an approximate permutation test introduced in Chapter~\ref{CI} for the hypothesis of independence of the amount of tobacco smoked and group membership (lung cancer or healthy control), we get <>= library("coin") set.seed(29) independence_test(Smoking_Mueller1940, teststat = "quad", distribution = approximate(100000)) @ and there is clearly a strong association between the number of cigarettes smoked and incidence of lung cancer. Because the amount of tobacco smoked is an ordered categorical variable, it is more appropriate to take this information into account, for example by means of a linear association test (see Chapter~\ref{CI}). Nonsmokers receive a score of zero, and for the remaining groups we choose the mid-point of the intervals of daily cigarettes smoked that were used by \cite{HSAUR:Mueller1940} to define his groups: <>= ssc <- c(0, 1 + 14 / 2, 16 + 9 / 2, 26 + 9 / 2, 40) independence_test(Smoking_Mueller1940, teststat = "quad", scores = list(Smoking = ssc), distribution = approximate(100000)) @ The result shows that the data are in favor of an ordered alternative. The $p$-values obtained from approximate permutation tests are attractive because no distributional assumptions are required, but it is hard to derive estimates and confidence intervals for interpretable parameters from such tests. We will therefore now switch to logistic regression models as described in Chapter~\ref{GLM} to model the odds of lung cancer in the different smoking groups. Before we start, let us define a small function for computing odds (for intercept parameters) and odds ratios (for difference parameters) and corresponding confidence intervals from a logistic regression model: <>= eci <- function(model) cbind("Odds (Ratio)" = exp(coef(model)), exp(confint(model))) @ We model the probability of developing lung cancer given the smoking behavior. Because our data was obtained from case-control studies where the groups (lung cancer patients and healthy controls) were defined first and only after that we observed data on the smoking behavior (in a so-called \stress{choice-based sampling}), this may seem the wrong model to start with. However, the marginal distribution of the two groups only changes the intercept in such a logistic model and the effects of smoking can still be interpreted in the way we require \citep[see][for example]{HSAUR:Tutz2012}. The formula for specifying a logistic regression model can be set up such that the response is a matrix with two columns for each smoking group consisting of the number of lung cancer deaths and the number of healthy controls. Although smoking is an ordered factor, we first fit the model with treatment contrasts, i.e., we can interpret the $\exp$ of the regression coefficients as odds ratios between each smoking group and nonsmokers: <>= smoking <- ordered(rownames(Smoking_Mueller1940), levels = rownames(Smoking_Mueller1940)) contrasts(smoking) <- "contr.treatment" eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) @ We see that all but one of the odds ratios increase with the amount of tobacco smoked with a maximum of almost $30$ for extreme smokers (more than $35$ cigarettes per day). The likelihood confidence intervals are rather wide due to the limited sample size, but also the lower limit increases with smoking. An alternative model formulation can help to compare each smoking group with the preceding group, the so-called split-coding \citep[for this and other codings see][]{HSAUR:Tutz2012}: <>= K <- diag(nlevels(smoking) - 1) K[lower.tri(K)] <- 1 contrasts(smoking) <- rbind(0, K) eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) @ The two largest differences are between moderate smokers and nonsmokers (\Robject{smoking1}) and between very heavy and heavy smokers (\Robject{smoking3}). The latter group difference seems, at least judged by the confidence interval, to be larger than expected under a model with no effect of smoking. For the analysis of the three remaining studies, we first perform permutation tests for the independence of smoking and the two groups (lung cancer and healthy controls) in males: <>= xSS44 <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) ap <- approximate(100000) pvalue(independence_test(xSS44, teststat = "quad", distribution = ap)) pvalue(independence_test(Smoking_Wassink1945, teststat = "quad", distribution = ap)) xDH50 <- as.table(Smoking_DollHill1950[,, "Male"]) pvalue(independence_test(xDH50, teststat = "quad", distribution = ap)) @ All $p$-values indicate that the data are not well-described by the independence model. \subsection{Joint Bayesian Analysis} For a Bayesian analysis, we first merge the data from all four studies into one data frame. In doing so, we also merge the smoking groups in a way that we only have three groups left: nonsmokers, moderate smokers, and heavy smokers. These groups are chosen in a way that the number of daily cigarettes is comparable. We first merge the heavy, very heavy, and extreme smokers from \cite{HSAUR:Mueller1940} <>= (M <- rbind(Smoking_Mueller1940[1:2,], colSums(Smoking_Mueller1940[3:5,]))) @ and proceed with the lung cancer patients and healthy controls from \cite{HSAUR:SchairerSchoeninger1944} in the same way <>= SS <- Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")] (SS <- rbind(SS[1,], colSums(SS[2:3,]), colSums(SS[4:5,]))) @ and finally perform the same exercise for the \cite{HSAUR:Wassink1945} and \cite{HSAUR:DollHill1950} data <>= (W <- rbind(Smoking_Wassink1945[1:2,], colSums(Smoking_Wassink1945[3:4,]))) DH <- Smoking_DollHill1950[,, "Male"] (DH <- rbind(DH[1,], colSums(DH[2:3,]), colSums(DH[4:6,]))) @ The three new groups are now called nonsmokers, moderate smokers, and heavy smokers, and we set up a data frame that contains the number of people in each of the possible groups for all studies: <>= smk <- c("Nonsmoker", "Moderate smoker", "Heavy smoker") x <- expand.grid(Smoking = ordered(smk, levels = smk), Diagnosis = factor(c("Lung cancer", "Control")), Study = c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945", "DollHill1950")) x$weights <- c(as.vector(M), as.vector(SS), as.vector(W), as.vector(DH)) @ Before we fit logistic regression models using the data organized in such a way, we define the contrasts for the smoking ordered factor and expand the data in a way that each row corresponds to one person. This is necessary because the \Rcmd{weights} argument to the \Rcmd{glm} function must not be used to define case weights: <>= contrasts(x$Smoking) <- "contr.treatment" x <- x[rep(1:nrow(x), x$weights),] @ We now compute one logistic regression model for each study for later comparisons: <>= models <- lapply(levels(x$Study), function(s) glm(Diagnosis ~ Smoking, data = x, family = binomial(), subset = Study == s)) names(models) <- levels(x$Study) @ In 1939, M\"uller was hardly in the position to come up with a reasonable prior for the odds ratios between moderate or heavy smokers and nonsmokers. So we also use a noninformative prior and just perform the maximum likelihood analysis: <>= eci(models[["Mueller1940"]]) @ Four years later, the maximum likelihood results obtained for the \cite{HSAUR:SchairerSchoeninger1944} data <>= eci(models[["SchairerSchoeniger1944"]]) @ could have been improved by using a normal prior for the difference in log odds whose distribution is the distribution of the maximum likelihood estimator obtained for M\"uller's data. At least approximately, we can compute posterior $90\%$ credibility intervals and the posterior mode from the Schairer and Sch\"oniger data by analyzing both data sets simultaneously. We should, however, keep in mind that the odds of developing lung cancer for nonsmokers is not really interesting for our analysis and that the four studies may very well differ with respect to this intercept parameter. Consequently, we don't want to specify a prior for the intercept. One way to implement such a strategy is to exclude the intercept term from the joint model while allowing a separate intercept for each of the studies: <>= mM40_SS44 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944")) eci(mM40_SS44) @ We observe two important differences between the maximum likelihood and Bayesian results for the Schairer and Sch\"oniger data: In the Bayesian analysis, the estimated odds ratio for moderate smokers is closer to the smaller value obtained from M\"uller's data and, more important, the credibility intervals are much narrower and, one has to say, more realistic now. An odds ratio as large as $40$ is hardly something one would expect to see in practice. If Wassink had been aware of Bayesian statistics, he could have used the posterior distribution of the parameters from our model \Robject{mM40\_SS44} as a prior distribution for analyzing his data. The maximum likelihood results for his data <>= eci(models[["Wassink1945"]]) @ would have changed to <>= mM40_SS44_W45 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945")) eci(mM40_SS44_W45) @ The rather small odds ratios obtained from the model fitted to the Wassink data only are now closer to the estimates obtained from the two previous studies and the variability, as given by the credibility intervals, is much smaller. Now, finally, the model for the Doll and Hill data reports rather large odds ratios with wide confidence intervals: <>= eci(models[["DollHill1950"]]) @ With a (now rather strong) prior defined by the three earlier studies, we get from the joint model for all four studies <>= m_all <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial()) eci(m_all) @ <>= r <- eci(m_all) xM <- round(r["SmokingModerate smoker", 2:3], 1) xH <- round(r["SmokingHeavy smoker", 2:3], 1) @ In 1950, the joint evidence based on such an analysis with an odds ratio between $\Sexpr{xM[1]}$ and $\Sexpr{xM[2]}$ for moderate smokers and between $\Sexpr{xH[1]}$ and $\Sexpr{xH[2]}$ for heavy smokers compared to nonsmokers, would have made a much stronger case than any of the single studies alone. It is interesting to see that with this strong prior for the Doll and Hill study, we also get relatively large odds ratios when comparing heavy to moderate smokers (see row labeled \Rcmd{Smoking2}): <>= K <- diag(nlevels(x$Smoking) - 1) K[lower.tri(K)] <- 1 contrasts(x$Smoking) <- rbind(0, K) eci(glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial())) @ \subsection{A Comparison with Meta Analysis} One may ask how the Bayesian approach of progressively updating the estimates considered here differs from a classical meta analysis described in Chapter~\ref{MA}. We first reshape the data into a form suitable for such an analysis <>= y <- xtabs(~ Study + Smoking + Diagnosis, data = x) ntrtM <- margin.table(y, 1:2)[,"Moderate smoker"] nctrl <- margin.table(y, 1:2)[,"Nonsmoker"] ptrtM <- y[,"Moderate smoker","Lung cancer"] pctrl <- y[,"Nonsmoker","Lung cancer"] ntrtH <- margin.table(y, 1:2)[,"Heavy smoker"] ptrtH <- y[,"Heavy smoker","Lung cancer"] @ and then compute joint odds ratios and confidence intervals for moderate and heavy smokers compared to nonsmokers: <>= library("rmeta") meta.MH(ntrt = ntrtM, nctrl = nctrl, ptrt = ptrtM, pctrl = pctrl) meta.MH(ntrt = ntrtH, nctrl = nctrl, ptrt = ptrtH, pctrl = pctrl) @ For moderate smokers, the effect is a little weaker compared with the results reported on earlier and for heavy smokers, the meta analysis identifies a stronger effect for heavy smokers. Nevertheless, the differences between the two rather different approaches are negligible and the conclusions would have been the same. \section{Summary of Findings} We have seen that, using a Bayesian approach to incorporate prior knowledge into a model, the odds of developing lung cancer increase with increased amounts of smoking. Of course, our analysis here is very simplistic, because we ignored that also pipe and cigar smokers were present in the data, we merged the data based on a very rough assessment of the number of cigarettes smoked per day, ignored whether or not the smokers inhaled the smoke into their lungs, or if nonsmokers were subject to passive-smoking, as we call it today. Most importantly, we must not misinterpret findings from case-control studies as casual and, in fact, none of the authors cited here did so. The debate on whether smoking, and which kind of smoking, actually \stress{causes} lung cancer was initiated by the publications cited in this chapter and many famous statisticians took part in the debate, for example, Sir Ronald Fisher \citep{HSAUR:Fisher1959}, took the view that the inference of causation was premature. In retrospect this was one issue (perhaps the only one) where Fisher was mistaken. \section{Final Comments} There remain a few hard-line opponents of Bayesian inference (just a few) who reject the method because of the use of subjective prior distributions which, these opponents feel, have no place in scientific investigations. And there are Bayesians who think that the only defense of using non-Bayesian methods is incompetence. But for an increasing number of statisticians Bayesian inference is very attractive, because we can use the posterior distribution of the parameters to draw conclusions from the data. Although this requires the specification of a prior distribution, we have seen in this chapter that, using data from previous experiments, priors can be defined in a reasonable way. It is not absolutely necessary to rely on rather complex numerical procedures to`estimate' a posterior distribution. When we are willing to cut some corners, we can implement simple Bayesian approaches using standard software. We should also keep in mind that the prior can be interpreted as a penalty on the parameters, and many penalization approaches therefore have an (often implicit) connection to the Bayesian way of doing statistics. Of course, just picking the prior that `works best' is dangerous and almost surely inappropriate. \section*{Exercises} \begin{description} \exercise Produce a forest plot as introduced in Chapter~\ref{MA} for the four smoking studies analyzed here. \exercise Produce a modified forest plot where one can see how the evidence for smoking being related to lung cancer evolved between 1940 and 1950. \exercise Use the \Rpackage{INLA} add-on package to perform a similar analysis by using the coefficients and their standard errors estimated from our initial logistic regression model \texttt{m[["Mueller1940"]]} as parameters of a normal prior for a logistic regression applied to the Schairer and Sch\"oniger data. Compare the resulting credibility intervals for the two odds-ratios with the approximate results obtained in this chapter. \end{description} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_multidimensional_scaling.Rnw0000644000175000017500000002740714133304452021551 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Multidimensional Scaling} %%\VignetteDepends{ape,wordcloud,MASS} \setcounter{chapter}{19} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= x <- library("ape") library("wordcloud") @ \chapter[Multidimensional Scaling]{Multidimensional Scaling: British Water Voles and Voting in US Congress \label{MDS}} \section{Introduction} \section{Multidimensional Scaling} \section{Analysis Using \R{}} We can apply classical scaling to the distance matrix for populations of water voles using the \R{} function \Rcmd{cmdscale}. The following code finds the classical scaling solution and computes the two criteria for assessing the required number of dimensions as described above. <>= data("watervoles", package = "HSAUR3") voles_mds <- cmdscale(watervoles, k = 13, eig = TRUE) voles_mds$eig @ Note that some of the eigenvalues are negative. The criterion $P_2$ can be computed by <>= sum(abs(voles_mds$eig[1:2]))/sum(abs(voles_mds$eig)) @ and the criterion suggested by \cite{HSAUR:Mardiaetal1979} is <>= sum((voles_mds$eig[1:2])^2)/sum((voles_mds$eig)^2) @ The two criteria for judging number of dimensions differ considerably, but both values are reasonably large, suggesting that the original distances between the water vole populations can be represented adequately in two dimensions. The two-dimensional solution can be plotted by extracting the coordinates from the \Robject{points} element of the \Robject{voles\_mds} object; the plot is shown in Figure~\ref{MDS-watervoles-plot}. The \Rcmd{textplot} function from package \Rpackage{wordcloud} can be used to annotate the plot with non-overlapping text. \begin{figure} \begin{center} <>= x <- voles_mds$points[,1] y <- voles_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") textplot(x, y, words = colnames(watervoles), new = FALSE) @ \caption{Two-dimensional solution from classical multidimensional scaling of distance matrix for water vole populations. \label{MDS-watervoles-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= library("ape") st <- mst(watervoles) plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") for (i in 1:nrow(watervoles)) { w1 <- which(st[i, ] == 1) segments(x[i], y[i], x[w1], y[w1]) } textplot(x, y, words = colnames(watervoles), new = FALSE) @ \caption{Minimum spanning tree for the \Robject{watervoles} data. \label{MDS-watervoles-mst}} \end{center} \end{figure} We shall now apply non-metric scaling to the voting behavior shown in Table~\ref{MDS-voting-tab}. Non-metric scaling is available with function \Rcmd{isoMDS} from package \Rpackage{MASS} \citep{HSAUR:VenablesRipley2002}: <>= library("MASS") data("voting", package = "HSAUR3") voting_mds <- isoMDS(voting) @ and we again depict the two-dimensional solution (Figure~\ref{MDS-voting-plot}). The Figure suggests that voting behavior is essentially along party lines, although there is more variation among Republicans. The voting behavior of one of the Republicans (Rinaldo) seems to be closer to his democratic colleagues rather than to the voting behavior of other Republicans. \begin{figure} \begin{center} <>= x <- voting_mds$points[,1] y <- voting_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(voting_mds$points[,1])*1.2, type = "n") textplot(x, y, words = colnames(voting), new = FALSE) voting_sh <- Shepard(voting[lower.tri(voting)], voting_mds$points) @ \caption{Two-dimensional solution from non-metric multidimensional scaling of distance matrix for voting matrix. \label{MDS-voting-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= plot(voting_sh, pch = ".", xlab = "Dissimilarity", ylab = "Distance", xlim = range(voting_sh$x), ylim = range(voting_sh$x)) lines(voting_sh$x, voting_sh$yf, type = "S") @ \caption{The Shepard diagram for the \Robject{voting} data shows some discrepancies between the original dissimilarities and the multidimensional scaling solution. \label{MDS-voting-shepard}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_missing_values.Rnw0000644000175000017500000006351314133304452017522 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Missing Values} %%\VignetteDepends{mice} \setcounter{chapter}{15} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Missing Values]{Missing Values: Lowering Blood Pressure During Surgery \label{MV}} \section{Introduction} \index{Blood pressure} It is sometimes necessary to lower a patient's blood pressure during surgery, using a hypotensive drug. Such drugs are administered continuously during the relevant phase of the operation; because the duration of this phase varies so does the total amount of drug administered. Patients also vary in the extent to which the drugs succeed in lowering blood pressure. The sooner the blood pressure rises again to normal after the drug is discontinued, the better. The data in Table~\ref{MV-bp-tab} \citep[a missing-value version of the data presented by][]{HSAUR:RobertsonArmitage1959} relate to a particular hypotensive drug and give the time in minutes before the patient's systolic blood pressure returned to 100mm of mercury (the recovery time), the logarithm (base 10) of the dose of drug in milligrams, and the average systolic blood pressure achieved while the drug was being administered. The question of interest is how is the recovery time related to the other two variables? For some patients the recovery time was not recorded and the missing values are indicated as NA in Table~\ref{MV-bp-tab}. <>= data("bp", package = "HSAUR3") toLatex(HSAURtable(bp), pcol = 2, caption = paste("Blood pressure data."), label = "MV-bp-tab") @ \section{Analyzing Multiply Imputed Data} \label{MI:ana} From the analysis of each data set we need to look at the estimates of the quantity of interest, say $Q$, and the variance of the estimates. We let $\hat{Q}_i$ be the estimate from the $i$th data set and $S_i$ its corresponding variance. The combined estimate of the quantity of interest is \begin{eqnarray*} \bar{Q} = \frac{1}{m}\sum_{i = 1}^m \hat{Q}_i. \end{eqnarray*} To find the combined variance involves first calculating the within-imputation variance, \begin{eqnarray*} \bar{S} = \frac{1}{m}\sum_{i = 1}^m S_i \end{eqnarray*} followed by the between-imputation variance, \begin{eqnarray*} B = \frac{1}{m - 1} \sum_{i = 1}^m (\hat{Q}_i - \bar{Q})^2 \end{eqnarray*} then the required total variance can now be found from \begin{eqnarray*} T = \bar{S} + (1 + m^{-1}) B \end{eqnarray*} This total variance is made up of two components; the first which preserves the natural variability, $\bar{S}$, is simply the average of the variance estimates for each imputed data set and is analogous to the variance that would be suitable if we did not need to account for missing data; the second component, $B$, estimates uncertainty caused by missing data by measuring how the point estimates vary from data set to data set. More explanation of how the formula for $T$ arises is given in \cite{HSAUR:vanBuuren2012}. The overall standard error is simply the square root of $T$. A significance test for $Q$ and a confidence interval is found from the usual test statistic, ($Q-$ hypothesized value of $Q$)/$\sqrt{T}$, the value of which is referred to a Student's $t$-distribution. The question arises however as to what is the appropriate value for the degrees of freedom of the test, say $v_0$? \cite{HSAUR:Rubin1987} suggests that the answer to this question is given by; \begin{eqnarray*} v_0 = (m - 1) (1 + 1/r^2) \end{eqnarray*} where \begin{eqnarray*} r = \frac{B + B / m}{\bar{S}} \end{eqnarray*} But \cite{HSAUR:BarnardRubin1999} noted that using this value of $v_0$ can produce values that are larger than the degrees of freedom in the complete data, a result which they considered `clearly inappropriate'. Consequently they developed an adapted version that does not lead to the same problem. Barnard and Rubin's revised value for the degrees of freedom of the $t$-test in which we are interested is $v_1$ given by; \begin{eqnarray*} v_1 = \frac{v_0 v_2}{v_0 + v_2} \end{eqnarray*} where \begin{eqnarray*} v_2 = \frac{n(n-1)(1 - \lambda)}{n + 2} \end{eqnarray*} and \begin{eqnarray*} \lambda = \frac{r}{\sqrt{r^2 + 1}}. \end{eqnarray*} The quantity $v_1$ is always less than or equal to the degrees of freedom of the test applied to the hypothetically complete data. \citep[For more details see][]{HSAUR:vanBuuren2012}. \index{Imputation|)} \section{Analysis Using \R{}} To begin we shall analyze the blood pressure data in Table~\ref{MV-bp-tab} using the complete-case approach, i.e., by simply removing the data for patients where the recovery time is missing. To begin we might simply count the number of missing values using the sapply function as follows: <>= sapply(bp, function(x) sum(is.na(x))) @ So there are ten missing values of recovery time but no missing values amongst the other two variables. Now we use the \Rcmd{summary} function to look at some basic statistics of the complete data for recovery time: <>= summary(bp$recovtime, na.rm = TRUE) @ And next we can calculate the complete data estimate of the standard deviation of recover time <>= sd(bp$recovtime, na.rm = TRUE) @ The final numerical results we might be interested in are the correlations of recovery time with blood pressure and of recovery time with logdose. These can be found as follows: <>= with(bp, cor(bloodp, recovtime, use = "complete.obs")) with(bp, cor(logdose, recovtime, use = "complete.obs")) @ And a useful graphic of the data is a scatterplot matrix which we can construct using \Rcmd{pairs}. The scatterplot matrix is given in Figure~\ref{MV-bp-pairs-cc}. \begin{figure} \begin{center} <>= layout(matrix(1:3, nrow = 1)) plot(bloodp ~ logdose, data = bp) plot(recovtime ~ bloodp, data = bp) plot(recovtime ~ logdose, data = bp) @ \caption{Scatterplots of the complete cases of the \Robject{bp} data. \label{MV-bp-pairs-cc}} \end{center} \end{figure} To investigate how recovery time is related to blood pressure and logdose we might begin by fitting a multiple linear regression model (see Chapter~\ref{MLR}). The relevant command and the summary of the results is shown in Figure~\ref{MV-bp-lm-cc}. Note that this summary output reports that ten observations with missing values were removed prior to the analysis; this is default for many models in \R. \renewcommand{\nextcaption}{\R{} output of the complete-case linear model for the \Robject{bp} data. \label{MV-bp-lm-cc}} \SchunkLabel <>= summary(lm(recovtime ~ bloodp + logdose, data = bp)) @ \SchunkRaw Now let us see what happens when we impute the missing values of the recovery time variable simply by the mean of the complete case; for this we will use the \Rpackage{mice} \citep{PKG:mice} package; <>= library("mice") @ We begin by creating a new data set, \Robject{imp}, which will contain the three variables log-dose, blood pressure, and recovery time with the missing values in the latter replaced by the mean recovery time of the complete cases; <>= imp <- mice(bp, method = "mean", m = 1, maxit = 1) @ So now we can find the summary statistics of recovery time to compare with those given previously <>= with(imp, summary(recovtime)) @ Making the comparison we see that only the values of the first and third quantile and the median have changed. The minimum and maximum values are the same and so, of course, is the mean. But of more interest is what happens to the sample standard deviation; its value for the imputed data can be found using: <>= with(imp, sd(recovtime)) @ The value for the imputed data, $\Sexpr{round(with(imp, sd(recovtime))[["analyses"]][[1]], 2)}$ is, as we would expect, lower than that for the complete data, $\Sexpr{round(with(bp, sd(recovtime, na.rm = TRUE)), 2)}$. What about the correlations? <>= with(imp, cor(bloodp, recovtime)) with(imp, cor(logdose, recovtime)) @ The correlations of blood pression and recovery time are very similar before ($\Sexpr{round(with(bp, cor(bloodp, recovtime, use = "complete.obs")), 2)}$) after ($\Sexpr{round(with(imp, cor(bloodp, recovtime))[["analyses"]][[1]], 2)}$) imputation. For log-dose, imputation changes the correlation from $\Sexpr{round(with(bp, cor(logdose, recovtime, use = "complete.obs")), 2)}$ to $\Sexpr{round(with(imp, cor(logdose, recovtime))[["analyses"]][[1]], 2)}$. The scatterplot of the imputed data is found as given by the code displayed with Figure~\ref{MV-bp-pairs-imp}. For mean imputation, the imputed value of the recovery time is constant for all observations and so they appear as a series of points along the value of the mean value of the observed recovery times namely, $\Sexpr{round(with(bp, mean(recovtime, na.rm = TRUE)), 2)}$. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) @ \caption{Scatterplots of the imputed \Robject{bp} data. Imputed observations are depicted as triangles. \label{MV-bp-pairs-imp}} \end{center} \end{figure} \renewcommand{\nextcaption}{\R{} output of the mean imputation linear model for the \Robject{bp} data. \label{MV-bp-lm-imp}} \SchunkLabel <>= with(imp, summary(lm(recovtime ~ bloodp + logdose))) @ \SchunkRaw Comparison of the multiple linear regression results in Figure~\ref{MV-bp-lm-imp} with those in Figure~\ref{MV-bp-lm-cc} show some interesting differences, for example, the standard errors of the regression coefficients are somewhat lower for the mean imputed data but the conclusions drawn from the results in each table would be broadly similar. \index{Predictive mean matching} The single imputation of a sample mean is not to be recommended and so we will move on to using a more sophisticated multiple imputation procedure know as \stress{predictive mean matching}. The method is described in detail in \cite{HSAUR:vanBuuren2012} who considers it both easy-to-use and versatile. And imputations outside the observed data range will not occur so that problems with meaningless imputations, for example, a negative recovery time, will not occur. The method is labeled \Robject{pmm} in the \Rpackage{mice} package and here we will apply it to the blood pressure data with $m = 10$ (we need to fix the seed in order to make the result reproducible): <>= imp_ppm <- mice(bp, m = 10, method = "pmm", print = FALSE, seed = 1) @ The scatterplot of the imputed data is found as given by the code displayed with Figure~\ref{MV-bp-pairs-imp-mice}. We only show the imputed recovery times from the first iteration ($m = 1$).The imputed recovery times now take different values. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) @ \caption{Scatterplots of the multiple imputed \Robject{bp} data (first iteration). Imputed observations are depicted as triangles. \label{MV-bp-pairs-imp-mice}} \end{center} \end{figure} From the resulting object we can compute the mean and standard deviations of recovery time for each of the $m = 10$ iterations. We first extract these numbers from the \Robject{analyses} element of the returned object, convert this list to a vector, and use the \Rcmd{summary} function to compute the usual summary statistics: <>= summary(unlist(with(imp_ppm, mean(recovtime))$analyses)) summary(unlist(with(imp_ppm, sd(recovtime))$analyses)) @ We do the same with the correlations as follows <>= summary(unlist(with(imp_ppm, cor(bloodp, recovtime))$analyses)) summary(unlist(with(imp_ppm, cor(logdose, recovtime))$analyses)) @ The estimate of the mean of the blood pressure data from the multiply imputed results is $\Sexpr{round(mean(unlist(with(imp_ppm, mean(recovtime))$analyses)) , 2)}$, very similar to the values found previously. Similarly the estimate of the standard deviation of the data is $\Sexpr{round(mean(unlist(with(imp_ppm, sd(recovtime))$analyses)) , 2)}$ which lies between the complete data estimate and the \emph{mean-imputed} value. The two correlation estimates are also very close to the previous values. The variation in the estimates of mean, standard deviation, and correlations across the ten imputation is relatively small apart from that for the correlation between log-dose and recovery time -- here there is considerable variation in the values for the ten imputations. Finally, we will fit a linear model to each of the imputed samples and then find the summary statistics for the ten sets of regression coefficients: the results are given in Figure~\ref{MV-bp-lm-cc-mice}: <>= fit <- with(imp_ppm, lm(recovtime ~ bloodp + logdose)) @ \renewcommand{\nextcaption}{\R{} output of the multiple imputed linear model for the \Robject{bp} data. \label{MV-bp-lm-cc-mice}} \SchunkLabel <>= summary(pool(fit)) @ \SchunkRaw The result for blood pressure is similar to the previous complete data and mean-imputed results with the regression coefficient for this variable being highly significant $(p = \Sexpr{round(summary(pool(fit))["bloodp", 5], 3)})$. But the result for log dose differs from those found previously; for the multiply imputed data the regression coefficient for log dose is not significant at the $5\%$ level $(p = \Sexpr{round(summary(pool(fit))["logdose", 5], 3)})$ whereas in both of the previous two analyses it was significant. This finding reflects the greater variation of the value of the correlation between log dose and recovery time in the ten imputations noted above. (Remember that the standard errors in Figure~\ref{MV-bp-lm-cc-mice} computed by \Rcmd{pool} arise from the formulae given in Section~\ref{MI:ana}.) Now suppose we wish to test the hypothesis that in the population from which the sample data in Table~\ref{MV-bp-tab} arises a mean recovery time of $27$ minutes. We will test this hypothesis in the usual way using Student's t-test applied to the complete-data, the singly imputed data, and the multiply imputed data: <>= with(bp, t.test(recovtime, mu = 27)) with(imp, t.test(recovtime, mu = 27))$analyses[[1]] @ For the multiply imputed data we need to use the \Rcmd{lm} function to get the equivalent of the $t$-test by modeling recovery time minus $27$ with an intercept only and testing for zero intercept. So the code needed is: <>= fit <- with(imp_ppm, lm(I(recovtime - 27) ~ 1)) summary(pool(fit)) @ Looking at the results of the three analyses we see that the complete-case analysis fails to reject the hypothesis at the $5\%$ level whereas the other two analyses lead to results that are statistically significant at the level. This simple (and perhaps rather artificial) example demonstrates that different conclusions can be reached by the different approaches. \section{Summary of Findings} The estimated standard deviation of the blood pressure is lower when computed from the mean-imputed data than from the complete data. The corresponding value from the multiply imputed data lies between these two values. The estimate of the mean from the multiply imputed data is very similar to the value obtained in the complete data analysis. (The value from the singly imputed data is, of course, the same as from the complete data.) The estimates of the correlations between blood pressure and recovery time and log dose and recovery time are very similar in all three analyses but the variation in the latter across the ten multiple imputations is considerable and this results in the regression coefficient for log dose being less significant than in the other two analyses. Testing the hypothesis that the population mean of recovery time is $27$ minutes using complete-case analysis leads to a different conclusion than is arrived at by the two multiple imputations approaches. \section{Final Comments} Missing values are an ever-present possibility in all types of studies although everything possible should be done to avoid them. But when data contain missing values multiple imputation can be used to provide valid inferences for parameter estimates from the incomplete data. If carefully handled, multiple imputation can cope with missing data in all types of variables. In this chapter we have given only a brief account of dealing with missing values; a detailed account is available in the issue of \stress{Statistical Methods in Medical Research entitled Multiple Imputation: Current Perspectives} (Volume 16, Number 3, 2007) and in \cite{HSAUR:vanBuuren2012}. \section*{Exercises} \begin{description} \exercise The data in Table~\ref{MI-UStemp-tab} give the lowest temperatures (in Fahrenheit) recorded in various months for cities in the US; missing values are indicated by NA. Calculate the correlation matrix of the data using \begin{enumerate} \item the complete-case approach, \item the available-data approach, and \item a multiple-imputation approach. \end{enumerate} Find the principal components of the data using each of three correlation matrices and plot the cities in the space of the first two components of each solution. <>= data("UStemp", package = "HSAUR3") toLatex(HSAURtable(UStemp), caption = "Lowest temperatures in Fahrenheit recorded in various months for cities in the US.", label = "MI-UStemp-tab", rownames = TRUE) @ \exercise Find $95\%$ confidence intervals for the population means of the lowest temperature in each month using \begin{enumerate} \item the complete-case approach, \item the mean value imputation, and \item a multiple-imputation approach. \end{enumerate} \exercise Find the correlation matrix for the four months in Table~\ref{MI-UStemp-tab} using complete-case analysis, listwise deletion, and multiple imputation. \end{description} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/graphics/0000755000175000017500000000000012451513136015162 5ustar nileshnileshHSAUR3/vignettes/graphics/Rlogo_bw.png0000644000175000017500000003234712357775400017464 0ustar nileshnileshPNG  IHDRFvZbKGD) pHYs."."ݒ vpAgO4IDATxy^}y/pIej_,[iIcɵ&Sum+q:viNfizvt4ĕ,YQ"E-" ;{syyb%5}.{~~G)2MAE8![::fD vKO`lũ_ܡ鸍f+Nۋkr.Т)%RLKiMWjTJX%fNhH'\8صqlI"E0b O8"$%A)) 葝F:4U,oiV3L4U8t$:%"EWP OA=e%5x PI8W3Y*F'"v\K41CڄT?RDjp>KZCӍ : dpR[qzF!2HsX/%A(#ZӤTCN'hpv%] {u#Np9<gDb1..5$HR#cPo&#Ixz7w{!P' _G1G@NR)1Ri]5{3 D$dt=uV|!ȏ܋$.Hd^LTZBo dgǤ$D$~cc[^wԉtN*fI|~NDIu] 1P1qstk/78&'Tτ4ߡPI}ET) '%u^Y<%cwXlvFN /v1;Ҵ x֮t_#Ӥ^3V*F0o@C7ol EoGf'`&c*gt:uBLDLʽkuů]kMb ABL@H}%P͟mp&荿}$BGg9ԣ<T1vC:R*$]@@WZO8VGQHFwʹcB^hGK0~v Ǽqﴈ)ǝEWui\NDkd$b!>a@)5NH^<ƍޘ 0:;k%;"R@,~Z)_#xPJG[ Ia``ҧK! ::AN#~$_EĘ2ns t4R"Fvy>/{'{+://A'10!Z/9.&&&&:g$SaqHJ#fFK)* & 11!R51!ޣbq% NóȳTɳ[$-D )6&:BSoLB`gP ޑHT>H! &*Iwv~{~ٲ}PnEN8eؔqiL!RCW_D_ɕE-LKP#XAS7P $",?O_޾sruyRR25,5e1PI 3.!q jУ~RH l i)Qg yp>̙+Qc)**( $ Ϗ\<@BKDe$H SRrlEK+Q""w4B:ژk4,JhxDJr(IYmkGA]}RrܠXTBüIP) C=X34et Y }\ 2y,r"5S;S KzݴZ%YեʡL0-Eftյ=B3|<2! 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Uc/3 Xdof%kT019b'?Cv r}mq3LSƥ$˛m6~ |ī_2G=3b2Ә4Ia+ֲEc ~'x ,I a2C[YG&N &XWfȳR{sN{7@|Ϥ鰓E(҆w/"JF Kuw\":N0d;SP&<֯GiOUn*ⰼ}cq;9AOG9l7r˚; &4]#%RwY=]e&mШ+x|֝[zdd ^%A->lU\ۈJTEsbKw m^$6_U@DIπe&+~ID̏j?XXisDqPw9͙Mɕ׮z;[{ Y,PL˕{=uJca[Mp9kYMNn2/M xWojAPt9q5)j;KG'",)dɃ۽TrE&q({܃\wzǺ܍d[*PXTƪ~r1|j4"vQU.fFJ9nD `ӗzj]`ܸ[ڡ|l %tEXtdate:create2010-10-13T15:42:15+02:00 P%tEXtdate:modify2010-10-13T15:42:15+02:00IENDB`HSAUR3/vignettes/Ch_analysis_of_variance.Rnw0000644000175000017500000004721114133304452020646 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analysis of Variance} %%\VignetteDepends{wordcloud} \setcounter{chapter}{4} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("wordcloud") @ \chapter[Analysis of Variance]{Analysis of Variance: Weight Gain, Foster Feeding in Rats, Water Hardness, and Male Egyptian Skulls \label{ANOVA}} \section{Introduction} \section{Analysis of Variance} \section{Analysis Using \R{}} \subsection{Weight Gain in Rats \label{ANOVA:rats}} Before applying analysis of variance to the data in Table~\ref{ANOVA-weightgain-tab} we should try to summarize the main features of the data by calculating means and standard deviations and by producing some hopefully informative graphs. The data is available in the \Rclass{data.frame} \Robject{weightgain}. The following \R{} code produces the required summary statistics <>= data("weightgain", package = "HSAUR3") tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), mean) tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), sd) @ \begin{figure} \begin{center} <>= plot.design(weightgain) @ \caption{Plot of mean weight gain for each level of the two factors. \label{ANOVA-weightgain-fig}} \end{center} \end{figure} To apply analysis of variance to the data we can use the \Rcmd{aov} function in \R{} and then the \Rcmd{summary} method to give us the usual analysis of variance table. The model \Rclass{formula} specifies a two-way layout with interaction terms, where the first factor is \Robject{source}, and the second factor is \Robject{type}. <>= wg_aov <- aov(weightgain ~ source * type, data = weightgain) @ \renewcommand{\nextcaption}{\R{} output of the ANOVA fit for the \Robject{weightgain} data. \label{ANOVA-weightgain-output}} \SchunkLabel <>= summary(wg_aov) @ \SchunkRaw \begin{figure} \begin{center} <>= interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain) @ <>= interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain, legend = FALSE) legend(1.5, 95, legend = levels(weightgain$source), title = "weightgain$source", lty = c(2,1), bty = "n") @ \caption{Interaction plot of type and source. \label{ANOVA-weightgain-fig2}} \end{center} \end{figure} The estimates of the intercept and the main and interaction effects can be extracted from the model fit by <>= coef(wg_aov) @ Note that the model was fitted with the restrictions $\gamma_1 = 0$ (corresponding to \Rlevel{Beef}) and $\beta_1 = 0$ (corresponding to \Rlevel{High}) because treatment contrasts were used as default as can be seen from <>= options("contrasts") @ Thus, the coefficient for \Robject{source} of $\Sexpr{coef(wg_aov)[2]}$ can be interpreted as an estimate of the difference $\gamma_2 - \gamma_1$. Alternatively, we can use the restriction $\sum_i \gamma_i = 0$ by <>= coef(aov(weightgain ~ source + type + source:type, data = weightgain, contrasts = list(source = contr.sum))) @ \subsection{Foster Feeding of Rats of Different Genotype} As in the previous subsection we will begin the analysis of the foster feeding data in Table~\ref{ANOVA-foster-tab} with a plot of the mean litter weight for the different genotypes of mother and litter (see Figure~\ref{ANOVA-foster-fig}). The data are in the \Rclass{data.frame} \Robject{foster} <>= data("foster", package = "HSAUR3") @ \begin{figure} \begin{center} <>= plot.design(foster) @ \caption{Plot of mean litter weight for each level of the two factors for the \Robject{foster} data. \label{ANOVA-foster-fig}} \end{center} \end{figure} We can derive the two analyses of variance tables for the foster feeding example by applying the \R{} code <>= summary(aov(weight ~ litgen * motgen, data = foster)) @ to give <>= summary(aov(weight ~ litgen * motgen, data = foster)) @ and then the code <>= summary(aov(weight ~ motgen * litgen, data = foster)) @ to give <>= summary(aov(weight ~ motgen * litgen, data = foster)) @ There are (small) differences in the sum of squares for the two main effects and, consequently, in the associated $F$-tests and $p$-values. \index{F-tests@$F$-tests} This would not be true if in the previous example in Subsection~\ref{ANOVA:rats} we had used the code <>= summary(aov(weightgain ~ type * source, data = weightgain)) @ instead of the code which produced Figure~\ref{ANOVA-weightgain-output} (readers should confirm that this is the case). We can investigate the effect of genotype B on litter weight in more detail by the use of \stress{multiple comparison procedures} \index{Multiple comparison procedures|(} \citep[see][and \Sexpr{ch("SIMC")}]{HSAUR:Everitt1996}. Such procedures allow a comparison of all pairs of levels of a factor whilst maintaining the nominal significance level at its specified value and producing adjusted confidence intervals for mean differences. One such procedure is called \stress{Tukey honest significant differences} \index{Tukey honest significant differences} suggested by \cite{HSAUR:Tukey1953}; see \cite{HSAUR:HochbergTamhane1987} also. Here, we are interested in simultaneous confidence intervals for the weight differences between all four genotypes of the mother. First, an ANOVA model is fitted <>= foster_aov <- aov(weight ~ litgen * motgen, data = foster) @ which serves as the basis of the multiple comparisons, here with all pair-wise differences by <>= foster_hsd <- TukeyHSD(foster_aov, "motgen") foster_hsd @ A convenient \Rcmd{plot} method exists for this object and we can get a graphical representation of the multiple confidence intervals as shown in Figure~\ref{ANOVA-foster-mc}. It appears that there is only evidence for a difference in the B and J genotypes. Note that the particular method implemented in \Rcmd{TukeyHSD} is applicable only to balanced and mildly unbalanced designs (which is the case here). Alternative approaches, applicable to unbalanced designs and more general research questions, will be introduced and discussed in \Sexpr{ch("SIMC")}. \begin{figure} \begin{center} <>= plot(foster_hsd) @ \caption{Graphical presentation of multiple comparison results for the \Robject{foster} feeding data. \label{ANOVA-foster-mc}} \end{center} \end{figure} \index{Multiple comparison procedures|)} \subsection{Water Hardness and Mortality} The water hardness and mortality data for $61$ large towns in England and Wales (see Table~2.3) was analyzed in \Sexpr{ch("SI")} and here we will extend the analysis by an assessment of the differences of both hardness and mortality in the North or South. The hypothesis that the two-dimensional mean-vector of water hardness and mortality is the same for cities in the North and the South can be tested by \stress{Hotelling-Lawley} test in a multivariate analysis of variance framework. The \R{} function \Rcmd{manova} can be used to fit such a model and the corresponding \Rcmd{summary} method performs the test specified by the \Rcmd{test} argument <>= data("water", package = "HSAUR3") summary(manova(cbind(hardness, mortality) ~ location, data = water), test = "Hotelling-Lawley") @ The \Rcmd{cbind} statement in the left-hand side of the formula indicates that a \stress{multivariate} response variable is to be modeled. \index{cbind function in formula@\texttt{cbind} function in \textit{formula}} The $p$-value associated with the \stress{Hotelling-Lawley} statistic is very small and there is strong evidence that the mean vectors of the two variables are not the same in the two regions. Looking at the sample means <>= tapply(water$hardness, water$location, mean) tapply(water$mortality, water$location, mean) @ we see large differences in the two regions both in water hardness and mortality, where low mortality is associated with hard water in the South and high mortality with soft water in the North (see Figure~\ref{SI-water-sp} also). \subsection{Male Egyptian Skulls} \index{Multivariate analysis of variance (MANOVA)|(} We can begin by looking at a table of mean values for the four measurements within each of the five epochs. The measurements are available in the \Rclass{data.frame} \Robject{skulls} and we can compute the means over all epochs by <>= data("skulls", package = "HSAUR3") means <- aggregate(skulls[,c("mb", "bh", "bl", "nh")], list(epoch = skulls$epoch), mean) means @ It may also be useful to look at these means graphically and this could be done in a variety of ways. Here we construct a scatterplot matrix of the means using the code attached to Figure~\ref{ANOVA-skulls-fig}. %% %% now uses wordcloud::textplot but xlim/ylim needs to be increased %% \begin{figure} \begin{center} <>= pairs(means[,-1], panel = function(x, y) { textplot(x, y, levels(skulls$epoch), new = FALSE, cex = 0.8) }) @ \caption{Scatterplot matrix of epoch means for Egyptian \Robject{skulls} data. \label{ANOVA-skulls-fig}} \end{center} \end{figure} There appear to be quite large differences between the epoch means, at least on some of the four measurements. We can now test for a difference more formally by using MANOVA with the following \R{} code to apply each of the four possible test criteria mentioned earlier; <>= skulls_manova <- manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls) summary(skulls_manova, test = "Pillai") summary(skulls_manova, test = "Wilks") summary(skulls_manova, test = "Hotelling-Lawley") summary(skulls_manova, test = "Roy") @ The $p$-value associated with each four test criteria is very small and there is strong evidence that the skull measurements differ between the five epochs. We might now move on to investigate which epochs differ and on which variables. We can look at the univariate $F$-tests \index{F-tests@$F$-tests} for each of the four variables by using the code <>= summary.aov(skulls_manova) @ We see that the results for the maximum breadths (\Robject{mb}) and basialiveolar length (\Robject{bl}) are highly significant, with those for the other two variables, in particular for nasal heights (\Robject{nh}), suggesting little evidence of a difference. To look at the pairwise multivariate tests (any of the four test criteria are equivalent in the case of a one-way layout with two levels only) we can use the \Rcmd{summary} method and \Rcmd{manova} function as follows: <>= summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c3300BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c1850BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c200BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "cAD150"))) @ To keep the overall significance level for the set of all pairwise multivariate tests under some control (and still maintain a reasonable power), \cite{HSAUR:Stevens2001} recommends setting the nominal level $\alpha = 0.15$ and carrying out each test at the $\alpha / m$ level where $m$ is the number of tests performed. The results of the four pairwise tests suggest that as the epochs become further separated in time the four skull measurements become increasingly distinct. \index{Multivariate analysis of variance (MANOVA)|)} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_simultaneous_inference.Rnw0000644000175000017500000005557314133304452021247 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Simultaneous Inference and Multiple Comparisons} %%\VignetteDepends{lme4,multcomp,coin,sandwich} \setcounter{chapter}{14} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("multcomp") library("coin") library("sandwich") library("lme4") @ \chapter[Simultaneous Inference and Multiple Comparisons]{Simultaneous Inference and Multiple Comparisons: Genetic Components of Alcoholism, Deer Browsing Intensities, and Cloud Seeding \label{SIMC}} \section{Introduction} \section{Simultaneous Inference and Multiple Comparisons} \section{Analysis Using \R{}} \subsection{Genetic Components of Alcoholism} We start with a graphical display of the data. Three parallel boxplots shown in Figure~\ref{SIMC-alpha-data-figure} indicate increasing expression levels of alpha synuclein mRNA for longer \textit{NACP}-REP1 alleles. %%\setkeys{Gin}{width=0.6\textwidth} \begin{figure}[t] \begin{center} <>= n <- table(alpha$alength) levels(alpha$alength) <- abbreviate(levels(alpha$alength), 4) plot(elevel ~ alength, data = alpha, varwidth = TRUE, ylab = "Expression Level", xlab = "NACP-REP1 Allele Length") axis(3, at = 1:3, labels = paste("n = ", n)) @ \caption{Distribution of levels of expressed alpha synuclein mRNA in three groups defined by the \textit{NACP}-REP1 allele lengths. \label{SIMC-alpha-data-figure}} \end{center} \end{figure} \index{Tukey honest significant differences|(} In order to model this relationship, we start fitting a simple one-way ANOVA model of the form $y_{ij} = \mu + \gamma_i + \varepsilon_{ij}$ to the data with independent normal errors $\varepsilon_{ij} \sim \N(0, \sigma^2)$, $j \in \{\text{short}, \text{intermediate}, \text{long}\}$, and $i = 1, \dots, n_j$. The parameters $\mu + \gamma_\text{short}$, $\mu + \gamma_\text{intermediate}$ and $\mu + \gamma_\text{long}$ can be interpreted as the mean expression levels in the corresponding groups. As already discussed in \Sexpr{ch("ANOVA")}, this model description is overparameterized. A standard approach is to consider a suitable re-parameterization. The so-called ``treatment contrast'' vector $% \theta = (\mu, \gamma_\text{intermediate} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{short})$ (the default re-parameterization used as elemental parameters in \R{}) is one possibility and is equivalent to imposing the restriction $\gamma_\text{short} = 0$. In addition, we define all comparisons among our three groups by choosing $\K$ such that $\K \theta$ contains all three group differences (Tukey's all-pairwise comparisons): %%' \begin{eqnarray*} \K_\text{Tukey} = \left( \begin{array}{rrr} 0 & 1 & 0 \\%% 0 & 0 & 1 \\%% 0 & -1 & 1% \end{array} \right) \end{eqnarray*} with parameters of interest \begin{eqnarray*} \vartheta_\text{Tukey} = \K_\text{Tukey} \theta = (\gamma_\text{intermediate} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{intermediate}). \end{eqnarray*} The function \Rcmd{glht} (for generalized linear hypothesis) from package \Rpackage{multcomp} \citep{PKG:multcomp,HSAUR:HothornBretzWestfall2008} takes the fitted \Rclass{aov} object and a description of the matrix $\K$. Here, we use the \Rcmd{mcp} function to set up the matrix of all pairwise differences for the model parameters associated with factor \Robject{alength}: <>= library("multcomp") amod <- aov(elevel ~ alength, data = alpha) amod_glht <- glht(amod, linfct = mcp(alength = "Tukey")) @ The matrix $\K$ reads <>= amod_glht$linfct @ The \Robject{amod\_glht} object now contains information about the estimated linear function $\hat{\vartheta}$ and their covariance matrix which can be inspected via the \Rcmd{coef} and \Rcmd{vcov} methods: <>= coef(amod_glht) vcov(amod_glht) @ The \Rcmd{summary} and \Rcmd{confint} methods can be used to compute a summary statistic including adjusted $p$-values and simultaneous confidence intervals, respectively: <>= confint(amod_glht) summary(amod_glht) @ Because of the variance heterogeneity that can be observed in Figure~\ref{SIMC-alpha-data-figure}, one might be concerned with the validity of the above results stating that there is no difference between any combination of the three allele lengths. A sandwich estimator might be more appropriate in this situation, and the \Rarg{vcov} argument can be used to specify a function to compute some alternative covariance estimator as follows: <>= amod_glht_sw <- glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich) summary(amod_glht_sw) @ We use the \Rcmd{sandwich} function from package \Rpackage{sandwich} \citep{PKG:sandwich, HSAUR:Zeileis2006} which provides us with a heteroscedasticity-consistent estimator of the covariance matrix. This result is more in line with previously published findings for this study obtained from non-parametric test procedures such as the Kruskal-Wallis test. A comparison of the simultaneous confidence intervals calculated based on the ordinary and sandwich estimator is given in Figure~\ref{SIMC-alpha-confint-plot}. %%\setkeys{Gin}{width=0.95\textwidth} \begin{figure}[h] \begin{center} <>= par(mai = par("mai") * c(1, 2.1, 1, 0.5)) layout(matrix(1:2, ncol = 2)) ci1 <- confint(glht(amod, linfct = mcp(alength = "Tukey"))) ci2 <- confint(glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich)) ox <- expression(paste("Tukey (ordinary ", bold(S)[n], ")")) sx <- expression(paste("Tukey (sandwich ", bold(S)[n], ")")) plot(ci1, xlim = c(-0.6, 2.6), main = ox, xlab = "Difference", ylim = c(0.5, 3.5)) plot(ci2, xlim = c(-0.6, 2.6), main = sx, xlab = "Difference", ylim = c(0.5, 3.5)) @ \caption{Simultaneous confidence intervals for the \Robject{alpha} data based on the ordinary covariance matrix (left) and a sandwich estimator (right). \label{SIMC-alpha-confint-plot}} \end{center} \end{figure} It should be noted that this data set is heavily unbalanced; see Figure~\ref{SIMC-alpha-data-figure}, and therefore the results obtained from function \Rcmd{TukeyHSD} might be less accurate. \index{Tukey honest significant differences|)} \subsection{Deer Browsing} \index{Generalized linear mixed model|(} Since we have to take the spatial structure of the deer browsing data into account, we cannot simply use a logistic regression model as introduced in \Sexpr{ch("GLM")}. One possibility is to apply a mixed logistic regression model \citep[using package \Rpackage{lme4},][]{PKG:lme4} with random intercept accounting for the spatial variation of the trees. These models have already been discussed in \Sexpr{ch("ALDII")}. For each plot nested within a set of five plots oriented on a 100m transect (the location of the transect is determined by a predefined equally spaced lattice of the area under test), a random intercept is included in the model. Essentially, trees that are close to each other are handled like repeated measurements in a longitudinal analysis. We are interested in probability estimates and confidence intervals for each tree species. Each of the five fixed parameters of the model corresponds to one species (in absence of a global intercept term); therefore, $\K = \text{diag}(5)$ is the linear function we are interested in: <>= trees513 <- subset(trees513, !species %in% c("fir", "ash/maple/elm/lime", "softwood (other)")) trees513$species <- trees513$species[,drop = TRUE] levels(trees513$species)[nlevels(trees513$species)] <- "hardwood" @ <>= mmod <- glmer(damage ~ species - 1 + (1 | lattice / plot), data = trees513, family = binomial()) K <- diag(length(fixef(mmod))) K @ In order to help interpretation, the names of the tree species and the corresponding sample sizes (computed via \Rcmd{table}) are added to $\K$ as row names; this information will carry through all subsequent steps of our analysis: <>= colnames(K) <- rownames(K) <- paste(gsub("species", "", names(fixef(mmod))), " (", table(trees513$species), ")", sep = "") K @ Based on $\K$, we first compute simultaneous confidence intervals for $\K \theta$ and transform these into probabilities. Note that $\left(1 + \exp(- \hat{\vartheta})\right)^{-1}$ (cf.~Equation~\ref{GLM:logitexp}) is the vector of estimated probabilities; simultaneous confidence intervals can be transformed to the probability scale in the same way: <>= ci <- confint(glht(mmod, linfct = K)) ci$confint <- 1 - binomial()$linkinv(ci$confint) ci$confint[,2:3] <- ci$confint[,3:2] @ The result is shown in Figure~\ref{SIMC-trees-plot}. Browsing is more frequent in hardwood but especially small oak trees are severely at risk. Consequently, the local authorities increased the number of roe deers to be harvested in the following years. %%The large confidence interval for ash, maple, elm and lime %%trees is caused by the small sample size. %%\setkeys{Gin}{width=0.8\textwidth} \begin{figure}[t] \begin{center} <>= plot(ci, xlab = "Probability of Damage Caused by Browsing", xlim = c(0, 0.5), main = "", ylim = c(0.5, 5.5)) @ \caption{Probability of damage caused by roe deer browsing for five tree species. Sample sizes are given in brackets. \label{SIMC-trees-plot}} \end{center} \end{figure} \index{Generalized linear mixed model|)} \subsection{Cloud Seeding} \index{Confidence band|(} In \Sexpr{ch("MLR")} we studied the dependency of rainfall on S-Ne values by means of linear models. Because the number of observations is small, an additional assessment of the variability of the fitted regression lines is interesting. Here, we are interested in a confidence band around some estimated regression line, i.e., a confidence region which covers the true but unknown regression line with probability greater or equal $1 - \alpha$. It is straightforward to compute \stress{pointwise} confidence intervals but we have to make sure that the type I error is controlled for all $x$ values simultaneously. Consider the simple linear regression model \begin{eqnarray*} \text{rainfall}_i = \beta_0 + \beta_1 \text{sne}_i + \varepsilon_i \end{eqnarray*} where we are interested in a confidence band for the predicted rainfall, i.e., the values $\hat{\beta}_0 + \hat{\beta}_1 \text{sne}_i$ for some observations $\text{sne}_i$. (Note that the estimates $\hat{\beta}_0$ and $\hat{\beta}_1$ are random variables.) We can formulate the problem as a linear combination of the regression coefficients by multiplying a matrix $\K$ to a grid of S-Ne values (ranging from $1.5$ to $4.5$, say) from the left to the elemental parameters $\theta = (\beta_0, \beta_1)$: \begin{eqnarray*} \K \theta = \left( \begin{array}{rr} 1 & 1.50 \\%% 1 & 1.75 \\%% \vdots & \vdots \\%% 1 & 4.25 \\%% 1 & 4.50 % \end{array} \right)\theta = (\beta_0 + \beta_1 1.50, \beta_0 + \beta_1 1.75, \dots, \beta_0 + \beta_1 4.50) = \vartheta. \end{eqnarray*} Simultaneous confidence intervals for all the parameters of interest $\vartheta$ form a confidence band for the estimated regression line. We implement this idea for the \Robject{clouds} data writing a small reusable function as follows: <>= confband <- function(subset, main) { mod <- lm(rainfall ~ sne, data = clouds, subset = subset) sne_grid <- seq(from = 1.5, to = 4.5, by = 0.25) K <- cbind(1, sne_grid) sne_ci <- confint(glht(mod, linfct = K)) plot(rainfall ~ sne, data = clouds, subset = subset, xlab = "S-Ne criterion", main = main, xlim = range(clouds$sne), ylim = range(clouds$rainfall)) abline(mod) lines(sne_grid, sne_ci$confint[,2], lty = 2) lines(sne_grid, sne_ci$confint[,3], lty = 2) } @ The function \Rcmd{confband} basically fits a linear model using \Rcmd{lm} to a subset of the data, sets up the matrix $\K$ as shown above and nicely plots both the regression line and the confidence band. Now, this function can be reused to produce plots similar to Figure~\ref{MLR-clouds-lmplot} separately for days with and without cloud seeding in Figure~\ref{SIMC-clouds-lmplot}. For the days without seeding, there is more uncertainty about the true regression line compared to the days with cloud seeding. Clearly, this is caused by the larger variability of the observations in the left part of the figure. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) confband(clouds$seeding == "no", main = "No seeding") confband(clouds$seeding == "yes", main = "Seeding") @ \caption{Regression relationship between S-Ne criterion and rainfall with and without seeding. The confidence bands cover the area within the dashed curves. \label{SIMC-clouds-lmplot}} \end{center} \end{figure} \index{Confidence band|)} \section{Summary of Findings} \begin{description} \item[Genetic components of alcoholism] We were interested in studying all pairwise differences in expression levels for three groups of subjects defined by allele length. Overall, there seem to be different expression levels for short and long alleles but no difference between these two groups and the intermediate group. \item[Deer browsing] For a number of tree species, the simultaneous confidence intervals for the probability of browsing damage show that there is rather precise information about browsing damage for spruce and pine with more variability for the broad-leaf species. For oak, more than $\Sexpr{round(ci$confint["oak (1258)", 2], 2)}\%$ of the trees are damaged. \item[Cloud seeding] Confidence bands for the estimated effects help to identify days where the uncertainty about rainfall is largest. \end{description} \section{Final Comments} Multiple comparisons in linear models have been in use for a long time. The \Rpackage{multcomp} package extends much of the theory to a broad class of parametric and semi-parametric statistical models, which allows for a unified treatment of multiple comparisons and other simultaneous inference procedures in generalized linear models, mixed models, models for censored data, robust models, etc. Honest decisions based on simultaneous inference procedures maintaining a pre-specified familywise error rate (at least asymptotically) can be derived from almost all classical and modern statistical models. The technical details and more examples can be found in \cite{HSAUR:HothornBretzWestfall2008} and the package vignettes of package \Rpackage{multcomp} \citep{PKG:multcomp}. \section*{Exercises} \begin{description} \exercise Compare the results of \Rcmd{glht} and \Rcmd{TukeyHSD} on the \Robject{alpha} data. \exercise Consider the linear model fitted to the clouds data as summarized in Figure~\ref{MLR-clouds-summary}. Set up a matrix $\K$ corresponding to the global null hypothesis that all interaction terms present in the model are zero. Test both the global hypothesis and all hypotheses corresponding to each of the interaction terms. Which interaction remains significant after adjustment for multiple testing? \exercise For the logistic regression model presented in Figure~\ref{GLM-womensrole-summary-2} perform a multiplicity adjusted test on all regression coefficients (except for the intercept) being zero. Do the conclusions drawn in \Sexpr{ch("GLM")} remain valid? \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/tables/0000755000175000017500000000000012451513136014634 5ustar nileshnileshHSAUR3/vignettes/tables/MLR-Xtab.tex0000644000175000017500000000047314133304452016706 0ustar nileshnilesh\begin{eqnarray*} \X = \left( \begin{array}{ccccc} 1 & x_{11} & x_{12} & \dots & x_{1q} \\ 1 & x_{21} & x_{22} & \dots & x_{2q} \\ \vdots & \vdots & \vdots & \ddots & \vdots \\ 1 & x_{n1} & x_{n2} & \dots & x_{nq} \\ \end{array} \right). \end{eqnarray*} HSAUR3/vignettes/tables/PCA_tab.tex0000644000175000017500000000056014133304452016606 0ustar nileshnilesh \begin{center} \begin{longtable}{cccccc} \caption{Correlations for calculus measurements for the six anterior mandibular teeth.} \\ \hline 1.00 & & & & & \\ 0.54 & 1.00 & & & & \\ 0.34 & 0.65 & 1.00 & & & \\ 0.37 & 0.65 & 0.84 & 1.00 & & \\ 0.36 & 0.59 & 0.67 & 0.80 & 1.00 & \\ 0.62 & 0.49 & 0.43 & 0.42 & 0.55 & 1.00 \\ \hline \end{longtable} \end{center} HSAUR3/vignettes/tables/CA_perm.tex0000644000175000017500000000057614133304452016672 0ustar nileshnilesh \begin{center} \begin{longtable}{rrl} \caption{Number of possible partitions depending on the sample size $n$ and number of clusters $k$. \label{CA:perm}} \\ $n$ & $k$ & Number of possible partitions \\ \hline $15$ & $3$ & $2,375,101$ \\ $20$ & $4$ & $45,232,115,901$ \\ $25$ & $8$ & $690,223,721,118,368,580$ \\ $100$ & $5$ & $10^{68}$ \\ \end{longtable} \end{center} HSAUR3/vignettes/tables/CI_rtimesc.tex0000644000175000017500000000123414133304452017375 0ustar nileshnilesh \begin{center} \begin{longtable}{cc|ccc|c} \caption{The general $r \times c$ table. \label{SI:rtimesc}} \\ & & & $y$ & & \\\ & & $1$ & $\dots$ & $c$ & \\ \hline & $1$ & $n_{11}$ & $\dots$ & $n_{1c}$ & $n_{1 \cdot}$ \\\ & $2$ & $n_{21}$ & $\dots$ & $n_{2c}$ & $n_{2 \cdot}$ \\\ $x$ & $\vdots$ & $\vdots$ & $\dots$ & $\vdots$ & $\vdots$ \\\ & $r$ & $n_{r1}$ & $\dots$ & $n_{rc}$ & $n_{r \cdot}$ \\ \hline & & $n_{\cdot 1}$ & $\dots$ & $n_{\cdot c}$ & $n$ \\\ \end{longtable} \end{center}HSAUR3/vignettes/tables/rec.tex0000644000175000017500000000120014133304534016117 0ustar nileshnilesh\begin{tabular}{llll} \Rpackage{KernSmooth} & \Rpackage{Matrix} & \Rpackage{boot} & \Rpackage{lattice}\\ \Rpackage{survival} & \Rpackage{MASS} & \Rpackage{base} & \Rpackage{class}\\ \Rpackage{cluster} & \Rpackage{codetools} & \Rpackage{compiler} & \Rpackage{datasets}\\ \Rpackage{foreign} & \Rpackage{grDevices} & \Rpackage{graphics} & \Rpackage{grid}\\ \Rpackage{methods} & \Rpackage{mgcv} & \Rpackage{nlme} & \Rpackage{nnet}\\ \Rpackage{parallel} & \Rpackage{rpart} & \Rpackage{spatial} & \Rpackage{splines}\\ \Rpackage{stats} & \Rpackage{stats4} & \Rpackage{tcltk} & \Rpackage{tools}\\ \Rpackage{utils} & & & \\ \end{tabular} HSAUR3/vignettes/tables/SI_rtimesc.tex0000644000175000017500000000123414133304452017415 0ustar nileshnilesh \begin{center} \begin{longtable}{cc|ccc|c} \caption{The general $r \times c$ table. \label{SI:rtimesc}} \\ & & & $y$ & & \\\ & & $1$ & $\dots$ & $c$ & \\ \hline & $1$ & $n_{11}$ & $\dots$ & $n_{1c}$ & $n_{1 \cdot}$ \\\ & $2$ & $n_{21}$ & $\dots$ & $n_{2c}$ & $n_{2 \cdot}$ \\\ $x$ & $\vdots$ & $\vdots$ & $\dots$ & $\vdots$ & $\vdots$ \\\ & $r$ & $n_{r1}$ & $\dots$ & $n_{rc}$ & $n_{r \cdot}$ \\ \hline & & $n_{\cdot 1}$ & $\dots$ & $n_{\cdot c}$ & $n$ \\\ \end{longtable} \end{center}HSAUR3/vignettes/tables/SI_mcnemar.tex0000644000175000017500000000042014133304452017365 0ustar nileshnilesh \begin{center} \begin{longtable}{cccc} \caption{Frequencies in matched samples data. \label{SI:mcnemartab}} \\ & & \multicolumn{2}{c}{Sample 1} \\ & & present & absent \\ Sample 2 & present & $a$ & $b$ \\ & absent & $c$ & $d$ \\ \end{longtable} \end{center} HSAUR3/vignettes/tables/Lanza.tex0000644000175000017500000000064714133304452016430 0ustar nileshnilesh \begin{center} \begin{longtable}{ll} \caption{Classification system for the response variable. \label{CI:scores}} \\ Classification & Endoscopy Examination \\ \hline 1 & No visible lesions \\ 2 & One haemorrhage or erosion \\ 3 & 2-10 haemorrhages or erosions \\ 4 & 11-25 haemorrhages or erosions \\ 5 & More than 25 haemorrhages or erosions \\ & or an invasive ulcer of any size\\ \hline \end{longtable} \end{center} HSAUR3/vignettes/tables/MA_table.tex0000644000175000017500000000031014133304452017012 0ustar nileshnilesh \begin{center} \begin{longtable}{cccc} & & \multicolumn{2}{c}{response} \\ & & success & failure \\ group & control & $a$ & $b$ \\ & treatment & $c$ & $d$ \\ \end{longtable} \end{center} HSAUR3/vignettes/tables/MLR-ANOVA-tab.tex0000644000175000017500000000067714133304452017426 0ustar nileshnilesh \begin{center} \begin{longtable}{lccc} \caption{Analysis of variance table for the multiple linear regression model. \label{MLR-ANOVA-tab}} \\ Source of variation & Sum of squares & Degrees of freedom \\ \hline Regression & $\sum\limits_{i = 1}^n (\hat{y}_i - \bar{y})^2$ & $q$ \\ Residual & $\sum\limits_{i = 1}^n (\hat{y}_i - y_i)^2$ & $n - q - 1$ \\ Total & $\sum\limits_{i = 1}^n (y_i - \bar{y})^2$ & $n - 1$ \\ \end{longtable} \end{center} HSAUR3/vignettes/tables/exMDS.tex0000644000175000017500000000044314133304452016335 0ustar nileshnilesh\begin{eqnarray*} s_{ij} = \left\{ \begin{array}{lcl} 9 & \text{if} & i = j \\ 8 & \text{if} & 1 \le | i - j | \le 3 \\ 7 & \text{if} & 4 \le | i - j | \le 6 \\ & \cdots & \\ 1 & \text{if} & 22 \le | i - j | \le 24 \\ 0 & \text{if} & | i - j | \ge 25 \\ \end{array} \right. \end{eqnarray*} HSAUR3/vignettes/tables/PCA_tab1.tex0000644000175000017500000000043112357775400016677 0ustar nileshnilesh\begin{table} \begin{center} \begin{tabular}{cccccc} 1.00 & & & & & \\\ 0.54 & 1.00 & & & & \\\ 0.34 & 0.65 & 1.00 & & & \\\ 0.37 & 0.65 & 0.84 & 1.00 & & \\\ 0.36 & 0.59 & 0.67 & 0.80 & 1.00 & \\\ 0.62 & 0.49 & 0.43 & 0.42 & 0.55 & 1.00 \\\ \end{tabular} \end{center} \end{table} HSAUR3/vignettes/Ch_density_estimation.Rnw0000644000175000017500000004716314133304452020410 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Density Estimation} %%\VignetteDepends{flexmix,KernSmooth,boot} \setcounter{chapter}{7} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} <>= x <- library("KernSmooth") x <- library("flexmix") x <- library("boot") @ \chapter[Density Estimation]{Density Estimation: Erupting Geysers and Star Clusters \label{DE}} \section{Introduction} \section{Density Estimation} The three kernel functions are implemented in \R{} as shown in lines 1--3 of Figure~\ref{DE-kernel-fig}. For some grid \Robject{x}, the kernel functions are plotted using the \R{} statements in lines 5--11 (Figure~\ref{DE-kernel-fig}). \numberSinput \begin{figure} \begin{center} <>= rec <- function(x) (abs(x) < 1) * 0.5 tri <- function(x) (abs(x) < 1) * (1 - abs(x)) gauss <- function(x) 1/sqrt(2*pi) * exp(-(x^2)/2) x <- seq(from = -3, to = 3, by = 0.001) plot(x, rec(x), type = "l", ylim = c(0,1), lty = 1, ylab = expression(K(x))) lines(x, tri(x), lty = 2) lines(x, gauss(x), lty = 3) legend(-3, 0.8, legend = c("Rectangular", "Triangular", "Gaussian"), lty = 1:3, title = "kernel functions", bty = "n") @ \caption{Three commonly used kernel functions. \label{DE-kernel-fig}} \end{center} \end{figure} \rawSinput <>= w <- options("width")$w options(width = 66) @ The kernel estimator $\hat{f}$ is a sum of `bumps' placed at the observations. %' The kernel function determines the shape of the bumps while the window width $h$ determines their width. \index{Windows, in kernel density estimation} Figure~\ref{DE-bumps} \citep[redrawn from a similar plot in][]{HSAUR:Silverman1986} shows the individual bumps $n^{-1}h^{-1} K((x - x_i) / h)$, as well as the estimate $\hat{f}$ obtained by adding them up for an artificial set of data points <>= x <- c(0, 1, 1.1, 1.5, 1.9, 2.8, 2.9, 3.5) n <- length(x) @ For a grid <>= xgrid <- seq(from = min(x) - 1, to = max(x) + 1, by = 0.01) @ on the real line, we can compute the contribution of each measurement in \Robject{x}, with $h = 0.4$, by the Gaussian kernel (defined in Figure~\ref{DE-kernel-fig}, line 3) as follows; <>= h <- 0.4 bumps <- sapply(x, function(a) gauss((xgrid - a)/h)/(n * h)) @ A plot of the individual bumps and their sum, the kernel density estimate $\hat{f}$, is shown in Figure~\ref{DE-bumps}. <>= options(width = w) @ \numberSinput \begin{figure} \begin{center} <>= plot(xgrid, rowSums(bumps), ylab = expression(hat(f)(x)), type = "l", xlab = "x", lwd = 2) rug(x, lwd = 2) out <- apply(bumps, 2, function(b) lines(xgrid, b)) @ \caption{Kernel estimate showing the contributions of Gaussian kernels evaluated for the individual observations with bandwidth $h = 0.4$. \label{DE-bumps}} \end{center} \end{figure} \rawSinput \begin{figure} \begin{center} <>= epa <- function(x, y) ((x^2 + y^2) < 1) * 2/pi * (1 - x^2 - y^2) x <- seq(from = -1.1, to = 1.1, by = 0.05) epavals <- sapply(x, function(a) epa(a, x)) persp(x = x, y = x, z = epavals, xlab = "x", ylab = "y", zlab = expression(K(x, y)), theta = -35, axes = TRUE, box = TRUE) @ \caption{Epanechnikov kernel for a grid between $(-1.1, -1.1)$ and $(1.1, 1.1)$. \label{DE-epakernel-fig}} \end{center} \end{figure} \section{Analysis Using \R{}} \numberSinput \begin{figure} \begin{center} <>= data("faithful", package = "datasets") x <- faithful$waiting layout(matrix(1:3, ncol = 3)) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Gaussian kernel", border = "gray") lines(density(x, width = 12), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Rectangular kernel", border = "gray") lines(density(x, width = 12, window = "rectangular"), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Triangular kernel", border = "gray") lines(density(x, width = 12, window = "triangular"), lwd = 2) rug(x) @ \caption{Density estimates of the geyser eruption data imposed on a histogram of the data. \label{DE:faithfuldens}} \end{center} \end{figure} \rawSinput \begin{figure} \begin{center} <>= library("KernSmooth") data("CYGOB1", package = "HSAUR3") CYGOB1d <- bkde2D(CYGOB1, bandwidth = sapply(CYGOB1, dpik)) contour(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity") @ \caption{A contour plot of the bivariate density estimate of the \Robject{CYGOB1} data, i.e., a two-dimensional graphical display for a three-dimensional problem. \label{DE:CYGOB12Dcontour}} \end{center} \end{figure} \begin{figure} \begin{center} <>= persp(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity", zlab = "estimated density", theta = -35, axes = TRUE, box = TRUE) @ \caption{The bivariate density estimate of the \Robject{CYGOB1} data, here shown in a three-dimensional fashion using the \Rcmd{persp} function. \label{DE:CYGOB12Dpersp}} \end{center} \end{figure} \subsection{A Parametric Density Estimate for the Old Faithful Data \label{DE-waiting}} <>= logL <- function(param, x) { d1 <- dnorm(x, mean = param[2], sd = param[3]) d2 <- dnorm(x, mean = param[4], sd = param[5]) -sum(log(param[1] * d1 + (1 - param[1]) * d2)) } startparam <- c(p = 0.5, mu1 = 50, sd1 = 3, mu2 = 80, sd2 = 3) opp <- optim(startparam, logL, x = faithful$waiting, method = "L-BFGS-B", lower = c(0.01, rep(1, 4)), upper = c(0.99, rep(200, 4))) @ \newpage <>= opp @ <>= print(opp[names(opp) != "message"]) @ Of course, optimizing the appropriate likelihood `by hand' %' is not very convenient. In fact, (at least) two packages offer high-level functionality for estimating mixture models. The first one is package \Rpackage{mclust} \citep{PKG:mclust} implementing the methodology described in \cite{HSAUR:FraleyRaftery2002}. Here, a Bayesian information criterion (BIC) is applied to choose the form of the mixture model: \index{Bayesian Information Criterion (BIC)} <>= library("mclust") @ <>= library("mclust") mc <- Mclust(faithful$waiting) mc @ and the estimated means are <>= mc$parameters$mean @ with estimated standard deviation (found to be equal within both groups) <>= sqrt(mc$parameters$variance$sigmasq) @ The proportion is $\hat{p} = \Sexpr{round(mc$parameters$pro[1], 2)}$. The second package is called \Rpackage{flexmix} whose functionality is described by \cite{HSAUR:Leisch2004}. A mixture of two normals can be fitted using <>= library("flexmix") fl <- flexmix(waiting ~ 1, data = faithful, k = 2) @ with $\hat{p} = \Sexpr{round(fl@prior, 2)}$ and estimated parameters <>= parameters(fl, component = 1) parameters(fl, component = 2) @ \begin{figure} \begin{center} <>= opar <- as.list(opp$par) rx <- seq(from = 40, to = 110, by = 0.1) d1 <- dnorm(rx, mean = opar$mu1, sd = opar$sd1) d2 <- dnorm(rx, mean = opar$mu2, sd = opar$sd2) f <- opar$p * d1 + (1 - opar$p) * d2 hist(x, probability = TRUE, xlab = "Waiting times (in min.)", border = "gray", xlim = range(rx), ylim = c(0, 0.06), main = "") lines(rx, f, lwd = 2) lines(rx, dnorm(rx, mean = mean(x), sd = sd(x)), lty = 2, lwd = 2) legend(50, 0.06, lty = 1:2, bty = "n", legend = c("Fitted two-component mixture density", "Fitted single normal density")) @ \caption{Fitted normal density and two-component normal mixture for geyser eruption data. \label{DE:2Dplot}} \end{center} \end{figure} \index{Bootstrap approach|(} We can get standard errors for the five parameter estimates by using a bootstrap approach \citep[see][]{HSAUR:EfronTibshirani1993}. The original data are slightly perturbed by drawing $n$ out of $n$ observations \stress{with replacement} and those artificial replications of the original data are called \stress{bootstrap samples}. Now, we can fit the mixture for each bootstrap sample and assess the variability of the estimates, for example using confidence intervals. \index{Confidence interval!derived from bootstrap samples} Some suitable \R{} code based on the \Rcmd{Mclust} function follows. First, we define a function that, for a bootstrap sample \Robject{indx}, fits a two-component mixture model and returns $\hat{p}$ and the estimated means (note that we need to make sure that we always get an estimate of $p$, not $1 - p$): <>= library("boot") fit <- function(x, indx) { a <- Mclust(x[indx], minG = 2, maxG = 2, modelNames="E")$parameters if (a$pro[1] < 0.5) return(c(p = a$pro[1], mu1 = a$mean[1], mu2 = a$mean[2])) return(c(p = 1 - a$pro[1], mu1 = a$mean[2], mu2 = a$mean[1])) } @ The function \Rcmd{fit} can now be fed into the \Rcmd{boot} function \citep{PKG:boot} for bootstrapping (here $1000$ bootstrap samples are drawn) \begin{Schunk} \begin{Sinput} R> bootpara <- boot(faithful$waiting, fit, R = 1000) \end{Sinput} \end{Schunk} <>= bootparafile <- system.file("cache", "DE-bootpara.rda", package = "HSAUR3") if (file.exists(bootparafile)) { load(bootparafile) } else { bootpara <- boot(faithful$waiting, fit, R = 1000) } @ We assess the variability of our estimates $\hat{p}$ by means of adjusted bootstrap percentile (BCa) confidence intervals, which for $\hat{p}$ can be obtained from <>= boot.ci(bootpara, type = "bca", index = 1) @ We see that there is a reasonable variability in the mixture model; however, the means in the two components are rather stable, as can be seen from <>= boot.ci(bootpara, type = "bca", index = 2) @ for $\hat{\mu}_1$ and for $\hat{\mu}_2$ from <>= boot.ci(bootpara, type = "bca", index = 3) @ Finally, we show a graphical representation of both the bootstrap distribution of the mean estimates \stress{and} the corresponding confidence intervals. For convenience, we define a function for plotting, namely <>= bootplot <- function(b, index, main = "") { dens <- density(b$t[,index]) ci <- boot.ci(b, type = "bca", index = index)$bca[4:5] est <- b$t0[index] plot(dens, main = main) y <- max(dens$y) / 10 segments(ci[1], y, ci[2], y, lty = 2) points(ci[1], y, pch = "(") points(ci[2], y, pch = ")") points(est, y, pch = 19) } @ The element \Robject{t} of an object created by \Rcmd{boot} contains the bootstrap replications of our estimates, i.e., the values computed by \Rcmd{fit} for each of the $1000$ bootstrap samples of the geyser data. First, we plot a simple density estimate and then construct a line representing the confidence interval. We apply this function to the bootstrap distributions of our estimates $\hat{\mu}_1$ and $\hat{\mu}_2$ in Figure~\ref{DE-bootplot}. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) bootplot(bootpara, 2, main = expression(mu[1])) bootplot(bootpara, 3, main = expression(mu[2])) @ \caption{Bootstrap distribution and confidence intervals for the mean estimates of a two-component mixture for the geyser data. \label{DE-bootplot}} \end{center} \end{figure} \index{Bootstrap approach|)} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_simple_inference.Rnw0000644000175000017500000005240414133304452017776 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Simple Inference} %%\VignetteDepends{vcd} \setcounter{chapter}{2} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Simple Inference]{Simple Inference: Guessing Lengths, Wave Energy, Water Hardness, Piston Rings, and Rearrests of Juveniles \label{SI}} \section{Introduction} <>= library("vcd") if (!interactive()) { print.htest <- function (x, digits = 4, quote = TRUE, prefix = "", ...) { cat("\n") cat(strwrap(x$method, prefix = "\t"), sep = "\n") cat("\n") cat("data: ", x$data.name, "\n") out <- character() if (!is.null(x$statistic)) out <- c(out, paste(names(x$statistic), "=", format(round(x$statistic, 4)))) if (!is.null(x$parameter)) out <- c(out, paste(names(x$parameter), "=", format(round(x$parameter, 3)))) if (!is.null(x$p.value)) { fp <- format.pval(x$p.value, digits = digits) out <- c(out, paste("p-value", if (substr(fp, 1, 1) == "<") fp else paste("=", fp))) } cat(strwrap(paste(out, collapse = ", ")), sep = "\n") if (!is.null(x$conf.int)) { cat(format(100 * attr(x$conf.int, "conf.level")), "percent confidence interval:\n", format(c(x$conf.int[1], x$conf.int[2])), "\n") } if (!is.null(x$estimate)) { cat("sample estimates:\n") print(x$estimate, ...) } cat("\n") invisible(x) } } @ \section{Statistical Tests} \section{Analysis Using \R{}} \subsection{Estimating the Width of a Room} The data shown in Table~\ref{SI-rw-tab} are available as \Robject{roomwidth} \Rclass{data.frame} from the \Rpackage{HSAUR3} package and can be attached by using <>= data("roomwidth", package = "HSAUR3") @ If we convert the estimates of the room width in meters into feet by multiplying each by $3.28$ then we would like to test the hypothesis that the mean of the population of `metre' estimates is equal to the mean %' of the population of `feet' estimates. We shall do this first %' by using an independent samples $t$-test, but first it is good practice to check, informally at least, the normality and equal variance assumptions. Here we can use a combination of numerical and graphical approaches. The first step should be to convert the meter estimates into feet by a factor <>= convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) @ which equals one for all feet measurements and $3.28$ for the measurements in meters. Now, we get the usual summary statistics and standard deviations of each set of estimates using <>= tapply(roomwidth$width * convert, roomwidth$unit, summary) tapply(roomwidth$width * convert, roomwidth$unit, sd) @ where \Rcmd{tapply} applies \Rcmd{summary}, or \Rcmd{sd}, to the converted widths for both groups of measurements given by \Robject{roomwidth\$unit}. A boxplot of each set of estimates might be useful and is depicted in Figure~\ref{SI-rw-bxp}. The \Rcmd{layout} function (line 1 in Figure~\ref{SI-rw-bxp}) divides the plotting area into three parts. The \Rcmd{boxplot} function produces a boxplot in the upper part and the two \Rcmd{qqnorm} statements in lines 7 and 10 set up the normal probability plots that can be used to assess the normality assumption of the $t$-test. \index{Normal probability plot} \numberSinput \begin{figure} \begin{center} <>= layout(matrix(c(1,2,1,3), nrow = 2, ncol = 2, byrow = FALSE)) boxplot(I(width * convert) ~ unit, data = roomwidth, ylab = "Estimated width (feet)", varwidth = TRUE, names = c("Estimates in feet", "Estimates in meters (converted to feet)")) feet <- roomwidth$unit == "feet" qqnorm(roomwidth$width[feet], ylab = "Estimated width (feet)") qqline(roomwidth$width[feet]) qqnorm(roomwidth$width[!feet], ylab = "Estimated width (meters)") qqline(roomwidth$width[!feet]) @ \caption{Boxplots of estimates of room width in feet and meters (after conversion to feet) and normal probability plots of estimates of room width made in feet and in meters. \label{SI-rw-bxp}} \end{center} \end{figure} \rawSinput The boxplots indicate that both sets of estimates contain a number of outliers and also that the estimates made in meters are skewed and more variable than those made in feet, a point underlined by the numerical summary statistics above. Both normal probability plots depart from linearity, suggesting that the distributions of both sets of estimates are not normal. The presence of outliers, the apparently different variances and the evidence of non-normality all suggest caution in applying the $t$-test, but for the moment we shall apply the usual version of the test using the \Rcmd{t.test} function in \R{}. The two-sample test problem is specified by a \Rclass{formula}, here by <>= I(width * convert) ~ unit @ where the response, \Robject{width}, on the left-hand side needs to be converted first and, because the star has a special meaning in formulae as will be explained in \Sexpr{ch("ANOVA")}, the conversion needs to be embedded by \texttt{I}. The factor \Robject{unit} on the right-hand side specifies the two groups to be compared. <>= tt <- t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) @ \renewcommand{\nextcaption}{\R{} output of the independent samples $t$-test for the \Robject{roomwidth} data. \label{SI-roomwidth-tt-fig}} \SchunkLabel <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the independent samples Welch test for the \Robject{roomwidth} data. \label{SI-roomwidth-welch-fig}} \SchunkLabel <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = FALSE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the Wilcoxon rank sum test for the \Robject{roomwidth} data. \label{SI-roomwidth-wilcox-fig}} \SchunkLabel <>= wilcox.test(I(width * convert) ~ unit, data = roomwidth, conf.int = TRUE) @ \SchunkRaw <>= pwt <- round(wilcox.test(I(width * convert) ~ unit, data = roomwidth)$p.value, 3) @ \subsection{Wave Energy Device Mooring} The data from Table~\ref{SI-m-tab} are available as \Rclass{data.frame} \Robject{waves} <>= data("waves", package = "HSAUR3") @ and requires the use of a matched pairs $t$-test to answer the question of interest. This test assumes that the differences between the matched observations have a normal distribution so we can begin by checking this assumption by constructing a boxplot and a normal probability plot -- see Figure~\ref{SI-w-bxp}. \begin{figure} \begin{center} <>= mooringdiff <- waves$method1 - waves$method2 layout(matrix(1:2, ncol = 2)) boxplot(mooringdiff, ylab = "Differences (Newton meters)", main = "Boxplot") abline(h = 0, lty = 2) qqnorm(mooringdiff, ylab = "Differences (Newton meters)") qqline(mooringdiff) @ \caption{Boxplot and normal probability plot for differences between the two mooring methods. \label{SI-w-bxp}} \end{center} \end{figure} \renewcommand{\nextcaption}{\R{} output of the paired $t$-test for the \Robject{waves} data. \label{SI-waves-tt-fig}} \SchunkLabel <>= t.test(mooringdiff) @ \SchunkRaw <>= pwt <- round(wilcox.test(mooringdiff)$p.value, 3) @ \renewcommand{\nextcaption}{\R{} output of the Wilcoxon signed rank test for the \Robject{waves} data. \label{SI-waves-ws-fig}} \SchunkLabel <>= wilcox.test(mooringdiff) @ \SchunkRaw \subsection{Mortality and Water Hardness} There is a wide range of analyses we could apply to the data in Table~\ref{SI-w-tab} available from <>= data("water", package = "HSAUR3") @ But to begin we will construct a scatterplot of the data enhanced somewhat by the addition of information about the marginal distributions of water hardness (calcium concentration) and mortality, and by adding the estimated linear regression fit (see \Sexpr{ch("MLR")}) for mortality on hardness. The plot and the required \R{} code are given along with Figure~\ref{SI-water-sp}. In line 1 of Figure~\ref{SI-water-sp}, we divide the plotting region into four areas of different size. The scatterplot (line 3) uses a plotting symbol depending on the location of the city (by the \Rarg{pch} argument); a legend for the location is added in line 6. We add a least squares fit (see \Sexpr{ch("MLR")}) to the scatterplot and, finally, depict the marginal distributions by means of a boxplot and a histogram. The scatterplot shows that as hardness increases mortality decreases, and the histogram for the water hardness shows it has a rather skewed distribution. \numberSinput \begin{figure} \begin{center} <>= nf <- layout(matrix(c(2, 0, 1, 3), 2, 2, byrow = TRUE), c(2, 1), c(1, 2), TRUE) psymb <- as.numeric(water$location) plot(mortality ~ hardness, data = water, pch = psymb) abline(lm(mortality ~ hardness, data = water)) legend("topright", legend = levels(water$location), pch = c(1,2), bty = "n") hist(water$hardness) boxplot(water$mortality) @ \caption{Enhanced scatterplot of water hardness and mortality, showing both the joint and the marginal distributions and, in addition, the location of the city by different plotting symbols. \label{SI-water-sp}} \end{center} \end{figure} \rawSinput \renewcommand{\nextcaption}{\R{} output of Pearsons' correlation coefficient %' for the \Robject{water} data. \label{SI-water-c-fig}} \SchunkLabel <>= cor.test(~ mortality + hardness, data = water) @ \SchunkRaw <>= cr <- round(cor.test(~ mortality + hardness, data = water)$estimate, 3) @ \subsection{Piston-ring Failures} <>= chisqt <- chisq.test(pistonrings) @ \renewcommand{\nextcaption}{\R{} output of the chi-squared test for the \Robject{pistonrings} data. \label{SI-pr-x2-fig}} \SchunkLabel <>= data("pistonrings", package = "HSAUR3") chisq.test(pistonrings) @ \SchunkRaw Rather than looking at the simple differences of observed and expected values for each cell which would be unsatisfactory since a difference of fixed size is clearly more important for smaller samples, it is preferable to consider a \stress{standardized residual} \index{Standardized residual, for chi-squared tests} given by dividing the observed minus the expected difference by the square root of the appropriate expected value. The $X^2$ statistic for assessing independence is simply the sum, over all the cells in the table, of the squares of these terms. We can find these values extracting the \Robject{residuals} element of the object returned by the \Rcmd{chisq.test} function <>= chisq.test(pistonrings)$residuals @ A graphical representation of these residuals is called an \stress{association plot} \index{Association plot} and is available via the \Rcmd{assoc} function from package \Rpackage{vcd} \citep{PKG:vcd} applied to the contingency table of the two categorical variables. Figure~\ref{SI-assoc-plot} depicts the residuals for the piston ring data. The deviations from independence are largest for C1 and C4 compressors in the center and south leg. \begin{figure} \begin{center} <>= library("vcd") assoc(pistonrings) @ \caption{Association plot of the residuals for the \Robject{pistonrings} data. \label{SI-assoc-plot}} \end{center} \end{figure} \subsection{Rearrests of Juveniles} The data in Table~\ref{SI-r-tab} are available as \Rclass{table} object via <>= data("rearrests", package = "HSAUR3") rearrests @ <>= mcs <- round(mcnemar.test(rearrests, correct = FALSE)$statistic, 2) @ and in \Robject{rearrests} the counts in the four cells refer to the matched pairs of subjects; for example, in $\Sexpr{rearrests[1,1]}$ pairs both members of the pair were rearrested. Here we need to use McNemar's %' test to assess whether rearrest is associated with the type of court where the juvenile was tried. We can use the \R{} function \Rcmd{mcnemar.test}. The test statistic shown in Figure~\ref{SI-ra-mc-fig} is $\Sexpr{mcs}$ with a single degree of freedom -- the associated $p$-value is extremely small and there is strong evidence that type of court and the probability of rearrest are related. It appears that trial at a juvenile court is less likely to result in rearrest (see Exercise~3.4). % An exact version of McNemar's test %%' can be obtained by testing whether $b$ and $c$ are equal using a binomial test (see Figure~\ref{SI-ra-mcbin-fig}). \renewcommand{\nextcaption}{\R{} output of McNemar's test %' for the \Robject{rearrests} data. \label{SI-ra-mc-fig}} \SchunkLabel <>= mcnemar.test(rearrests, correct = FALSE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of an exact version of McNemar's test %' for the \Robject{rearrests} data computed via a binomial test. \label{SI-ra-mcbin-fig}} \SchunkLabel <>= binom.test(rearrests[2], n = sum(rearrests[c(2,3)])) @ \SchunkRaw \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/chapman.cls0000644000175000017500000007263312357775400015520 0ustar nileshnilesh% CHAPMAN.STY % v0.17 --- released 6th April 1993 % v0.16 --- released 11th November 1991 % v0.15 --- released 8th November 1991 % v0.14 --- first release 3rd November 1991 % % A LaTeX style file for Chapman and Hall books % Copyright 1993 Cambridge University Press %Modified Sept 1995 to work under Latex 2e % % based on the BOOK DOCUMENT STYLE -- Released 26 April 88 % for LaTeX version 2.09 % Copyright (C) 1988 by Leslie Lamport % \typeout{Document Style `chapman' v0.17 <6th April 1993>} % % Books use two-sided printing. % %\usepackage{times,mathtime}%for latex 2e user to use mathtimes font \@twosidetrue \@mparswitchtrue % % draft option % \def\ds@draft{\overfullrule 5pt} \@options % **************************************** % * FONTS * % **************************************** % \lineskip 1pt \normallineskip 1pt \def\baselinestretch{1} \def\normalsize{\@setsize\normalsize{12pt}\xpt\@xpt \abovedisplayskip 6pt plus 1pt minus 1pt% \belowdisplayskip \abovedisplayskip \abovedisplayshortskip \z@ plus3pt% \belowdisplayshortskip 3.25pt plus 1pt minus 1pt% \let\@listi\@listI} 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\normalsize % **************************************** % * PAGE LAYOUT * % **************************************** % % All margin dimensions measured from a point one inch from top and side % of page. % % SIDE MARGINS: % \oddsidemargin 6pc %5pc \evensidemargin 5.7pc %5pc \marginparwidth 4pc \marginparsep 1pc \topmargin 12pt %0pt \headheight 12pt \headsep 8pt \footskip 2pc % % DIMENSION OF TEXT: % \textheight = 45\baselineskip %\advance\textheight by \topskip \addtolength\textheight{3pt} \textwidth 28pc \addtolength\textwidth{.5pt} % \textheight = 43\baselineskip % %\advance\textheight by \topskip %\addtolength\textheight{3pt} % \textwidth 26pc %\addtolength\textwidth{.5pt} \columnsep 1pc \columnseprule 0pt % % FOOTNOTES % \footnotesep 6.65pt \skip\footins 12pt plus 3pt minus 1.5pt % % FLOATS % % FOR FLOATS ON A TEXT PAGE: % ONE-COLUMN MODE OR SINGLE-COLUMN FLOATS IN TWO-COLUMN MODE: \floatsep 12pt plus 2pt minus 2pt \textfloatsep 18pt plus 2pt minus 4pt \intextsep 12pt plus 2pt minus 2pt % TWO-COLUMN FLOATS IN TWO-COLUMN MODE: \dblfloatsep 12pt plus 2pt minus 2pt \dbltextfloatsep 18pt plus 2pt minus 4pt % % FOR FLOATS ON A SEPARATE FLOAT PAGE OR COLUMN: % ONE-COLUMN MODE OR SINGLE-COLUMN FLOATS IN TWO-COLUMN MODE: \@fptop 0pt plus 0fil \@fpsep 12pt plus 0fil \@fpbot 0pt plus 3fil % % DOUBLE-COLUMN FLOATS IN TWO-COLUMN MODE. \@dblfptop 0pt plus 0fil \@dblfpsep 12pt plus 0fil \@dblfpbot 0pt plus 3fil % % MARGINAL NOTES: % \marginparpush 5pt % **************************************** % * PARAGRAPHING * % **************************************** % \parskip 0pt plus .25pt \parindent 1em \partopsep 2pt plus 1pt minus 1pt % % The following page-breaking penalties are defined % \@lowpenalty 51 \@medpenalty 151 \@highpenalty 301 \@beginparpenalty -\@lowpenalty \@endparpenalty -\@lowpenalty \@itempenalty -\@lowpenalty % \clubpenalty=0 % 'Club line' at bottom of page. \widowpenalty=10000 % 'Widow line' at top of page. % \displaywidowpenalty % Math display widow line. % \predisplaypenalty % Breaking before a math display. % \postdisplaypenalty % Breaking after a math display. % \interlinepenalty % Breaking at a line within a paragraph. % \brokenpenalty % Breaking after a hyphenated line. % \def\thin@rule{{\parindent0pt\par\rule{\textwidth}{0.5pt}\par}} \def\thick@rule{{\parindent0pt\par\rule{\textwidth}{1pt}\par}} % **************************************** % * CHAPTERS AND SECTIONS * % **************************************** % % DEFINE COUNTERS: % \newcounter{part} \newcounter{chapter} \newcounter{section}[chapter] \newcounter{subsection}[section] \newcounter{subsubsection}[subsection] \newcounter{paragraph}[subsubsection] \newcounter{subparagraph}[paragraph] \def\thepart {\Roman{part}} \def\thechapter {\arabic{chapter}} \def\thesection {\thechapter.\arabic{section}} \def\thesubsection {\thesection.\arabic{subsection}} \def\thesubsubsection{\thesubsection .\arabic{subsubsection}} \def\theparagraph {\thesubsubsection.\arabic{paragraph}} \def\thesubparagraph {\theparagraph.\arabic{subparagraph}} \def\@chapapp{CHAPTER} % **************************************** % * PARTS * % **************************************** % \def\part{% \cleardoublepage \thispagestyle{empty}% \if@twocolumn \onecolumn \@tempswatrue \else \@tempswafalse \fi \secdef\@part\@spart } % % Heading for the \part command. % \def\@part[#1]#2{% \ifnum \c@secnumdepth >-2\relax \refstepcounter{part}% \addcontentsline{toc}{part}{\thepart \hspace{1em}#1}% \typeout{PART \number\c@part.}% \else \addcontentsline{toc}{part}{#1}% \fi \markboth{}{}% \vspace*{-17pt}% \vbox{\thin@rule\par \parindent 0pt \centering \vskip 17pt% \ifnum \c@secnumdepth >\m@ne \normalfont PART \thepart\par \else \normalfont \phantom{PART \thepart}\par \fi \vskip 17pt% \LARGE \bfseries #1\par \nobreak \addvspace{-4pt}% \thick@rule \vskip 25pt}% \@endpart } % % Heading for the \part* command. % \def\@spart#1{% \vspace*{-17pt}% \vbox{\thin@rule\par \parindent 0pt \centering \vskip 17pt% \normalfont\phantom{PART \thepart}\par \vskip 17pt% \LARGE \bfseries #1\par \nobreak \addvspace{-4pt}% \thick@rule \vskip 25pt}% \@endpart } % % \@endpart finishes the part page. % \def\@endpart{% \vfil\newpage \if@twoside \hbox{}% \thispagestyle{empty}% \newpage \fi \if@tempswa \twocolumn\fi } % **************************************** % * CHAPTERS * % **************************************** % % Chapter text macros % \newif\if@chptxt \newbox\@chptxtbox % \def\chaptertext{\global\@chptxttrue\global\setbox\@chptxtbox=\vbox\bgroup% \hsize=\textwidth\normalfont\small\noindent\ignorespaces} \def\endchaptertext{\egroup} % % Heading for the \chapter command. % \def\@makechapterhead#1{% \vspace*{-17pt}% \vbox{\thin@rule\par \parindent 0pt \centering \vskip 17pt% \ifnum \c@secnumdepth >\m@ne \normalfont \@chapapp{} \thechapter\par \else \normalfont \phantom{\@chapapp{} \thechapter}\par \fi \vskip 17pt% \LARGE \bfseries #1\par \nobreak \addvspace{-4pt}% \thick@rule \if@chptxt \addvspace{24pt plus 2pt}\unvbox\@chptxtbox \addvspace{6pt}\global\@chptxtfalse \else \vskip 23.5pt% \fi}% } % % Heading for the \chapter* command. % \def\@makeschapterhead#1{% \vspace*{-17pt}% \vbox{\thin@rule\par \parindent 0pt \centering \vskip 17pt% \normalfont\phantom{\@chapapp{} \thechapter}\par \vskip 17pt% \LARGE \bf #1\par \nobreak \addvspace{-4pt}% \thick@rule \if@chptxt \addvspace{24pt plus 2pt}\unvbox\@chptxtbox \addvspace{6pt}\global\@chptxtfalse \else \vskip 23.5pt% \fi}% } % % \secdef{UNSTARCMDS}{STARCMDS} : % \def\chapter{% \cleardoublepage \thispagestyle{plain}% \global\@topnum\z@ \@afterindentfalse \secdef\@chapter\@schapter } % \def\@chapter[#1]#2{% \ifnum \c@secnumdepth >\m@ne \refstepcounter{chapter}% \typeout{\@chapapp\space\thechapter.}% \addcontentsline{toc}{chapter}{\protect\numberline{\thechapter}#1}% \else \addcontentsline{toc}{chapter}{#1}% \fi \chaptermark{#1}% \addtocontents{lof}{\protect\addvspace{10pt}}% \addtocontents{lot}{\protect\addvspace{10pt}}% \if@twocolumn \@topnewpage[\@makechapterhead{#2}]% \else \@makechapterhead{#2}\@afterheading \fi } % \def\@schapter#1{% \chaptermark{#1}% \addtocontents{lof}{\protect\addvspace{10pt}}% \addtocontents{lot}{\protect\addvspace{10pt}}% \thispagestyle{empty}% %% \if@nocntentry %% \else %% \addcontentsline{toc}{chapter}{#1}% %% \fi \if@twocolumn \@topnewpage[\@makeschapterhead{#1}]% \else \@makeschapterhead{#1}\@afterheading \fi } % **************************************** % * SECTIONS * % **************************************** % % \@startsection {NAME}{LEVEL}{INDENT}{BEFORESKIP}{AFTERSKIP}{STYLE} % optional * [ALTHEADING]{HEADING} % \def\section{\@startsection{section}{1}{\z@} {-1.5pc plus -1pt minus -2pt} {6pt plus 1pt} {\normalsize\bf\raggedright}} \def\subsection{\@startsection{subsection}{2}{\z@} {-1.5pc plus -1pt minus -2pt} {6pt plus 1pt} {\normalsize\it\raggedright}} \def\subsubsection{\@startsection{subsubsection}{3}{\z@} {-1.0pc plus -1pt minus -2pt} {6pt plus 1pt} {\normalsize\it\raggedright}} \def\paragraph{\@startsection{paragraph}{4}{\z@} {3.25pt plus 1pt minus .2pt} {-1em} {\normalsize\it}} \def\subparagraph{\@startsection{subparagraph}{4}{\parindent} {3.25pt plus 1pt minus.2pt} {-1em} {\normalsize\normalfont}} % % Default initializations of \...mark commands % \def\chaptermark#1{} \setcounter{secnumdepth}{2} % % APPENDIX % \def\appendix{\par \setcounter{chapter}{0} \setcounter{section}{0} \def\@chapapp{APPENDIX} \def\thechapter{\Alph{chapter}}} % **************************************** % * LISTS * % **************************************** % \leftmargini 1pc \leftmarginii 1pc \leftmarginiii 1pc \leftmarginiv 1pc \leftmarginv 1pc \leftmarginvi 1pc \leftmargin\leftmargini \labelsep 0.5em \labelwidth\leftmargini\advance\labelwidth-\labelsep \def\@listI{\leftmargin\leftmargini \parsep 3pt plus 1pt minus 1pt% \topsep 3pt plus 1pt minus 2pt% \itemsep \z@ plus 2pt} \let\@listi\@listI \@listi \def\@listii{\leftmargin\leftmarginii \labelwidth\leftmarginii\advance\labelwidth-\labelsep \topsep 3pt plus 2pt minus 1pt \parsep 2pt plus 1pt minus 1pt \itemsep \z@ plus 2pt} \def\@listiii{\leftmargin\leftmarginiii \labelwidth\leftmarginiii\advance\labelwidth-\labelsep \topsep 3pt plus 1pt minus 1pt \parsep \z@ \partopsep 1pt plus 0pt minus 1pt \itemsep \z@ plus 2pt} \def\@listiv{\leftmargin\leftmarginiv \labelwidth\leftmarginiv\advance\labelwidth-\labelsep} \def\@listv{\leftmargin\leftmarginv \labelwidth\leftmarginv\advance\labelwidth-\labelsep} \def\@listvi{\leftmargin\leftmarginvi \labelwidth\leftmarginvi\advance\labelwidth-\labelsep} % % ENUMERATE -- with optional argument to set left margin % % label macros for Range-Left and Range-Right labels \def\makeRLlabel#1{\rlap{#1}\hss} \def\makeRRlabel#1{\hss\llap{#1}} % \def\enumerate{\ifnum \@enumdepth >3 \@toodeep \else \advance\@enumdepth \@ne \edef\@enumctr{enum\romannumeral\the\@enumdepth}% \fi \@ifnextchar [{\@enumeratetwo}{\@enumerateone}% } \def\@enumeratetwo[#1]{% \list{\csname label\@enumctr\endcsname}% {\settowidth\labelwidth{[#1]} \leftmargin\labelwidth \advance\leftmargin\labelsep \usecounter{\@enumctr} \let\makelabel\makeRRlabel} } \def\@enumerateone{% \list{\csname label\@enumctr\endcsname}% {\usecounter{\@enumctr} \let\makelabel\makeRRlabel}} % \def\labelenumi{\theenumi} \def\theenumi{\arabic{enumi}.} \def\labelenumii{\theenumii} \def\theenumii{(\alph{enumii})} \def\p@enumii{\theenumi} \def\labelenumiii{\theenumiii} \def\theenumiii{\roman{enumiii}.} \def\p@enumiii{\theenumi(\theenumii)} \def\labelenumiv{\theenumiv} \def\theenumiv{\Alph{enumiv}.} \def\p@enumiv{\p@enumiii\theenumiii} % % ITEMIZE % \def\labelitemi{$\bullet$} \def\labelitemii{\bf --} \def\labelitemiii{$\ast$} \def\labelitemiv{$\cdot$} % % VERSE % \def\verse{\let\\=\@centercr \list{}{\itemsep\z@ \itemindent -1em\listparindent \itemindent \rightmargin\leftmargin\advance\leftmargin 1em}\item[]} \let\endverse\endlist % % QUOTATION % \def\quotation{\list{}{\listparindent 1em \itemindent\listparindent \rightmargin\z@ \parsep 0pt plus 1pt}\item[]\small} \let\endquotation=\endlist % % QUOTE % \def\quote{\list{}{\rightmargin\z@}\item[]\small} \let\endquote=\endlist % % DESCRIPTION % \def\descriptionlabel#1{\hspace\labelsep \bf #1} \def\description{\list{}{\labelwidth\z@ \itemindent-\leftmargin \let\makelabel\descriptionlabel}} \let\enddescription\endlist \newdimen\descriptionmargin \descriptionmargin=3em % **************************************** % * OTHER ENVIRONMENTS * % **************************************** % % PROOF \def\proof{\normalfont \trivlist \item[\hskip \labelsep{\itshape Proof.}]} \def\endproof{\hspace*{1em}{\begin{picture}(6.5,6.5)% \put(0,0){\framebox(6.5,6.5){}}\end{picture}}\endtrivlist} \@namedef{proof*}{\normalfont\trivlist \item[\hskip \labelsep{\itshape Proof.}]} \@namedef{endproof*}{\endtrivlist} \def\proofbox{\begin{picture}(6.5,6.5)% \put(0,0){\framebox(6.5,6.5){}}\end{picture}} % % ARRAY AND TABULAR % \arraycolsep 5pt \tabcolsep 6pt \arrayrulewidth .5pt \doublerulesep 0pt % % TABBING % \tabbingsep \labelsep % % MINIPAGE % % \skip\@mpfootins : plays same role for footnotes in a minipage as % \skip\footins does for ordinary footnotes \skip\@mpfootins = \skip\footins \def\thempfootnote{\mbox{{$\fnsymbol{mpfootnote}$}}} % % FRAMEBOX % \fboxsep = 3pt \fboxrule = .5pt % **************************************** % * TABLE OF CONTENTS, ETC. * % **************************************** % \def\@pnumwidth{2.5em} \def\@tocrmarg {2.55em} \def\@dotsep{4.5} \setcounter{tocdepth}{1} % % \@dottedtocline{LEVEL}{INDENT}{NUMWIDTH}{TITLE}{PAGE} : % \def\@dottedtocline#1#2#3#4#5{% \ifnum #1>\c@tocdepth \else \vskip \z@ plus .2pt {\leftskip #2\relax \rightskip \@tocrmarg plus2em% v.0.16 \parfillskip -\rightskip \parindent #2\relax \@afterindenttrue \interlinepenalty\@M \leavevmode \@tempdima #3\relax \advance\leftskip \@tempdima \hbox{}\hskip -\leftskip #4\nobreak % \leaders\hbox{$\m@th \mkern \@dotsep mu.\mkern \@dotsep mu$} \hfill \nobreak \hbox to\@pnumwidth{\hfil\normalfont #5}\par}% \fi } % TABLEOFCONTENTS % \newif\if@nocntentry % \def\tableofcontents{\@restonecolfalse \if@twocolumn \@restonecoltrue\onecolumn \fi \@nocntentrytrue \chapter*{Contents}% \@nocntentryfalse % \@mkboth{Contents}{Contents}% \@starttoc{toc}% \if@restonecol\twocolumn\fi } \def\l@chapter#1#2{\pagebreak[3] \vskip 12pt plus 1pt \@tempdima 1.5em \begingroup \parindent \z@ \rightskip \@pnumwidth \parfillskip -\@pnumwidth \bf \leavevmode \advance\leftskip\@tempdima \hskip -\leftskip {\raggedright #1}\nobreak \hfil \nobreak\hbox to\@pnumwidth{\hss #2}\par \endgroup} % \let\l@part=\l@chapter % \def\l@section {\@dottedtocline{1}{15.0pt}{22.5pt}} \def\l@subsection {\@dottedtocline{2}{37.5pt}{30.0pt}} \def\l@subsubsection{\@dottedtocline{3}{67.5pt}{20.0pt}} \def\l@paragraph {\@dottedtocline{4}{87.5pt}{20.0pt}} \def\l@subparagraph {\@dottedtocline{5}{107.5pt}{20.0pt}} % % The default width of TOC entries for sections in CHAPMAN.STY % will only cater for sections with numbers up to 10.9. Numbers larger % than this result in the section number leaving no space between the % number and the title. % % This can be fixed by placing the \widetocentries command before % the \tableofcontents command (but after the \documentstyle line). % \def\widetocentries{% \def\l@section {\@dottedtocline{1}{15.0pt}{27.5pt}}% \def\l@subsection {\@dottedtocline{2}{42.5pt}{40.0pt}}% \def\l@subsubsection{\@dottedtocline{3}{82.5pt}{20.0pt}}% \def\l@paragraph {\@dottedtocline{4}{102.5pt}{20.0pt}}% \def\l@subparagraph {\@dottedtocline{5}{120.5pt}{20.0pt}}% } % % LIST OF FIGURES % \def\listoffigures{\@restonecolfalse \if@twocolumn \@restonecoltrue\onecolumn \fi \chapter*{List of Figures} % \@mkboth{List of Figures}{List of Figures} \@starttoc{lof} \if@restonecol \twocolumn \fi } \def\l@figure{\@dottedtocline{1}{1.5em}{2.3em}} % % LIST OF TABLES % \def\listoftables{\@restonecolfalse \if@twocolumn \@restonecoltrue \onecolumn \fi \chapter*{List of Tables} % \@mkboth{List of Tables}{List of Tables} \@starttoc{lot} \if@restonecol \twocolumn\fi } \let\l@table\l@figure % **************************************** % * BIBLIOGRAPHY * % **************************************** % \newcounter{dummy} % \def\thebibliography#1{% \chapter*{References} % \@mkboth{References}{References} \typeout{References.} \list{}{\labelwidth\z@ \leftmargin 1em \itemsep \z@ plus .1pt \itemindent-\leftmargin \usecounter{dummy}} \small \parindent\z@ \parskip\z@ plus .1pt\relax \def\newblock{\hskip .11em plus .33em minus .07em} \sloppy\clubpenalty4000\widowpenalty4000 \sfcode`\.=1000\relax } \let\endthebibliography=\endlist % \def\@biblabel#1{[#1]\hfill} % \def\@cite#1{[#1]} % **************************************** % * THE INDEX * % **************************************** % % The theindex, theauthorindex and thesubjectindex environment's % \newif\if@restonecol \newif\if@royalflag \def\theindex{\the@index{Index}} \def\endtheindex{\par\endthe@index} \def\theauthorindex{\the@index{Author index}} \def\endtheauthorindex{\par\endthe@index} \def\thesubjectindex{\the@index{Subject index}} \def\endthesubjectindex{\par\endthe@index} \def\the@index#1{\@restonecoltrue\if@twocolumn\@restonecolfalse\fi \columnseprule \z@ \columnsep 1pc% %%\twocolumn[\vspace*{11pt}\@makeschapterhead{#1}]% \twocolumn[\vspace*{11pt}] \if@royalflag % If royal 1 or 2 is in use \chapter*{Index}% %%TH \@mkboth{#1}{#1}% \else \chapter*{Index}% %%TH \@mkboth{\uppercase{#1}}{\uppercase{#1}}% \fi \typeout{#1.}% %%TH \addcontentsline{toc}{chapter}{#1}% %%TH \thispagestyle{empty}% \parindent\z@ \parskip\z@ plus .3pt% \small\raggedright \relax \let\item\@idxitem } \def\endthe@index{\if@restonecol\onecolumn\else\clearpage\fi} \def\@idxitem{\par\hangindent 10pt} \def\subitem{\par\hangindent 20pt \hspace*{10pt}} \def\subsubitem{\par\hangindent 30pt \hspace*{20pt}} \def\indexspace{\par\vskip 16pt plus 2pt minus 2pt\relax} % **************************************** % * FOOTNOTES * % **************************************** % \newskip\@footindent \@footindent=1em \def\footnoterule{\kern-3\p@ \hrule width 0\columnwidth \kern 2.6\p@} \@addtoreset{footnote}{chapter} \long\def\@makefntext#1{\@setpar{\@@par\@tempdima \hsize \advance\@tempdima-\@footindent \parshape \@ne \@footindent \@tempdima}\par \noindent \hbox to \z@{\hss$^{\@thefnmark}$\ }#1} \renewcommand{\thefootnote}{\mbox{{$\fnsymbol{footnote}$}}} \def\@fnsymbol#1{\ifcase#1\or * \or \dagger\or \ddagger\or \S \or \P \or \|\or **\or \dagger\dagger \or \ddagger\ddagger \or \S\S \or \P\P \else\@ctrerr\fi\relax} % **************************************** % * FIGURES AND TABLES * % **************************************** % % Float placement parameters. % \setcounter{topnumber}{2} \def\topfraction{.9} \setcounter{bottomnumber}{2} \def\bottomfraction{.5} \setcounter{totalnumber}{4} \def\textfraction{.1} \def\floatpagefraction{.8} \setcounter{dbltopnumber}{2} \def\dbltopfraction{.9} \def\dblfloatpagefraction{.8} % % \@makecaption{NUMBER}{TEXT} : Macro to make a figure or table caption. % %\long\def\@makecaption#1#2{% % \vskip 10pt% % \setbox\@tempboxa\hbox{\small \normalfont #1\enskip \itshape #2}% % \ifdim \wd\@tempboxa >\hsize % \small \normalfont #1\enskip \itshape #2\par % \else % \hbox to\hsize{\hfil\box\@tempboxa\hfil}% % \fi% %} \long\def\@makecaption#1#2{% \vskip 10pt% \setbox\@tempboxa\hbox{\small \normalfont #1\unskip\hskip10pt #2}% \ifdim \wd\@tempboxa >\hsize \small \normalfont \@hangfrom{#1\unskip\hskip10pt\ignorespaces}#2\par \else \hbox to\hsize{\hfil\box\@tempboxa\hfil}% \fi% } % % FIGURE % \newcounter{figure}[chapter] \def\thefigure{\thechapter.\@arabic\c@figure} \def\fps@figure{tbp} \def\ftype@figure{1} \def\ext@figure{lof} \def\fnum@figure{{\bf Figure \thefigure}} \def\figure{\@float{figure}} \let\endfigure\end@float \@namedef{figure*}{\@dblfloat{figure}} \@namedef{endfigure*}{\end@dblfloat} % % TABLE % \newcounter{table}[chapter] \def\thetable{\thechapter.\@arabic\c@table} \def\fps@table{tbp} \def\ftype@table{2} \def\ext@table{lot} \def\fnum@table{{\bf Table \thetable}} \def\table{\@float{table}} \let\endtable\end@float \@namedef{table*}{\@dblfloat{table}} \@namedef{endtable*}{\end@dblfloat} % **************************************** % * TITLE * % **************************************** % % TITLEPAGE % \def\titlepage{\@restonecolfalse \if@twocolumn \@restonecoltrue\onecolumn \else \newpage \fi \thispagestyle{empty} } \def\endtitlepage{\if@restonecol\twocolumn \else \newpage \fi} % \def\maketitle{\make@cornermarks\begin{titlepage} \let\footnotesize\small \let\footnoterule\relax \setcounter{page}{1} \null \vspace*{-17pt}% {\parindent 0pt \centering \par \LARGE \bfseries \@title \par \nobreak \vskip 0pt \thick@rule \vskip 25pt \par \large \normalfont \begin{tabular}[t]{c} \@author \end{tabular}\par } \vfill \@thanks \null \end{titlepage} \setcounter{footnote}{0} \let\thanks\relax \gdef\@thanks{} \gdef\@author{} \gdef\@title{} \let\maketitle\relax } % **************************************** % * PAGE STYLES * % **************************************** \def\cleardoublepage{% \clearpage \if@twoside \ifodd\c@page \else \hbox{}% \pagestyle{empty}% \newpage \if@twocolumn \hbox{}% \newpage\fi\fi\fi} \newdimen\htrim \newdimen\vtrimtop \newdimen\vtrimbot % \htrim.75in % \vtrimtop.8607in % \vtrimbot1.027in % \hoffset-.49in % \voffset-.63in%.04in \htrim4.42pc \vtrimtop6.26pc \vtrimbot6.37pc % \hoffset-5pt \voffset39pt %\fi \newsavebox\ul@box \newsavebox\ur@box \newsavebox\ll@box \newsavebox\lr@box \def\top@cornermarks{% \hskip-\htrim \vbox to 0\p@{\vskip-\vtrimtop\llap{\copy\ul@box}\vss}% \vbox to 0\p@{\vskip-\vtrimtop\rlap{\hskip\textwidth\hskip2\htrim\copy\ur@box}\vss}% \vbox to 0\p@{\vskip\textheight\vskip\vtrimbot\llap{\copy\ll@box}\vss}% \vbox to 0\p@{\vskip\textheight\vskip\vtrimbot\rlap{\hskip\textwidth\hskip2\htrim\copy\lr@box}\vss}% \hskip\htrim} \def\make@cornermarks{% \sbox\ul@box{\rule{18\p@}{.25\p@}\hskip8\p@\hbox to.25\p@{\vbox to26\p@{\noindent\rule{.25\p@}{18\p@}}}}% \sbox\ur@box{\hbox to.25\p@{\vbox to26\p@{\noindent\rule{.25\p@}{18\p@}}}\hskip8\p@\rule{18\p@}{.25\p@}}% \sbox\ll@box{\rule{18\p@}{.25\p@}\hskip8\p@\lower34\p@\hbox to.25\p@{\vbox to26\p@{\noindent\rule{.25\p@}{18\p@}}}}% \sbox\lr@box{\lower34\p@\hbox to.25\p@{\vbox to26\p@{\noindent\rule{.25\p@}{18\p@}}}\hskip8\p@\rule{18\p@}{.25\p@}}} \def\even@head{% \top@cornermarks \@the@page {%\RunningHeadFont \hfil {%\MakeUppercase \leftmark } }}%\hfil \def\odd@head{% \top@cornermarks {%\RunningHeadFont {%\MakeUppercase \rightmark } } \hfil \@the@page } \def\@the@page{{\thepage}} %\def\@the@page{{\PageNumFont\thepage}} \def\ps@empty{% \let\@mkboth\@gobbletwo \let\@oddhead\top@cornermarks \let\@evenhead\top@cornermarks \let\@oddfoot\@empty \let\@evenfoot\@empty } \def\ps@folio{% \let\@mkboth\@gobbletwo \let\@oddhead\top@cornermarks \def\@oddfoot{% \parindent\z@ \baselineskip7\p@ \hbox{% \textwidth\@ciprulewidth \vbox{% \if@cip\rule{\@ciprulewidth}{.25pt}\par \hbox{\vbox{\noindent\copy\@cipboxa\par\noindent\copy\@cipboxb}}\fi}} \hfill\@the@page} \let\@evenhead\odd@head \let\@evenfoot\@oddfoot } \def\ps@headings{% \let\@mkboth\@gobbletwo \let\@oddfoot\@empty \let\@evenfoot\@empty \let\@evenhead\even@head \let\@oddhead\odd@head \def\chaptermark##1{\markboth {\uppercase{##1}}{\uppercase{##1}}} \def\sectionmark##1{\markright{\uppercase{##1}}} } \def\ps@opening{% \let\@mkboth\@gobbletwo \make@cornermarks \let\@oddhead\top@cornermarks \let\@evenhead\top@cornermarks \def\@oddfoot{% \parindent\z@ \baselineskip7\p@ \hbox{% \textwidth\@ciprulewidth \vbox{% \if@cip\rule{\@ciprulewidth}{.25pt}\par \hbox{\vbox{\noindent\copy\@cipboxa\par\noindent\copy\@cipboxb}}\fi}} \hfill\@the@page} \let\@evenfoot\@oddfoot } % % Initializes TeX's marks % \mark{{}{}} % % \ps@empty and \ps@plain defined in LATEX.TEX % \def\ps@plain{% \let\@mkboth\@gobbletwo \let\@oddhead\top@cornermarks \let\@evenhead\top@cornermarks \def\@oddfoot{\hfil{\footnotesize\rm \thepage}\hfil}% 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nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Quantile Regression} %%\VignetteDepends{lattice,quantreg} \setcounter{chapter}{11} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 80} <>= library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) data("db", package = "gamlss.data") nboys <- with(db, sum(age > 2)) @ \chapter[Quantile Regression]{Quantile Regression: Head Circumference for Age\label{QR}} \section{Introduction} \section{Quantile Regression} \section{Analysis Using \R{}} We begin with a graphical inspection of the influence of age on head circumference by means of a scatterplot. Plotting all pairs of age and head circumference in one panel gives more weight to the teens and 20s, so we produce one plot for younger boys between two and nine years old and one additional plot for boys older than nine years (or $>108$ months, to be precise). The \Rcmd{cut} function is very convenient for constructing a factor representing these two groups <>= summary(db) db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) @ which can then be used as a conditioning variable for conditional scatterplots produced with the \Rcmd{xyplot} function \citep[package \Rpackage{lattice}]{PKG:lattice}. Because we draw $\Sexpr{nboys}$ points in total, we use transparent shading (via \Rcmd{rgb(.1, .1, .1, .1)}) in order to obtain a clearer picture for the more populated areas in the plot. \begin{figure} \begin{center} <>= db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", scales = list(x = list(relation = "free")), layout = c(2, 1), pch = 19, col = rgb(.1, .1, .1, .1)) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys. \label{QR-db-plot}} \end{center} \end{figure} Figure~\ref{QR-db-plot}, as expected, shows that head circumference increases with age. It also shows that there is considerable variation and also quite a number of extremely large or small head circumferences in the respective age cohorts. It should be noted that each point corresponds to one boy participating in the study due to its cross-sectional study design. No longitudinal measurements (cf.~Chapter~\ref{ALDI}) were taken and we can safely assume independence between observations. We start with a simple linear model, computed separately for the younger and older boys, for regressing the mean head circumference on age <>= (lm2.9 <- lm(head ~ age, data = db, subset = age < 9)) (lm9.23 <- lm(head ~ age, data = db, subset = age > 9)) @ This approach is equivalent to fitting two intercepts and two slopes in the joint model <>= (lm_mod <- lm(head ~ age:I(age < 9) + I(age < 9) - 1, data = db)) @ while omitting the global intercept. Because the median of the normal distribution is equal to its mean, the two models can be interpreted as conditional median models under the normal assumption. The model states that within one year, the head circumference increases by $\Sexpr{round(coef(lm_mod)["age:I(age < 9)TRUE"], 3)}$ cm for boys less than nine years old and by $\Sexpr{round(coef(lm_mod)["age:I(age < 9)FALSE"], 3)}$ for older boys. We now relax this distributional assumption and compute a median regression model using the \Rcmd{rq} function from package \Rpackage{quantreg} \citep{PKG:quantreg}: <>= library("quantreg") (rq_med2.9 <- rq(head ~ age, data = db, tau = 0.5, subset = age < 9)) (rq_med9.23 <- rq(head ~ age, data = db, tau = 0.5, subset = age > 9)) @ When we construct confidence intervals for the intercept and slope parameters from both models for the younger boys <>= cbind(coef(lm2.9)[1], confint(lm2.9, parm = "(Intercept)")) cbind(coef(lm2.9)[2], confint(lm2.9, parm = "age")) summary(rq_med2.9, se = "rank") @ we see that the two intercepts are almost identical but there seems to be a larger slope parameter for age in the median regression model. For the older boys, we get the confidence intervals via <>= cbind(coef(lm9.23)[1], confint(lm9.23, parm = "(Intercept)")) cbind(coef(lm9.23)[2], confint(lm9.23, parm = "age")) summary(rq_med9.23, se = "rank") @ with again almost identical intercepts and only a slightly increased slope for age in the median regression model. Since one of our aims was the construction of growth curves, we first use the linear models regressing head circumference on age to plot such curves. Based on the two normal linear models, we can compute the quantiles of head circumference for age. For the following values of $\tau$ <>= tau <- c(.01, .1, .25, .5, .75, .9, .99) @ and a grid of age values <>= gage <- c(2:9, 9:23) i <- 1:8 @ (the index \Rcmd{i} denoting younger boys), we compute the standard prediction intervals \index{Prediction interval} taking the randomness of the estimated intercept, slope, and variance parameters into account. We first set up a data frame with our grid of age values and then use the \Rcmd{predict} function for a linear model to compute prediction intervals, here with a coverage of $50\%$. The lower limit of such a $50\%$ prediction interval is equivalent to the conditional $25\%$ quantile for the given age and the upper limit corresponds to the $75\%$ quantile. The conditional mean is also reported and is equivalent to the conditional median: <>= idf <- data.frame(age = gage[i]) p <- predict(lm2.9, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p @ We now proceed with $80\%$ prediction intervals for constructing the $10\%$ and $90\%$ quantiles, and with $98\%$ prediction intervals corresponding to the $1\%$ and $99\%$ quantiles and repeat the exercise also for the older boys: <>= p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") p2.9 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] idf <- data.frame(age = gage[-i]) p <- predict(lm9.23, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") @ We now reorder the columns of this table and get the following conditional quantiles, estimated under the normal assumption of head circumference: <>= p9.23 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] round((q2.23 <- rbind(p2.9, p9.23)), 3) @ We can now superimpose these conditional quantiles on our scatterplot. To do this, we need to write our own little panel function that produces the scatterplot using the \Rcmd{panel.xyplot} function and then adds the just computed conditional quantiles by means of the \Rcmd{panel.lines} function called for every column of $\Robject{q2.23}$. Figure~\ref{QR-db-lm-plot} shows parallel lines owing to the fact that the linear model assumes an error variance independent from age; this is the so-called variance homogeneity. Compared to a plot with only a single (mean) regression line, we plotted a whole bunch of conditional distributions here, one for each value of age. Of course, we did so under extremely simplifying assumptions like linearity and variance homogeneity that we're going to drop now. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), q2.23[nrow(q2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), q2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed normal quantiles. \label{QR-db-lm-plot}} \end{center} \end{figure} For the production of a nonparametric version of our growth curves, we start with fitting not only one but multiple quantile regression models, one for each value of $\tau$. We start with the younger boys <>= (rq2.9 <- rq(head ~ age, data = db, tau = tau, subset = age < 9)) @ and continue with the older boys <>= (rq9.23 <- rq(head ~ age, data = db, tau = tau, subset = age > 9)) @ Naturally, the intercept parameters vary but there is also a considerable variation in the slopes, with the largest value for the $1\%$ quantile regression model for younger boys. The parameters $\beta_\tau$ have to be interpreted with care. In general, they cannot be interpreted on an individual-specific level. A boy who happens to be at the $\tau \times 100\%$ quantile of head circumference conditional on his age would not be at the same quantile anymore when he gets older. When knowing $\beta_\tau$, the only conclusion that can be drawn is how the $\tau \times 100\%$ quantile of a population with a specific age differs from the $\tau \times 100\%$ quantile of a population with a different age. Because the linear functions estimated by linear quantile regression, here in model \Robject{rq9.23}, directly correspond to the conditional quantiles of interest, we can use the \Rcmd{predict} function to compute the estimated conditional quantiles: <>= p2.23 <- rbind(predict(rq2.9, newdata = data.frame(age = gage[i])), predict(rq9.23, newdata = data.frame(age = gage[-i]))) @ It is important to note that these numbers were obtained without assuming anything about the continuous distribution of head circumference given any age. Again, we produce a scatterplot with superimposed quantiles, this time each line corresponds to a specific model. For the sake of comparison with the linear model, we add the linear model quantiles as dashed lines to Figure~\ref{QR-db-rq-plot}. For the older boys, there seems to be almost no difference but the more extreme $1\%$ and $99\%$ quantiles for the younger boys differ considerably. So, at least for the younger boys, we might want to allow for age-specific variability in the distribution of head circumference. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), p2.23[nrow(p2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed regression quantiles (solid lines) and normal quantiles (dashed lines). \label{QR-db-rq-plot}} \end{center} \end{figure} Still, with the quantile regression models shown in Figure~\ref{QR-db-rq-plot} we assume that the quantiles of head circumference depend on age in a linear way. Additive quantile regression is one way to approach the estimation of non-linear quantile functions. By considering two different models for younger and older boys, we allowed for a certain type of non-linear function in the results shown so far. Additive quantile regression should be able to deal with this problem and we therefore fit these models to all boys simultaneously. For our different choices of $\tau$, we fit one additive quantile regression model using the \Rcmd{rqss} function from the \Rpackage{quantreg} and allow smooth quantile functions of age via the \Rcmd{qss} function in the right-hand side of the model formula. Note that we transformed age by the third root prior to model fitting. This does not affect the model since it is a monotone transformation, however, it helps to avoid fitting a function with large derivatives for very young boys resulting in a low penalty parameter $\lambda$: <>= rqssmod <- vector(mode = "list", length = length(tau)) db$lage <- with(db, age^(1/3)) for (i in 1:length(tau)) rqssmod[[i]] <- rqss(head ~ qss(lage, lambda = 1), data = db, tau = tau[i]) @ For the analysis of the head circumference, we choose a penalty parameter $\lambda = 1$, which is the default for the \Rcmd{qss} function. Simply using the default without a careful hyperparameter tuning, for example using crossvalidation or similar procedures, is almost always a mistake. By visual inspection (Figure~\ref{QR-db-rqss-plot}) we find this choice appropriate but ask the readers to make a second guess (Exercise 3). For a finer grid of age values, we compute the conditional quantiles from the \Rcmd{predict} function: <>= gage <- seq(from = min(db$age), to = max(db$age), length = 50) p <- sapply(1:length(tau), function(i) { predict(rqssmod[[i]], newdata = data.frame(lage = gage^(1/3))) }) @ Using very similar code as for plotting linear quantiles, we produce again a scatterplot of age and head circumference but this time overlaid with non-linear regression quantiles. Given that the results from the linear models presented in Figure~\ref{QR-db-rq-plot} looked pretty convincing, the quantile curves in Figure~\ref{QR-db-rqss-plot} shed a surprising new light on the data. For the younger boys, we expected to see a larger variability than for boys between two and three years old, but in fact the distribution seems to be more complex. The distribution seems to be positively skewed with a heavy lower tail and the degree of skewness varies with age (note that the median is almost linear for boys older than four years). Also in the right part of Figure~\ref{QR-db-rqss-plot}, we see an age-varying skewness, although less pronounced as for the younger boys. The median increases up to 16 years but then the growth rate is much smaller. This does not seem to be the case for the $1\%, 10\%, 90\%$, and $99\%$ quantiles. Note that the discontinuity in the quantiles between the two age groups is only due to the overlapping abscissae. However, the deviations between the growth curves obtained from a linear model under normality assumption on the one hand and quantile regression on the other hand as shown in Figures~\ref{QR-db-rq-plot} and \ref{QR-db-rqss-plot} are hardly dramatic for the head circumference data. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) apply(p, 2, function(x) panel.lines(gage, x)) panel.text(rep(max(db$age), length(tau)), p[nrow(p),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed non-linear regression quantiles. \label{QR-db-rqss-plot}} \end{center} \end{figure} \section{Summary of Findings} We can conclude that the whole distribution of head circumference changes with age and that assumptions like symmetry and variance homogeneity might be questionable for such type of analysis. One alternative to the estimation of conditional quantiles is the estimation of conditional distributions. One very interesting parametric approach are generalized additive models for location, scale, and shape \citep[GAMLSS,][]{HSAUR:RigbyStasinopoulos2005}. In \cite{HSAUR:StasinopoulosRigby2007}, an analysis of the age and head circumference by means of the \Rpackage{gamlss} package can be found. One practical problem associated with contemporary methods in quantile regression is quantile crossing. Because we fitted one quantile regression model for each of the quantiles of interest, we cannot guarantee that the conditional quantile functions are monotone, so the $90\%$ quantile may well be larger than the $95\%$ quantile in some cases. Postprocessing of the estimated quantile curves may help in this situation \citep{HSAUR:DetteVolgushev2008}. \section{Final Comments} When estimating regression models, we have to be aware of the implications of model assumptions when interpreting the results. Symmetry, linearity, and variance homogeneity are among the strongest but common assumptions. Quantile regression, both in its linear and additive formulation, is an intellectually stimulating and practically very useful framework where such assumptions can be relaxed. At a more basic level, one should always ask \stress{Am I really interested in the mean?} before using the regression models discussed in other chapters of this book. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_logistic_regression_glm.Rnw0000644000175000017500000011117014133304452021377 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Logistic Regression and Generalized Linear Models} %%\VignetteDepends{survival,MASS,multcomp,lattice} \setcounter{chapter}{6} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Logistic Regression and Generalized Linear Models]{Logistic Regression and Generalized Linear Models: Blood Screening, Women's Role in %' Society, Colonic Polyps, Driving and Back Pain, and Happiness in China \label{GLM}} \section{Introduction} \section{Logistic Regression and Generalized Linear Models} \section{Analysis Using \R{}} \subsection{ESR and Plasma Proteins} \begin{figure} \begin{center} <>= data("plasma", package = "HSAUR3") layout(matrix(1:2, ncol = 2)) cdplot(ESR ~ fibrinogen, data = plasma) cdplot(ESR ~ globulin, data = plasma) @ \caption{Conditional density plots of the erythrocyte sedimentation rate (ESR) given fibrinogen and globulin. \label{GLM:plasma1}} \end{center} \end{figure} We can now fit a logistic regression model to the data using the \Rcmd{glm} function. We start with a model that includes only a single explanatory variable, \Robject{fibrinogen}. The code to fit the model is <>= plasma_glm_1 <- glm(ESR ~ fibrinogen, data = plasma, family = binomial()) @ The formula implicitly defines a parameter for the global mean (the intercept term) as discussed in \Sexpr{ch("ANOVA")} and \Sexpr{ch("MLR")}. The distribution of the response is defined by the \Robject{family} argument, a binomial distribution in our case. \index{family argument@\Rcmd{family} argument} \index{Binomial distribution} (The default link function when the binomial family is requested is the logistic function.) \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to ESR and fibrigonen. \label{GLM-plasma-summary-1}} \SchunkLabel <>= summary(plasma_glm_1) @ \SchunkRaw From the results in Figure~\ref{GLM-plasma-summary-1} we see that the regression coefficient for fibrinogen is significant at the $5\%$ level. An increase of one unit in this variable increases the log-odds in favor of an ESR value greater than $20$ by an estimated $\Sexpr{round(coef(plasma_glm_1)["fibrinogen"], 2)}$ with 95\% confidence interval <>= ci <- confint(plasma_glm_1)["fibrinogen",] @ <>= confint(plasma_glm_1, parm = "fibrinogen") @ <>= print(ci) @ These values are more helpful if converted to the corresponding values for the odds themselves by exponentiating the estimate <>= exp(coef(plasma_glm_1)["fibrinogen"]) @ and the confidence interval <>= ci <- exp(confint(plasma_glm_1, parm = "fibrinogen")) @ <>= exp(confint(plasma_glm_1, parm = "fibrinogen")) @ <>= print(ci) @ The confidence interval is very wide because there are few observations overall and very few where the ESR value is greater than $20$. Nevertheless it seems likely that increased values of fibrinogen lead to a greater probability of an ESR value greater than $20$. We can now fit a logistic regression model that includes both explanatory variables using the code <>= plasma_glm_2 <- glm(ESR ~ fibrinogen + globulin, data = plasma, family = binomial()) @ and the output of the \Rcmd{summary} method is shown in Figure \ref{GLM-plasma-summary-2}. \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to ESR and both globulin and fibrinogen. \label{GLM-plasma-summary-2}} \SchunkLabel <>= summary(plasma_glm_2) @ \SchunkRaw <>= plasma_anova <- anova(plasma_glm_1, plasma_glm_2, test = "Chisq") @ The coefficient for gamma globulin is not significantly different from zero. Subtracting the residual deviance of the second model from the corresponding value for the first model we get a value of $\Sexpr{round(plasma_anova$Deviance[2], 2)}$. Tested using a $\chi^2$-distribution with a single degree of freedom this is not significant at the 5\% level and so we conclude that gamma globulin is not associated with ESR level. In \R{}, the task of comparing the two nested models can be performed using the \Rcmd{anova} function <>= anova(plasma_glm_1, plasma_glm_2, test = "Chisq") @ Nevertheless we shall use the predicted values from the second model and plot them against the values of \stress{both} explanatory variables using a \stress{bubbleplot} to illustrate the use of the \Rcmd{symbols} function. \index{Bubbleplot} The estimated conditional probability of a ESR value larger $20$ for all observations can be computed, following formula (\ref{GLM:logitexp}), by <>= prob <- predict(plasma_glm_2, type = "response") @ and now we can assign a larger circle to observations with larger probability as shown in Figure~\ref{GLM:bubble}. The plot clearly shows the increasing probability of an ESR value above $20$ (larger circles) as the values of fibrinogen, and to a lesser extent, gamma globulin, increase. \begin{figure} \begin{center} <>= plot(globulin ~ fibrinogen, data = plasma, xlim = c(2, 6), ylim = c(25, 55), pch = ".") symbols(plasma$fibrinogen, plasma$globulin, circles = prob, add = TRUE) @ \caption{Bubbleplot of fitted values for a logistic regression model fitted to the \Robject{plasma} data. \label{GLM:bubble}} \end{center} \end{figure} \subsection{Women's Role in Society} %' Originally the data in Table~\ref{GLM-womensrole-tab} would have been in a completely equivalent form to the data in Table~\ref{GLM-plasma-tab} data, but here the individual observations have been grouped into counts of numbers of agreements and disagreements for the two explanatory variables, \Robject{gender} and \Robject{education}. To fit a logistic regression model to such grouped data using the \Rcmd{glm} function we need to specify the number of agreements and disagreements as a two-column matrix on the left-hand side of the model formula. We first fit a model that includes the two explanatory variables using the code <>= data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ gender + education womensrole_glm_1 <- glm(fm1, data = womensrole, family = binomial()) @ \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to the \Robject{womensrole} data. \label{GLM-womensrole-summary-1}} \SchunkLabel <>= summary(womensrole_glm_1) @ \SchunkRaw From the \Rcmd{summary} output in Figure~\ref{GLM-womensrole-summary-1} it appears that education has a highly significant part to play in predicting whether a respondent will agree with the statement read to them, but the respondent's %' gender is apparently unimportant. As years of education increase the probability of agreeing with the statement declines. We now are going to construct a plot comparing the observed proportions of agreeing with those fitted by our fitted model. Because we will reuse this plot for another fitted object later on, we define a function which plots years of education against some fitted probabilities, e.g., <>= role.fitted1 <- predict(womensrole_glm_1, type = "response") @ and labels each observation with the person's gender: %%' \numberSinput <>= myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } @ \rawSinput \begin{figure} \begin{center} <>= myplot(role.fitted1) @ \caption{Fitted (from \Robject{womensrole\_glm\_1}) and observed probabilities of agreeing for the \Robject{womensrole} data. The size of the symbols is proportional to the sample size. \label{GLM-role1plot}} \end{center} \end{figure} In lines 3--5 of function \Rcmd{myplot}, an empty scatterplot of education and fitted probabilities (\Rcmd{type = "n"}) is set up, basically to set the scene for the following plotting actions. Then, two lines are drawn (using function \Rcmd{lines} in lines 6 and 7), one for males (with line type 1) and one for females (with line type 2, i.e., a dashed line), where the logical vector \Robject{f} describes both genders. In line 9 a legend is added. Finally, in lines 12 onwards we plot `observed' values, i.e., the frequencies of agreeing in each of the groups (\Robject{y} as computed in lines 10 and 11) and use the Venus and Mars symbols to indicate gender. The size of the plotted symbol is proportional to the numbers of observations in the corresponding group of gender and years of education. The two curves for males and females in Figure~\ref{GLM-role1plot} are almost the same reflecting the non-significant value of the regression coefficient for gender in \Robject{womensrole\_glm\_1}. But the observed values plotted on Figure~\ref{GLM-role1plot} suggest that there might be an interaction of education and gender, a possibility that can be investigated by applying a further logistic regression model using \index{Interaction} <>= fm2 <- cbind(agree,disagree) ~ gender * education womensrole_glm_2 <- glm(fm2, data = womensrole, family = binomial()) @ The \Robject{gender} and \Robject{education} interaction term is seen to be highly significant, as can be seen from the \Rcmd{summary} output in Figure~\ref{GLM-womensrole-summary-2}. \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to the \Robject{womensrole} data. \label{GLM-womensrole-summary-2}} \SchunkLabel <>= summary(womensrole_glm_2) @ \SchunkRaw \begin{figure} \begin{center} <>= role.fitted2 <- predict(womensrole_glm_2, type = "response") myplot(role.fitted2) @ \caption{Fitted (from \Robject{womensrole\_glm\_2}) and observed probabilities of agreeing for the \Robject{womensrole} data. \label{GLM-role2plot}} \end{center} \end{figure} We can obtain a plot of deviance residuals plotted against fitted values using the following code above Figure~\ref{GLM:devplot}. \begin{figure} \begin{center} <>= res <- residuals(womensrole_glm_2, type = "deviance") plot(predict(womensrole_glm_2), res, xlab="Fitted values", ylab = "Residuals", ylim = max(abs(res)) * c(-1,1)) abline(h = 0, lty = 2) @ \caption{Plot of deviance residuals from logistic regression model fitted to the \Robject{womensrole} data. \label{GLM:devplot}} \end{center} \end{figure} The residuals fall into a horizontal band between $-2$ and $2$. This pattern does not suggest a poor fit for any particular observation or subset of observations. \subsection{Colonic Polyps} The data on colonic polyps in Table~\ref{GLM-polyps-tab} involves \stress{count} data. We could try to model this using multiple regression but there are two problems. The first is that a response that is a count can take only positive values, and secondly such a variable is unlikely to have a normal distribution. Instead we will apply a GLM with a log link function, ensuring that fitted values are positive, and a Poisson error distribution, i.e., \index{Poisson error distribution} \index{Poisson regression} \begin{eqnarray*} \P(y) = \frac{e^{-\lambda}\lambda^y}{y!}. \end{eqnarray*} This type of GLM is often known as \stress{Poisson regression}. We can apply the model using <>= data("polyps", package = "HSAUR3") polyps_glm_1 <- glm(number ~ treat + age, data = polyps, family = poisson()) @ (The default link function when the Poisson family is requested is the log function.) \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the Poisson regression model fitted to the \Robject{polyps} data. \label{GLM-polyps-summary-1}} \SchunkLabel <>= summary(polyps_glm_1) @ \SchunkRaw We can deal with overdispersion by using a procedure known as \stress{quasi-likelihood}, \index{Quasi-likelihood} which allows the estimation of model parameters without fully knowing the error distribution of the response variable. \cite{HSAUR:McCullaghNelder1989} give full details of the quasi-likelihood approach. In many respects it simply allows for the estimation of $\phi$ from the data rather than defining it to be unity for the binomial and Poisson distributions. We can apply quasi-likelihood estimation to the colonic polyps data using the following \R{} code <>= polyps_glm_2 <- glm(number ~ treat + age, data = polyps, family = quasipoisson()) summary(polyps_glm_2) @ The regression coefficients for both explanatory variables remain significant but their estimated standard errors are now much greater than the values given in Figure~\ref{GLM-polyps-summary-1}. A possible reason for overdispersion in these data is that polyps do not occur independently of one another, but instead may `cluster' together. %' \index{Overdispersion|)} \subsection{Driving and Back Pain} A frequently used design in medicine is the matched case-control study in which each patient suffering from a particular condition of interest included in the study is matched to one or more people without the condition. The most commonly used matching variables are age, ethnic group, mental status, etc. A design with $m$ controls per case is known as a $1:m$ matched study. In many cases $m$ will be one, and it is the $1:1$ matched study that we shall concentrate on here where we analyze the data on low back pain given in Table~\ref{GLM-backpain-tab}. To begin we shall describe the form of the logistic model appropriate for case-control studies in the simplest case where there is only one binary explanatory variable. With matched pairs data the form of the logistic model involves the probability, $\varphi$, that in matched pair number $i$, for a given value of the explanatory variable the member of the pair is a case. Specifically the model is \begin{eqnarray*} \text{logit}(\varphi_i) = \alpha_i + \beta x. \end{eqnarray*} The odds that a subject with $x=1$ is a case equals $\exp(\beta)$ times the odds that a subject with $x=0$ is a case. The model generalizes to the situation where there are $q$ explanatory variables as \begin{eqnarray*} \text{logit}(\varphi_i) = \alpha_i + \beta_1 x_1 + \beta_2 x_2 + \dots \beta_q x_q. \end{eqnarray*} Typically one $x$ is an explanatory variable of real interest, such as past exposure to a risk factor, with the others being used as a form of statistical control in addition to the variables already controlled by virtue of using them to form matched pairs. This is the case in our back pain example where it is the effect of car driving on lower back pain that is of most interest. The problem with the model above is that the number of parameters increases at the same rate as the sample size with the consequence that maximum likelihood estimation is no longer viable. We can overcome this problem if we regard the parameters $\alpha_i$ as of little interest and so are willing to forgo their estimation. If we do, we can then create a \stress{conditional likelihood function} that will yield maximum likelihood estimators of the coefficients, $\beta_1, \dots, \beta_q$, that are consistent and asymptotically normally distributed. The mathematics behind this are described in \cite{HSAUR:Collett2003}. The model can be fitted using the \Rcmd{clogit} function from package \Rpackage{survival}; the results are shown in Figure~\ref{GLM-backpain-print}. <>= library("survival") backpain_glm <- clogit(I(status == "case") ~ driver + suburban + strata(ID), data = backpain) @ The response has to be a logical (\Rcmd{TRUE} for cases) and the \Rcmd{strata} command specifies the matched pairs. \renewcommand{\nextcaption}{\R{} output of the \Robject{print} method for the conditional logistic regression model fitted to the \Robject{backpain} data. \label{GLM-backpain-print}} \SchunkLabel <>= print(backpain_glm) @ \SchunkRaw The estimate of the odds ratio of a herniated disc occurring in a driver relative to a nondriver is $\Sexpr{round(exp(coef(backpain_glm)[1]),2)}$ with a $95\%$ confidence interval of $\Sexpr{paste("(", paste(round(exp(confint(backpain_glm)[1,]), 2), collapse = ","),")", sep = "")}$. Conditional on residence we can say that the risk of a herniated disc occurring in a driver is about twice that of a nondriver. There is no evidence that where a person lives affects the risk of lower back pain. \subsection{Happiness in China} We model the probability distribution of reported happiness using a proportional odds model. In \R{}, the function \Rcmd{polr} from the \Rpackage{MASS} package \citep{HSAUR:VenablesRipley2002, PKG:MASS} implements such models, but in a slightly different form as explained in Section~\ref{GLM:polr}. The model we are going to fit reads \begin{eqnarray*} \log\left(\frac{\P(y \le k | x_1, \dots, x_q)}{\P(y > k | x_1, \dots, x_q)}\right) & = & \zeta_k - (\beta_1 x_1 + \dots + \beta_q x_q) \end{eqnarray*} and we have to take care when interpreting the signs of the estimated regression coefficients. Another issue needs our attention before we start. Three of the explanatory variables are itself ordered (\Robject{R\_edu}, the level of education of the responding woman; \Robject{R\_health}, the health status of the responding woman in the last year; and \Robject{A\_edu}, the level of education of the woman's partner). For unordered factors, the default treatment contrasts, see Chapters~\ref{ANOVA}, \ref{MLR}, and \ref{SIMC}, compares the effect of each level to the first level. This coding does not take the ordinal nature of an ordered factor into account. One more appropriate coding is called \stress{Helmert} contrasts. \index{Helmert constrast} Here, we compare each level $k$ to the average of the preceding levels, i.e., the second level to the first, the third to the average of the first and the second, and so on (these contrasts are also sometimes called \stress{reverse Helmert contrasts}). The \Rcmd{option} function can be used to specify the default contrasts for unordered (we don't change the default \Robject{contr.treatment} option) and ordered factors. The returned \Robject{opts} variable stores the options before manipulation and can be used to conveniently restore them after we fitted the proportional odds model: <>= library("MASS") opts <- options(contrasts = c("contr.treatment", "contr.helmert")) CHFLS_polr <- polr(R_happy ~ ., data = CHFLS, Hess = TRUE) options(opts) @ \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the proportional odds model fitted to the \Robject{CHFLS} data. \label{GLM-CHFLS-polr-summary}} \SchunkLabel <>= summary(CHFLS_polr) @ \SchunkRaw As (almost) always, the \Rcmd{summary} function can be used to display the fitted model, see Figure~\ref{GLM-CHFLS-polr-summary}. The largest absolute values of the $t$-statistics are associated with the self-reported health variable. To interpret the results correctly, we first make sure to understand the definition of the Helmert contrasts. <>= H <- with(CHFLS, contr.helmert(table(R_health))) rownames(H) <- levels(CHFLS$R_health) colnames(H) <- paste(levels(CHFLS$R_health)[-1], "- avg") H @ Let's focus on the probability of being very unhappy. A positive regression coefficient for the first contrast of health means that the probability of being very unhappy is smaller (because of the sign switch in the regression coefficients) for women that reported their health as not good compared to women that reported a poor health. Thus, the results given in Figure~\ref{GLM-CHFLS-polr-summary} indicate that better health leads to happier women, a finding that sits well with our expectations. The other effects are less clear to interpret, also because formal inference is difficult and no $p$-values are displayed in the summary output of Figure~\ref{GLM-CHFLS-polr-summary}. As a remedy, making use of the asymptotic distribution of maximum-likelihood-based estimators, we use the \Rcmd{cftest} function from the \Rpackage{multcomp} package \citep{PKG:multcomp} to compute normal $p$-values assuming that the estimated regression coefficients follow a normal limiting distribution (which is, for \Sexpr{nrow(CHFLS) - 3} observations, not completely unrealistic); the results are given in Figure~\ref{GLM-CHFLS-polr-cftest}. %% mess with the output function <>= library("multcomp") op <- options(digits = 2) cf <- cftest(CHFLS_polr) cftest <- function(x, digits = max(3, getOption("digits") - 3)) { x <- cf cat("\n\t", "Simultaneous Tests for General Linear Hypotheses\n\n") if (!is.null(x$type)) cat("Multiple Comparisons of Means:", x$type, "Contrasts\n\n\n") call <- if (isS4(x$model)) x$model@call else x$model$call if (!is.null(call)) { cat("Fit: ") print(call) cat("\n") } pq <- x$test mtests <- cbind(pq$coefficients, pq$sigma, pq$tstat, pq$pvalues) error <- attr(pq$pvalues, "error") pname <- switch(x$alternativ, less = paste("Pr(<", ifelse(x$df == 0, "z", "t"), ")", sep = ""), greater = paste("Pr(>", ifelse(x$df == 0, "z", "t"), ")", sep = ""), two.sided = paste("Pr(>|", ifelse(x$df == 0, "z", "t"), "|)", sep = "")) colnames(mtests) <- c("Estimate", "Std. Error", ifelse(x$df == 0, "z value", "t value"), pname) type <- pq$type if (!is.null(error) && error > .Machine$double.eps) { sig <- which.min(abs(1/error - (10^(1:10)))) sig <- 1/(10^sig) } else { sig <- .Machine$double.eps } cat("Linear Hypotheses:\n") alt <- switch(x$alternative, two.sided = "==", less = ">=", greater = "<=") rownames(mtests) <- rownames(mtests) printCoefmat(mtests, digits = digits, has.Pvalue = TRUE, P.values = TRUE, eps.Pvalue = sig) switch(type, univariate = cat("(Univariate p values reported)"), `single-step` = cat("(Adjusted p values reported -- single-step method)"), Shaffer = cat("(Adjusted p values reported -- Shaffer method)"), Westfall = cat("(Adjusted p values reported -- Westfall method)"), cat("(Adjusted p values reported --", type, "method)")) cat("\n\n") invisible(x) } @ \renewcommand{\nextcaption}{\R{} output of the \Robject{cftest} function for the proportional odds model fitted to the \Robject{CHFLS} data. \label{GLM-CHFLS-polr-cftest}} \SchunkLabel <>= library("multcomp") cftest(CHFLS_polr) @ \SchunkRaw <>= options(op) @ There seem to be geographical differences and also older and larger women seem to be happier. Other than that, education and income don't seem to contribute much in this model. One remarkable thing about the proportional odds model is that, similar to the quantile regression models presented in Chapter~\ref{QR}, it directly formulates a regression problem in terms of conditional distributions, not only conditional means (the same is trivially true for the binary case in logistic regression). Consequently, the model allows making distributional predictions, in other words, we can infer the predicted distribution or density of happiness in a woman with certain values for the explanatory variables that entered the model. To do so, we focus on the woman corresponding to the first row of the data set: \clearpage <>= CHFLS[1,] @ and repeat these values as often as there are levels in the \Robject{R\_health} factor, and each row is assigned one of these levels <>= nd <- CHFLS[rep(1, nlevels(CHFLS$R_health)),] nd$R_health <- ordered(levels(nd$R_health), labels = levels(nd$R_health)) @ We can now use the \Rcmd{predict} function to compute the density of the response variable \Rcmd{R\_happy} for each of these five hypothetical women: <>= (dens <- predict(CHFLS_polr, newdata = nd, type = "probs")) @ From each row, we get the predicted probability that the self-reported happiness will correspond to the levels shown in the column name. These densities, one for each row in \Robject{nd} and therefore for each level of health, can now be plotted, for example using a conditional barchart, see Figure~\ref{GLM-CHFLS-pred-plot}. We clearly see that better health is associated with greater happiness. \begin{figure} \begin{center} <>= library("lattice") D <- expand.grid(R_health = nd$R_health, R_happy = ordered(LETTERS[1:4])) D$dens <- as.vector(dens) barchart(dens ~ R_happy | R_health, data = D, ylab = "Density", xlab = "Happiness",) @ \caption{Predicted distribution of happiness for hypothetical women with health conditions rating from poor to excellent, with the remaining explanatory variables being the same as for the woman corresponding to the first row in the \Robject{CHFLS} data frame. The levels of happiness have been abbreviated (A: very unhappy, B: not too happy, C: somewhat happy; D: very happy). \label{GLM-CHFLS-pred-plot}} \end{center} \end{figure} We'll present an alternative and maybe simpler model in Chapter~\ref{RP}. \section{Summary of Findings} <>= ci <- round(exp(confint(plasma_glm_1, parm = "fibrinogen")), 2) ci <- paste("(", paste(ci, collapse = ","), ")", sep = "") @ \begin{description} \item[Blood screening] Application of logistic regression shows that an increase of one unit in the fibrinogen value produces approximately a six fold increase in the odds of an ESR value greater than $20$. However, because the number of observations is small the corresponding $95\%$ confidence interval for the odds is rather wide namely, $\Sexpr{ci}$. Gamma globulin values do not help in the prediction of ESR values greater than $20$ over and above the fibrinogen values. \item[Women's role in society] Modeling the probability of agreeing with the statement about women's role in society using logistic regression demonstrates that it is the interaction of education and gender which is of most importance; for fewer years of education women have a higher probability of agreeing with the statement than men, but when the years of education exceed about ten then this situation reverses. \item[Colonic polyps] Fitting a Poisson regression allowing for overdispersion shows that the drug treatment is effective in reducing the number of polyps with age having only a marginal effect. \item[Driving and back pain] Application of conditional logistic regression shows that the odds ratio of a herniated disc occurring in a driver relative to a nondriver is $\Sexpr{round(exp(coef(backpain_glm)[1]),2)}$ with a $95\%$ confidence interval of $\Sexpr{paste("(", paste(round(exp(confint(backpain_glm)[1,]), 2), collapse = ","),")", sep = "")}$. There is no evidence that where a person lives affects the risk of suffering lower back pain. \item[Happiness in China] Better health is associated with greater happiness -- what a surprise! \end{description} \section{Final Comments} Generalized linear models provide a very powerful and flexible framework for the application of regression models to a variety of non-normal response variables, for example, logistic regression to binary responses and Poisson regression to count data. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_analysing_longitudinal_dataI.Rnw0000644000175000017500000003373214133304452022332 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analyzing Longitudinal Data I} %%\VignetteDepends{lme4,multcomp} \setcounter{chapter}{12} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("lme4") library("multcomp") residuals <- function(object) { y <- getME(object, 'y') y - fitted(object) } @ \chapter[Analyzing Longitudinal Data I]{Analyzing Longitudinal Data I: Computerized Delivery of Cognitive Behavioral Therapy -- Beat the Blues \label{ALDI}} \section{Introduction} \section{Analyzing Longitudinal Data} \section{Analysis Using \R{}} \begin{figure} \begin{center} <>= data("BtheB", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) ylim <- range(BtheB[,grep("bdi", names(BtheB))], na.rm = TRUE) tau <- subset(BtheB, treatment == "TAU")[, grep("bdi", names(BtheB))] boxplot(tau, main = "Treated as Usual", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) btheb <- subset(BtheB, treatment == "BtheB")[, grep("bdi", names(BtheB))] boxplot(btheb, main = "Beat the Blues", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) @ \caption{Boxplots for the repeated measures by treatment group for the \Robject{BtheB} data. \label{ALDI:boxplots}} \end{center} \end{figure} We shall fit both random intercept and random intercept and slope models to the data including the baseline BDI values (\Robject{pre.bdi}), \Robject{treatment} group, \Robject{drug}, and \Robject{length} as fixed effect covariates. Linear mixed effects models are fitted in \R{} by using the \Rcmd{lmer} function contained in the \Rpackage{lme4} package \citep{PKG:lme4,HSAUR:PinheiroBates2000,HSAUR:Bates2005}, but an essential first step is to rearrange the data from the `wide form' in which they appear in the \Robject{BtheB} data frame %%' into the `long form' in which each separate repeated measurement %%' and associated covariate values appear as a separate row in a \Rclass{data.frame}. This rearrangement can be made using the following code: <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) @ such that the data are now in the form (here shown for the first three subjects) <>= subset(BtheB_long, subject %in% c("1", "2", "3")) @ The resulting \Rclass{data.frame} \Robject{BtheB\_long} contains a number of missing values \index{Missing values} and in applying the \Rcmd{lmer} function these will be dropped. But notice it is only the missing values that are removed, \stress{not} participants that have at least one missing value. All the available data is used in the model fitting process. The \Rcmd{lmer} function is used in a similar way to the \Rcmd{lm} function met in \Sexpr{ch("MLR")} with the addition of a random term to identify the source of the repeated measurements, here \Robject{subject}. We can fit the two models (\ref{ALDI:ModelA}) and (\ref{ALDI:ModelB}) and test which is most appropriate using <>= library("lme4") BtheB_lmer1 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (1 | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) BtheB_lmer2 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (time | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) anova(BtheB_lmer1, BtheB_lmer2) @ \renewcommand{\nextcaption}{\R{} output of the linear mixed-effects model fit for the \Robject{BtheB} data. \label{ALDI-BtheB-summary}} \SchunkLabel <>= summary(BtheB_lmer1) @ \SchunkRaw The \Rcmd{summary} method for \Rclass{lmer} objects doesn't print $p$-values for Gaussian mixed models because the degrees of freedom of the $t$ reference distribution are not obvious. However, one can rely on the asymptotic normal distribution for computing univariate $p$-values for the fixed effects using the \Rcmd{cftest} function from package \Rpackage{multcomp}. The asymptotic $p$-values are given in Figure~\ref{ALDI-BtheB-summary-p}. \renewcommand{\nextcaption}{\R{} output of the asymptotic $p$-values for linear mixed-effects model fit for the \Robject{BtheB} data. \label{ALDI-BtheB-summary-p}} \SchunkLabel <>= cftest(BtheB_lmer1) @ \SchunkRaw We can check the assumptions of the final model fitted to the \Robject{BtheB} data, i.e., the normality of the random effect terms and the residuals, by first using the \Rcmd{ranef} method to \stress{predict} the former and the \Rcmd{residuals} method to calculate the differences between the observed data values and the fitted values, and then using normal probability plots on each. How the random effects are predicted is explained briefly in Section~\ref{ALDI:predictrandom}. The necessary \R{} code to obtain the effects, residuals, and plots is shown with Figure~\ref{ALDI:qqplots}. There appear to be no large departures from linearity in either plot. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) qint <- ranef(BtheB_lmer1)$subject[["(Intercept)"]] qres <- residuals(BtheB_lmer1) qqnorm(qint, ylab = "Estimated random intercepts", xlim = c(-3, 3), ylim = c(-20, 20), main = "Random intercepts") qqline(qint) qqnorm(qres, xlim = c(-3, 3), ylim = c(-20, 20), ylab = "Estimated residuals", main = "Residuals") qqline(qres) @ \caption{Quantile-quantile plots of predicted random intercepts and residuals for the random intercept model \Robject{BtheB\_lmer1} fitted to the \Robject{BtheB} data. \label{ALDI:qqplots}} \end{center} \end{figure} \begin{figure} \begin{center} <>= bdi <- BtheB[, grep("bdi", names(BtheB))] plot(1:4, rep(-0.5, 4), type = "n", axes = FALSE, ylim = c(0, 50), xlab = "Months", ylab = "BDI") axis(1, at = 1:4, labels = c(0, 2, 3, 5)) axis(2) for (i in 1:4) { dropout <- is.na(bdi[,i + 1]) points(rep(i, nrow(bdi)) + ifelse(dropout, 0.05, -0.05), jitter(bdi[,i]), pch = ifelse(dropout, 20, 1)) } @ \caption{Distribution of BDI values for patients that do (circles) and do not (bullets) attend the next scheduled visit. \label{ALDI-dropout}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_meta_analysis.Rnw0000644000175000017500000003654214133304452017325 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Meta-Analysis} %%\VignetteDepends{rmeta} \setcounter{chapter}{16} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Meta-Analysis]{Meta-Analysis: Nicotine Gum and Smoking Cessation and the Efficacy of BCG Vaccine in the Treatment of Tuberculosis \label{MA}} \section{Introduction} \section{Systematic Reviews and Meta-Analysis} \section{Analysis Using \R{}} The aim in collecting the results from the randomized trials of using nicotine gum to help smokers quit was to estimate the overall \stress{odds ratio}, the odds of quitting smoking for those given the gum, divided by the odds of quitting for those not receiving the gum. Following formula (\ref{MA:barY}), we can compute the pooled odds ratio as follows: <>= data("smoking", package = "HSAUR3") odds <- function(x) (x[1] * (x[4] - x[3])) / ((x[2] - x[1]) * x[3]) weight <- function(x) ((x[2] - x[1]) * x[3]) / sum(x) W <- apply(smoking, 1, weight) Y <- apply(smoking, 1, odds) sum(W * Y) / sum(W) @ Of course, the computations are more conveniently done using the functionality provided in package \Rpackage{rmeta}. The odds ratios and corresponding confidence intervals are computed by means of the \Rcmd{meta.MH} function for fixed effects meta-analysis as shown here <>= library("rmeta") smokingOR <- meta.MH(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking)) @ and the results can be inspected via a \Rcmd{summary} method -- see Figure~\ref{MA-smoking-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{smokingOR}. \label{MA-smoking-summary}} \SchunkLabel <>= summary(smokingOR) @ \SchunkRaw \begin{figure} \begin{center} <>= plot(smokingOR, ylab = "") @ \caption{Forest plot of observed effect sizes and $95\%$ confidence intervals for the nicotine gum studies. \label{MA:smokingplot}} \end{center} \end{figure} We shall use both the fixed effects and random effects approaches here so that we can compare results. For the fixed effects model (see Figure~\ref{MA-smoking-summary}) the estimated overall log-odds ratio is \Sexpr{round(smokingOR$logMH, 3)} with a standard error of \Sexpr{round(smokingOR$selogMH, 3)}. This leads to an estimate of the overall odds ratio of \Sexpr{round(exp(smokingOR$logMH), 3)}, with a 95\% confidence interval as given above. For the random effects model, which is fitted by applying function \Rcmd{meta.DSL} to the \Robject{smoking} data as follows \vspace{1cm} <>= (smokingDSL <- meta.DSL(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking))) @ the corresponding estimate is \Sexpr{round(exp(smokingDSL$logDSL), 3)}. Both models suggest that there is clear evidence that nicotine gum increases the odds of quitting. The random effects confidence interval is considerably wider than that from the fixed effects model; here the test of homogeneity of the studies is not significant implying that we might use the fixed effects results. But the test is not particularly powerful and it is more sensible to assume a priori that heterogeneity is present and so we use the results from the random effects model. \section{Meta-Regression} The examination of heterogeneity of the effect sizes from the studies in a meta-analysis begins with the formal test for its presence, although in most meta-analyses such heterogeneity can almost be assumed to be present. There will be many possible sources of such heterogeneity and estimating how these various factors affect the observed effect sizes in the studies chosen is often of considerable interest and importance, indeed usually more important than the relatively simplistic use of meta-analysis to determine a single summary estimate of overall effect size. We can illustrate the process using the BCG vaccine data. We first find the estimate of the overall effect size from applying the fixed effects and the random effects models described previously: <>= data("BCG", package = "HSAUR3") BCG_OR <- meta.MH(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) BCG_DSL <- meta.DSL(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) @ The results are inspected using the \Rcmd{summary} method as shown in Figures~\ref{MA-BCGOR-summary} and \ref{MA-BCGDSL-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_OR}. \label{MA-BCGOR-summary}} \SchunkLabel <>= summary(BCG_OR) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_DSL}. \label{MA-BCGDSL-summary}} \SchunkLabel <>= summary(BCG_DSL) @ \SchunkRaw To assess how the two covariates, latitude and year, relate to the observed effect sizes we shall use multiple linear regression but will weight each observation by $W_i = (\hat{\sigma}^2 + V_i^2)^{-1}, i = 1, \dots, 13$, where $\hat{\sigma}^2$ is the estimated between-study variance and $V_i^2$ is the estimated variance from the $i$th study. The required \R{} code to fit the linear model via weighted least squares is: \index{Meta-Analysis!weighted least squares regression} <>= studyweights <- 1 / (BCG_DSL$tau2 + BCG_DSL$selogs^2) y <- BCG_DSL$logs BCG_mod <- lm(y ~ Latitude + Year, data = BCG, weights = studyweights) @ and the results of the \Rcmd{summary} method are shown in Figure~\ref{MA-mod-summary}. There is some evidence that latitude is associated with observed effect size, the log-odds ratio becoming increasingly negative as latitude increases, as we can see from a scatterplot of the two variables with the added weighted regression fit seen in Figure~\ref{MA-BCG}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_mod}. \label{MA-mod-summary}} \SchunkLabel <>= summary(BCG_mod) @ \SchunkRaw \begin{figure} \begin{center} <>= plot(y ~ Latitude, data = BCG, ylab = "Estimated log-OR") abline(lm(y ~ Latitude, data = BCG, weights = studyweights)) @ \caption{Plot of observed effect size for the \Robject{BCG} vaccine data against latitude, with a weighted least squares regression fit shown in addition. \label{MA-BCG}} \end{center} \end{figure} \section{Publication Bias} \begin{figure} \begin{center} <>= set.seed(290875) sigma <- seq(from = 1/10, to = 1, length.out = 35) y <- rnorm(35) * sigma gr <- (y > -0.5) layout(matrix(1:2, ncol = 1)) plot(y, 1/sigma, xlab = "Effect size", ylab = "1 / standard error") plot(y[gr], 1/(sigma[gr]), xlim = range(y), xlab = "Effect size", ylab = "1 / standard error") @ \caption{Example funnel plots from simulated data. The asymmetry in the lower plot is a hint that a publication bias might be a problem. \label{MA-funnel}} \end{center} \end{figure} We can construct a funnel plot for the nicotine gum data using the \R{} code depicted with Figure~\ref{MA:funnel}. There does not appear to be any strong evidence of publication bias here. \begin{figure} \begin{center} <>= funnelplot(smokingDSL$logs, smokingDSL$selogs, summ = smokingDSL$logDSL, xlim = c(-1.7, 1.7)) abline(v = 0, lty = 2) @ \caption{Funnel plot for nicotine gum data. \label{MA:funnel}} \end{center} \end{figure} \index{Meta-analysis!funnel plots|)} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_survival_analysis.Rnw0000644000175000017500000004023614133304452020245 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Survival Analysis} %%\VignetteDepends{survival,coin,partykit} \setcounter{chapter}{10} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= x <- library("survival") x <- library("coin") x <- library("partykit") @ \chapter[Survival Analysis]{Survival Analysis: \\ Glioma Treatment and \\ Breast Cancer Survival \label{SA}} \section{Introduction} \section{Survival Analysis} \section{Analysis Using \R{}} \subsection{Glioma Radioimmunotherapy} \begin{figure} \begin{center} <>= data("glioma", package = "coin") library("survival") layout(matrix(1:2, ncol = 2)) g3 <- subset(glioma, histology == "Grade3") plot(survfit(Surv(time, event) ~ group, data = g3), main = "Grade III Glioma", lty = c(2, 1), ylab = "Probability", xlab = "Survival Time in Month", legend.text = c("Control", "Treated"), legend.bty = "n") g4 <- subset(glioma, histology == "GBM") plot(survfit(Surv(time, event) ~ group, data = g4), main = "Grade IV Glioma", ylab = "Probability", lty = c(2, 1), xlab = "Survival Time in Month", xlim = c(0, max(glioma$time) * 1.05)) @ \caption{Survival times comparing treated and control patients. \label{SA-glioma-plot}} \end{center} \end{figure} Figure~\ref{SA-glioma-plot} leads to the impression that patients treated with the novel radioimmunotherapy survive longer, regardless of the tumor type. In order to assess if this informal finding is reliable, we may perform a log-rank test via \index{Log-rank test} <>= survdiff(Surv(time, event) ~ group, data = g3) @ which indicates that the survival times are indeed different in both groups. However, the number of patients is rather limited and so it might be dangerous to rely on asymptotic tests. As shown in \Sexpr{ch("CI")}, conditioning on the data and computing the distribution of the test statistics without additional assumptions are one alternative. The function \Rcmd{surv\_test} from package \Rpackage{coin} \citep{HSAUR:Hothorn:2006:AmStat,PKG:coin} can be used to compute an exact conditional test answering the question whether the survival times differ for grade III patients. For all possible permutations of the groups on the censored response variable, the test statistic is computed and the fraction of whose being greater than the observed statistic defines the exact $p$-value: <>= library("coin") logrank_test(Surv(time, event) ~ group, data = g3, distribution = "exact") @ which, in this case, confirms the above results. The same exercise can be performed for patients with grade IV glioma <>= logrank_test(Surv(time, event) ~ group, data = g4, distribution = "exact") @ which shows a difference as well. However, it might be more appropriate to answer the question whether the novel therapy is superior for both groups of tumors simultaneously. This can be implemented by \stress{stratifying}, or \stress{blocking}, with respect to tumor grading: <>= logrank_test(Surv(time, event) ~ group | histology, data = glioma, distribution = approximate(B = 10000)) @ Here, we need to approximate the exact conditional distribution since the exact distribution is hard to compute. The result supports the initial impression implied by Figure~\ref{SA-glioma-plot}. \subsection{Breast Cancer Survival} Before fitting a Cox model to the \Robject{GBSG2} data, we again derive a Kaplan-Meier estimate of the survival function of the data, here stratified with respect to whether a patient received hormonal therapy or not (see Figure~\ref{SA-GBSG2-plot}). \begin{figure} \begin{center} <>= data("GBSG2", package = "TH.data") plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2), lty = 1:2, mark.time = FALSE, ylab = "Probability", xlab = "Survival Time in Days") legend(250, 0.2, legend = c("yes", "no"), lty = c(2, 1), title = "Hormonal Therapy", bty = "n") @ \caption{Kaplan-Meier estimates for breast cancer patients who either received hormonal therapy or not. \label{SA-GBSG2-plot}} \end{center} \end{figure} Fitting a Cox model follows roughly the same rules as shown for linear models in \Sexpr{ch("MLR")} with the exception that the response variable is again coded as a \Rclass{Surv} object. For the \Robject{GBSG2} data, the model is fitted via <>= GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2) @ and the results as given by the \Rcmd{summary} method are given in Figure~\ref{GBSG2-coxph-summary}. Since we are especially interested in the relative risk for patients who underwent hormonal therapy, we can compute an estimate of the relative risk and a corresponding confidence interval via <>= ci <- confint(GBSG2_coxph) exp(cbind(coef(GBSG2_coxph), ci))["horThyes",] @ This result implies that patients treated with hormonal therapy had a lower risk and thus survived longer compared to women who were not treated this way. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{GBSG2\_coxph}. \label{GBSG2-coxph-summary}} \SchunkLabel <>= summary(GBSG2_coxph) @ \SchunkRaw Model checking and model selection for proportional hazards models are complicated by the fact that easy-to-use residuals, such as those discussed in \Sexpr{ch("MLR")} for linear regression models, are not available, but several possibilities do exist. A check of the proportional hazards assumption can be done by looking at the parameter estimates $\beta_1, \dots, \beta_q$ over time. We can safely assume proportional hazards when the estimates don't vary much over time. %' The null hypothesis of constant regression coefficients can be tested, both globally as well as for each covariate, by using the \Rcmd{cox.zph} function <>= GBSG2_zph <- cox.zph(GBSG2_coxph) GBSG2_zph @ There seems to be some evidence of time-varying effects, \index{Time-varying effects} especially for age and tumor grading. A graphical representation of the estimated regression coefficient over time is shown in Figure~\ref{SA-GBSG2-zph-plot}. We refer to \cite{HSAUR:TherneauGrambsch2000} for a detailed theoretical description of these topics. \begin{figure} \begin{center} <>= plot(GBSG2_zph, var = "age") @ \caption{Estimated regression coefficient for \Robject{age} depending on time for the \Robject{GBSG2} data. \label{SA-GBSG2-zph-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:3, ncol = 3)) res <- residuals(GBSG2_coxph) plot(res ~ age, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "Martingale Residuals") abline(h = 0, lty = 3) plot(res ~ pnodes, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) plot(res ~ log(progrec), data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) @ \caption{Martingale residuals for the \Robject{GBSG2} data. \label{SA-GBSG2-mart-plot}} \end{center} \end{figure} The tree-structured regression models applied to continuous and binary responses in \Sexpr{ch("RP")} are applicable to censored responses in survival analysis as well. Such a simple prognostic model with only a few terminal nodes might be helpful for relating the risk to certain subgroups of patients. Both \Rcmd{rpart} and the \Rcmd{ctree} function from package \Rpackage{partykit} can be applied to the GBSG2 data, where the conditional trees of the latter select cutpoints based on log-rank statistics \index{Conditional tree} <>= GBSG2_ctree <- ctree(Surv(time, cens) ~ ., data = GBSG2) @ and the \Rcmd{plot} method applied to this tree produces the graphical representation in Figure~\ref{SA-GBSG2-ctree-plot}. The number of positive lymph nodes (\Robject{pnodes}) is the most important variable in the tree, corresponding to the $p$-value associated with this variable in Cox's %%'s regression; see Figure~\ref{GBSG2-coxph-summary}. Women with not more than three positive lymph nodes who have undergone hormonal therapy seem to have the best prognosis whereas a large number of positive lymph nodes and a small value of the progesterone receptor indicates a bad prognosis. \begin{figure} \begin{center} <>= plot(GBSG2_ctree) @ \caption{Conditional inference tree for the \Robject{GBSG2} data with the survival function, estimated by Kaplan-Meier, shown for every subgroup of patients identified by the tree. \label{SA-GBSG2-ctree-plot}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/vignettes/Ch_recursive_partitioning.Rnw0000644000175000017500000005514114133304452021266 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Recursive Partitioning} %%\VignetteDepends{vcd,lattice,randomForest,partykit} \setcounter{chapter}{8} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("vcd") library("lattice") library("randomForest") library("partykit") ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) mai <- par("mai") options(SweaveHooks = list(nullmai = function() { par(mai = rep(0, 4)) }, twomai = function() { par(mai = c(0, mai[2], 0, 0)) }, threemai = function() { par(mai = c(0, mai[2], 0.1, 0)) })) numbers <- c("zero", "one", "two", "three", "four", "five", "six", "seven", "eight", "nine") @ \chapter[Recursive Partitioning]{Recursive Partitioning: Predicting Body Fat, Glaucoma Diagnosis, and Happiness in China \label{RP}} \section{Introduction} \section{Recursive Partitioning} \section{Analysis Using \R{}} \subsection{Predicting Body Fat Content} The \Rcmd{rpart} function from \Rpackage{rpart} can be used to grow a regression tree. The response variable and the covariates are defined by a model formula in the same way as for \Rcmd{lm}, say. By default, a large initial tree is grown, we restrict the number of observations required to establish a potential binary split to at least ten: <>= library("rpart") data("bodyfat", package = "TH.data") bodyfat_rpart <- rpart(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat, control = rpart.control(minsplit = 10)) @ A \Rcmd{print} method for \Rclass{rpart} objects is available; however, a graphical representation \citep[here utilizing functionality offered from package \Rpackage{partykit},][]{PKG:partykit} shown in Figure~\ref{RP-bodyfat-plot} is more convenient. Observations that satisfy the condition shown for each node go to the left and observations that don't are an element of the right branch in each node. %' As expected, higher values for waist and hip circumferences and wider knees correspond to higher values of body fat content. The rightmost terminal node consists of only three rather extreme observations. \begin{figure} \begin{center} <>= library("partykit") plot(as.party(bodyfat_rpart), tp_args = list(id = FALSE)) @ \caption{Initial tree for the body fat data with the distribution of body fat in terminal nodes visualized via boxplots. \label{RP-bodyfat-plot}} \end{center} \end{figure} \index{Cross-validation} To determine if the tree is appropriate or if some of the branches need to be subjected to pruning we can use the \Robject{cptable} element of the \Rclass{rpart} object: <>= print(bodyfat_rpart$cptable) opt <- which.min(bodyfat_rpart$cptable[,"xerror"]) @ The \Robject{xerror} column contains estimates of cross-validated prediction error for different numbers of splits (\Robject{nsplit}). The best tree has \Sexpr{numbers[bodyfat_rpart$cptable[opt, "nsplit"] + 1]} splits. Now we can prune back the large initial tree using <>= cp <- bodyfat_rpart$cptable[opt, "CP"] bodyfat_prune <- prune(bodyfat_rpart, cp = cp) @ The result is shown in Figure~\ref{RP-bodyfat-pruneplot}. Note that the inner nodes three and six have been removed from the tree. Still, the rightmost terminal node might give very unreliable extreme predictions. \begin{figure} \begin{center} <>= plot(as.party(bodyfat_prune), tp_args = list(id = FALSE)) @ \caption{Pruned regression tree for body fat data. \label{RP-bodyfat-pruneplot}} \end{center} \end{figure} Given this model, one can predict the (unknown, in real circumstances) body fat content based on the covariate measurements. Here, using the known values of the response variable, we compare the model predictions with the actually measured body fat as shown in Figure~\ref{RP-bodyfat-predict}. The three observations with large body fat measurements in the rightmost terminal node can be identified easily. \begin{figure} \begin{center} <>= DEXfat_pred <- predict(bodyfat_prune, newdata = bodyfat) xlim <- range(bodyfat$DEXfat) plot(DEXfat_pred ~ DEXfat, data = bodyfat, xlab = "Observed", ylab = "Predicted", ylim = xlim, xlim = xlim) abline(a = 0, b = 1) @ \caption{Observed and predicted DXA measurements. \label{RP-bodyfat-predict}} \end{center} \end{figure} \subsection{Glaucoma Diagnosis} <>= set.seed(290875) @ <>= data("GlaucomaM", package = "TH.data") glaucoma_rpart <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 100)) glaucoma_rpart$cptable opt <- which.min(glaucoma_rpart$cptable[,"xerror"]) cp <- glaucoma_rpart$cptable[opt, "CP"] glaucoma_prune <- prune(glaucoma_rpart, cp = cp) @ \setkeys{Gin}{width = 0.65\textwidth} \begin{figure} \begin{center} <>= plot(as.party(glaucoma_prune), tp_args = list(id = FALSE)) @ \caption{Pruned classification tree of the glaucoma data with class distribution in the leaves. \label{RP:gl}} \end{center} \end{figure} \setkeys{Gin}{width=0.95\textwidth} \index{Classification tree!choice of tree size} \index{Tree size} As we discussed earlier, the choice of the appropriately sized tree is not a trivial problem. For the glaucoma data, the above choice of three leaves is very unstable across multiple runs of cross-validation. As an illustration of this problem we repeat the very same analysis as shown above and record the optimal number of splits as suggested by the cross-validation runs. <>= nsplitopt <- vector(mode = "integer", length = 25) for (i in 1:length(nsplitopt)) { cp <- rpart(Class ~ ., data = GlaucomaM)$cptable nsplitopt[i] <- cp[which.min(cp[,"xerror"]), "nsplit"] } @ \newpage <>= table(nsplitopt) @ Although for \Sexpr{sum(nsplitopt == 1)} runs of cross-validation a simple tree with one split only is suggested, larger trees would have been favored in \Sexpr{sum(nsplitopt > 1)} of the cases. This short analysis shows that we should not trust the tree in Figure~\ref{RP:gl} too much. \index{Bagging} \index{Bootstrap approach!glaucoma diagnosis data} One way out of this dilemma is the aggregation of multiple trees via bagging. In \R{}, the bagging idea can be implemented by three or four lines of code. Case count or weight vectors representing the bootstrap samples can be drawn from the multinominal distribution with parameters $n$ and $p_1 = 1/n, \dots, p_n = 1/n$ via the \Rcmd{rmultinom} function. For each weight vector, one large tree is constructed without pruning and the \Rclass{rpart} objects are stored in a list, here called \Robject{trees}: <>= trees <- vector(mode = "list", length = 25) n <- nrow(GlaucomaM) bootsamples <- rmultinom(length(trees), n, rep(1, n)/n) mod <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 0)) for (i in 1:length(trees)) trees[[i]] <- update(mod, weights = bootsamples[,i]) @ The \Rcmd{update} function re-evaluates the call of \Robject{mod}, however, with the weights being altered, i.e., fits a tree to a bootstrap sample specified by the weights. It is interesting to have a look at the structures of the multiple trees. For example, the variable selected for splitting in the root of the tree is not unique as can be seen by <>= table(sapply(trees, function(x) as.character(x$frame$var[1]))) @ Although \Robject{varg} is selected most of the time, other variables such as \Robject{vari} occur as well -- a further indication that the tree in Figure~\ref{RP:gl} is questionable and that hard decisions are not appropriate for the glaucoma data. In order to make use of the ensemble of trees in the list \Robject{trees} we estimate the conditional probability of suffering from glaucoma given the covariates for each observation in the original data set by <>= classprob <- matrix(0, nrow = n, ncol = length(trees)) for (i in 1:length(trees)) { classprob[,i] <- predict(trees[[i]], newdata = GlaucomaM)[,1] classprob[bootsamples[,i] > 0,i] <- NA } @ Thus, for each observation we get \Sexpr{length(trees)} estimates. However, each observation has been used for growing one of the trees with probability $0.632$ and thus was not used with probability $0.368$. Consequently, the estimate from a tree where an observation was not used for growing is better for judging the quality of the predictions and we label the other estimates with \Robject{NA}. Now, we can average the estimates and we vote for glaucoma when the average of the estimates of the conditional glaucoma probability exceeds $0.5$. The comparison between the observed and the predicted classes does not suffer from overfitting since the predictions are computed from those trees for which each single observation was \stress{not} used for growing. <>= avg <- rowMeans(classprob, na.rm = TRUE) predictions <- factor(ifelse(avg > 0.5, "glaucoma", "normal")) predtab <- table(predictions, GlaucomaM$Class) predtab @ Thus, an honest estimate of the probability of a glaucoma prediction when the patient is actually suffering from glaucoma is <>= round(predtab[1,1] / colSums(predtab)[1] * 100) @ per cent. For <>= round(predtab[2,2] / colSums(predtab)[2] * 100) @ percent of normal eyes, the ensemble does not predict glaucomateous damage. \begin{figure} \begin{center} <>= library("lattice") gdata <- data.frame(avg = rep(avg, 2), class = rep(as.numeric(GlaucomaM$Class), 2), obs = c(GlaucomaM[["varg"]], GlaucomaM[["vari"]]), var = factor(c(rep("varg", nrow(GlaucomaM)), rep("vari", nrow(GlaucomaM))))) panelf <- function(x, y) { panel.xyplot(x, y, pch = gdata$class) panel.abline(h = 0.5, lty = 2) } print(xyplot(avg ~ obs | var, data = gdata, panel = panelf, scales = "free", xlab = "", ylab = "Estimated Class Probability Glaucoma")) @ \caption{Estimated class probabilities depending on two important variables. The $0.5$ cut-off for the estimated glaucoma probability is depicted as a horizontal line. Glaucomateous eyes are plotted as circles and normal eyes are triangles. \label{RP:glplot}} \end{center} \end{figure} \index{Random forest} The bagging procedure is a special case of a more general approach called \stress{random forest} \citep{HSAUR:Breiman2001b}. The package \Rpackage{randomForest} \citep{PKG:randomForest} can be used to compute such ensembles via <>= library("randomForest") rf <- randomForest(Class ~ ., data = GlaucomaM) @ and we obtain out-of-bag estimates for the prediction error via <>= table(predict(rf), GlaucomaM$Class) @ \subsection{Trees Revisited} For the body fat data, such a \stress{conditional inference tree} can be computed using the \Rcmd{ctree} function \index{Conditional tree} <>= bodyfat_ctree <- ctree(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat) @ This tree doesn't require a pruning procedure because an internal stop criterion based on formal statistical tests prevents the procedure from overfitting the data. The tree structure is shown in Figure~\ref{RP-bodyfat-ctree-plot}. Although the structure of this tree and the tree depicted in Figure~\ref{RP-bodyfat-pruneplot} are rather different, the corresponding predictions don't vary too much. \begin{figure} \begin{center} <>= plot(bodyfat_ctree, tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of body fat content shown for each terminal leaf. \label{RP-bodyfat-ctree-plot}} \end{center} \end{figure} Very much the same code is needed to grow a tree on the glaucoma data: <>= glaucoma_ctree <- ctree(Class ~ ., data = GlaucomaM) @ and a graphical representation is depicted in Figure~\ref{RP-glaucoma-ctree-plot} showing both the cutpoints and the $p$-values of the associated independence tests for each node. The first split is performed using a cutpoint defined with respect to the volume of the optic nerve above some reference plane, but in the inferior part of the eye only (\Robject{vari}). \begin{figure} \begin{center} <>= plot(glaucoma_ctree, tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of glaucomateous eyes shown for each terminal leaf. \label{RP-glaucoma-ctree-plot}} \end{center} \end{figure} \subsection{Happiness in China} \index{Chinese Health and Family Life Survey} A conditional inference tree is a simple alternative to the proportional odds model for the regression analysis of the happiness variable from the Chinese Health and Family Life Survey. In each node, a linear association test introduced in Section~\ref{CI:Lanza} taking the ordering of the happiness levels into account is applied for selecting variables and split-points. Before we fit the tree with the \Rcmd{ctree} function, we recode the levels of the happiness variable to allow plotting of these symbols with restricted page space: \newpage <>= levels(CHFLS$R_happy) levels(CHFLS$R_happy) <- LETTERS[1:4] CHFLS_ctree <- ctree(R_happy ~ ., data = CHFLS) @ The resulting tree is depicted in Figure~\ref{RP-CHFLS-ctree-plot} and very nicely backs up the results obtained from the proportional odds model in Chapter~\ref{GLM}. The distribution of self-reported happiness is shifted from very unhappy to very happy with increasing values of self-reported health, i.e., women that reported excellent health (mind the $>$ sign in the right label of the root split!) were at least somewhat happy with only a few exceptions. Women with poor or not good health reported being not too happy much more often. There seems to be further differentiation with respect to geography and also income but the differences in the distributions depicted in the terminal leaves are negligible. \begin{figure} \begin{center} <>= plot(CHFLS_ctree, ep_args = list(justmin = 10), tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of self-reported happiness shown for each terminal leaf. The levels of happiness have been abbreviated (A: very unhappy, B: not too happy, C: somewhat happy; D: very happy). The \Rcmd{justmin} argument ensures that split descriptions longer than $10$ characters are displayed over two lines. \label{RP-CHFLS-ctree-plot}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/build/0000755000175000017500000000000014133304605012447 5ustar nileshnileshHSAUR3/build/vignette.rds0000644000175000017500000000224014133304605015004 0ustar nileshnileshV͓4&a] C? 0Mݙ%anV d$9dKlI9rpb>~O~E(D1!<0DG: g[I*8[QUV+|q2g7}2x,!@- )[AڀdTD4` zWW{Wp&/ξΚݙp `boPȇWߧvF+2;F1.r m|lˌ;{1!-rnz fSԱlMSYk.ӪÅl ݕfɢTBɺtjj^. II'zqA\CQ8"ӪJB:>7I񉀨CMlLufPձh>}Y"% N{s,WܼKΌ ߐ&t$͉=. 1) { nr <- ceiling(nrow(object$data) / pcol) object$data <- rbind(object$data, matrix(" ", nrow = nr * pcol - nrow(object$data), ncol = nc)) d <- NULL for (i in 1:pcol) d <- cbind(d, object$data[((i - 1) * nr + 1):(i * nr),]) object$data <- d } RET <- c() if (index) RET <- c(RET, paste("\\index{", object$xname, " data@\\Robject{", object$xname, "} data}", sep = "")) RET <- c(RET, "\\begin{center}") if (rownames) RET <- c(RET, paste("\\begin{longtable}{l", paste(rep(paste(rep("r", nc), collapse = ""), pcol), collapse = "|"), "}", collapse = "")) else RET <- c(RET, paste("\\begin{longtable}{", paste(rep(paste(rep("r", nc), collapse = ""), pcol), collapse = "|"), "}", collapse = "")) if (topcaption) RET <- c(RET, caption(object$xname, label, caption, object$pkg), "\\\\") RET <- c(RET, "\\hline") vn <- rep(object$varnames, pcol) vn <- paste(paste("\\Robject{", vn, sep = ""), "}", sep = "") if (rownames) { RET <- c(RET, paste(" & ", isep(vn), "\\\\ \\hline")) RET <- c(RET, "\\endfirsthead") RET <- c(RET, paste("\\caption[]{\\Robject{", object$xname, "} data (continued).} \\\\", sep = "", collapse = "")) RET <- c(RET, "\\hline") RET <- c(RET, paste(" & ", isep(vn), "\\\\ \\hline")) RET <- c(RET, "\\endhead") for (i in 1:nrow(object$data)) RET <- c(RET, paste(object$rownames[i], " & ", isep(object$data[i,]), "\\\\")) } else { RET <- c(RET, paste(isep(vn), "\\\\ \\hline")) RET <- c(RET, "\\endfirsthead") RET <- c(RET, paste("\\caption[]{\\Robject{", object$xname, "} data (continued).} \\\\", sep = "", collapse = "")) RET <- c(RET, "\\hline") RET <- c(RET, paste(isep(vn), "\\\\ \\hline")) RET <- c(RET, "\\endhead") RET <- c(RET, apply(object$data, 1, function(x) paste(isep(x), "\\\\"))) } RET <- c(RET, "\\hline") if (!topcaption) RET <- c(RET, caption(object$xname, label, caption, object$pkg)) RET <- c(RET, "\\end{longtable}") RET <- c(RET, "\\end{center}") class(RET) <- "Latex" return(RET) } HSAUR3/R/isi2bibtex.R0000644000175000017500000000727412357775376014001 0ustar nileshnilesh isi2bibtex <- function(file) { journals <- rbind(c("J. Am. Stat. Assoc.", "Journal of the American Statistical Association", "JASA"), c("J. Stat. Plan. Infer.", "Journal of Statistical Planning and Inference", "JSPI"), c("Biom. J.", "Biometrical Journal", "BJ"), c("Stat. Med.", "Statistics in Medicine", "SiM")) colnames(journals) <- c("Abbr", "Title", "ID") tfile <- tempfile() isitxt <- readLines(file) isitxt <- gsub("(^[A-Z][A-Z,0-9])", "\\1:", isitxt, perl = TRUE) writeLines(isitxt, con = tfile) isidcf <- read.dcf(tfile, fields = c("PT", "AU", "TI", "SO", "LA", "DT", "DE", "ID", "AB", "C1", "RP", "EM", "NR", "TC", "PU", "PI", "PA", "SN", "J9", "JI", "PD", "PY", "VL", "IS", "BP", "EP", "PG", "SC", "GA", "UT")) ### journals only isidcf <- isidcf[isidcf[,"PT"] == "J",] ### missings isidcf <- isidcf[!apply(isidcf, 1, function(x) all(is.na(x))),] ### rename interesting fields cn <- colnames(isidcf) colnames(isidcf)[cn == "AU"] <- "author" colnames(isidcf)[cn == "TI"] <- "title" colnames(isidcf)[cn == "JI"] <- "journal" colnames(isidcf)[cn == "PD"] <- "month" colnames(isidcf)[cn == "PY"] <- "year" colnames(isidcf)[cn == "VL"] <- "volumne" colnames(isidcf)[cn == "IS"] <- "number" colnames(isidcf)[cn == "UT"] <- "isitag" colnames(isidcf)[cn == "DE"] <- "keywords" colnames(isidcf)[cn == "TC"] <- "timescited" colnames(isidcf)[cn == "AB"] <- "abstract" rownames(isidcf) <- 1:nrow(isidcf) isidcf[,"title"] <- gsub("\n", " ", isidcf[,"title"]) ### author names for (i in 1:nrow(isidcf)) { au <- strsplit(isidcf[i,"author"], "\n") names <- strsplit(au[[1]], ", ") for (j in 1:length(names)) names[[j]][2] <- paste(strsplit(names[[j]][2], "")[[1]], ". ", sep = "", collapse = "") lastnames <- sapply(names, function(x) gsub(" ", "", x[1])) if (length(lastnames) > 3) lastnames <- lastnames[1:3] jour <- isidcf[i,"journal"] indx <- journals[, "Abbr"] == jour if (sum(indx) == 1) { isidcf[i, "journal"] <- journals[indx, "Title"] jkey <- journals[indx, "ID"] } else { jkey <- gsub("\\.* ", "", jour) } label <- paste(paste(lastnames, collapse = "+"), ":", jkey, ":", isidcf[i,"year"], sep = "") rownames(isidcf)[i] <- label isidcf[i,"author"] <- paste(sapply(names, function(x) paste(x[2], x[1], sep = "")), collapse = " and ") title <- isidcf[i, "title"] if (!identical(toupper(title), title)) { ttmp <- strsplit(title, " ")[[1]] lower <- tolower(ttmp) != ttmp lower[1] <- FALSE ttmp[lower] <- paste("{", ttmp[lower], "}", sep = "") isidcf[i, "title"] <- paste(ttmp, collapse = " ") } } tags <- c("author", "title", "journal", "month", "year", "volumne", "number", "isitag", "abstract", "keywords", "timescited") isidcf[is.na(isidcf[,"month"]), "month"] <- "" for (tag in tags) isidcf[,tag] <- paste(tag, " = {", isidcf[,tag], "},", sep = "") pages <- paste("pages = {", isidcf[, "BP"], "--", isidcf[, "EP"], "},", sep = "") headerkey <- paste("@article{", rownames(isidcf), ",", sep = "") ret <- vector(mode = "list", length = nrow(isidcf)) for (i in 1:nrow(isidcf)) ret[[i]] <- c(headerkey[i], paste(" ", isidcf[i, tags]), paste(" ", pages[i]), "}", " ") unlist(ret) } HSAUR3/R/Rwelcome.R0000644000175000017500000000240312357775376013477 0ustar nileshnilesh Rwelcome <- function() { tversion <- paste(version$major, version$minor, sep = ".") tdate <- paste(version$year, version$month, version$day, sep = "-") x <- c(paste("R : Copyright", version$year, "The R Foundation for Statistical Computing"), paste("Version", tversion, paste("(", tdate, "),", sep = ""), "ISBN 3-900051-07-0"), " ", "R is free software and comes with ABSOLUTELY NO WARRANTY.", "You are welcome to redistribute it under certain conditions.", "Type 'license()' or 'licence()' for distribution details.", " ", "R is a collaborative project with many contributors.", "Type 'contributors()' for more information and", "'citation()' on how to cite R or R packages in publications.", " ", "Type 'demo()' for some demos, 'help()' for on-line help, or", "'help.start()' for an HTML browser interface to help.", "Type 'q()' to quit R.", ">") cat(paste(x, collapse = "\n")) } exename <- function() { tversion <- paste(version$major, "0", substr(version$minor, 1, 1), substr(version$minor,3,3), sep = "") return(paste("rw", tversion, ".exe", sep = "")) } HSAUR3/R/tools.R0000644000175000017500000001765612374663573013074 0ustar nileshnilesh ### some tools that make life easier ### copy *Rout to *Rout.save cpRoutsave <- function(Routdir = NULL, Routsavedir = NULL) { Routfiles <- list.files(path = Routdir, pattern = "\\.Rout$", full.names = FALSE) srcfiles <- file.path(Routdir, Routfiles) destfiles <- file.path(Routsavedir, paste(Routfiles, ".save", sep = "")) file.copy(srcfiles, destfiles, overwrite = TRUE) } ### attach all data frames in the global environment gattach <- function() { env <- globalenv() var <- eval(parse(text = "ls()"), envir = env) df <- sapply(var, function(x) eval(parse(text = paste("is.data.frame(", x, ")", sep = "", collapse = "")), envir = env)) if (any(df)) { var <- var[df] out <- sapply(var, function(x) eval(parse(text = paste("attach(", x, ")", sep = "", collapse = "")), envir = env)) } } ### extract and check Robject or Rcmd LaTeX markup extRact <- function(file, what = "Robject") { x <- readLines(file) indx <- grep(what, x) out <- sapply(indx, function(i) { obj <- NULL while (TRUE) { where <- regexpr(what, x[i]) if (where != -1) { x[i] <- substring(x[i], where) dm <- delimMatch(x[i]) obj <- c(obj, (substring(x[i], dm + 1, dm + attr(dm, "match.length") - 2))) x[i] <- substring(x[i], dm + attr(dm, "match.length")) } else { break } } return(obj) }) cmds <- unique(gsub("\\\\", "", out)) gattach() for (cmd in cmds) { a <- try(eval(parse(text = cmd))) if (class(a) == "try-error") print(a) } cmds } ### try to polish S{in,out}put environments, this needs ### manual refinements in some places prettyS <- function(file, texenvironment = c("Sinput", "Soutput"), width = 63, split = " ", write = TRUE) { ### handle Sinput or Soutput environments texenvironment <- match.arg(texenvironment) if (texenvironment == "Sinput" && split == " ") split <- c(", ", "/", " ") ### dirty hack: in `Makefile's I want to call `prettyS' ### right after weaving and thus have only `file.Rnw' available if (length(grep("Rnw$", file)) > 0) file <- gsub("Rnw$", "tex", file) ### read file x <- readLines(file) ### remove all end-line spaces x <- gsub("\\s+$", "", x) ### determine begin and end lines of environment start <- grep(paste("^\\\\begin\\{", texenvironment, "\\}$", sep = "", collapse = ""), x) end <- grep(paste("^\\\\end\\{", texenvironment, "\\}$", sep = "", collapse = ""), x) if (length(start) == 0) return(NULL) if (length(start) != length(end)) stop("unbalanced begin and end statements") n <- length(start) for (i in 1:n) { ### iterate over all lines longer than width lines <- (start[i]):(end[i]) lines <- lines[sapply(x[lines], nchar) > width] for (line in lines) { cat("prettyS: line ", line, " too long: \n", x[line], "\n") y <- x[line] add <- sapply(split, function(s) ifelse(length(grep(s, y)) > 0, nchar(s), 0)) if (all(add == 0)) next() s <- split[min(which(add > 0))] y <- unlist(strsplit(y, split = s)) nc <- sapply(y, nchar) + add[min(which(add > 0))] pos <- cumsum(nc) <= width if (!any(pos)) next() newline <- cumsum(nc)[max(which(pos))] plus <- length(grep("^\\+", x[line])) > 0 && substr(x[line], newline - 1, newline) != ", " x[line] <- paste(substr(x[line], 1, newline), "\n", ifelse(texenvironment == "Sinput", options("continue"), ""), ifelse(plus, " ", ""), " ", substr(x[line], newline + 1, nchar(x[line])), sep = "", collapse = "") # if (length(grep("^\\+", x[line + 1])) > 0 && # (nchar(x[line + 1]) + (nchar(x[line]) - newline) < width)) { # y <- x[line + 1] # y <- gsub("^\\+ ", "", y) # x[line] <- paste(x[line], y, sep = "", collapse = "") # x[line + 1] <- "" # } cat("prettyS: ", x[line], "\n") } } if (write) writeLines(x, con = file) } ### extract all Sinput environments from tex files chkS <- function(file, texenvironment = "Sinput") { ### read file x <- readLines(file) ### determine begin and end lines of environment start <- grep(paste("^\\\\begin\\{", texenvironment, "\\}$", sep = "", collapse = ""), x) end <- grep(paste("^\\\\end\\{", texenvironment, "\\}$", sep = "", collapse = ""), x) if (length(start) == 0) return(NULL) if (length(start) != length(end)) stop("unbalanced begin and end statements") n <- length(start) y <- NULL for (i in 1:n) { ### iterate over all lines longer than width lines <- (start[i] + 1):(end[i] - 1) x[lines] <- gsub("^R>", "", x[lines]) x[lines] <- gsub("^\\+", "", x[lines]) y <- c(y, x[lines]) } y } ### read in a BibTeX file and return as list readBibtex <- function(file = NULL) { bib <- readLines(file) entries <- grep("^@", bib) labels <- gsub(",$", "", gsub("^@[A-Za-z].*\\{", "", bib[entries])) if (any(duplicated(labels))) { print(labels[duplicated(labels)]) stop("non-unique BibTeX labels in ", file) } biblist <- vector(mode = "list", length = length(entries)) for (i in 1:length(entries)) { nexte <- ifelse(i == length(entries), length(entries), entries[i + 1] - 1) biblist[[i]] <- bib[entries[i]:nexte] empty <- grep("^$", biblist[[i]]) if (length(empty) > 0) biblist[[i]] <- biblist[[i]][-empty] } names(biblist) <- labels class(biblist) <- "txtBibtex" return(biblist) } ### the subset of a BibTeX database actually used in `file' extractBibtex <- function(file, bibtex) { if (class(bibtex) != "txtBibtex") bibtex <- readBibtex(bibtex) tex <- readLines(file) tex <- tex[grep("\\cite", tex)] enames <- gsub("\\+", "\\\\+", names(bibtex)) cited <- sapply(enames, function(name) length(grep(name, tex)) > 0) biblist <- bibtex[cited] class(biblist) <- "txtBibtex" return(biblist) } ### output to a file toBibtex.txtBibtex <- function(object, ...) { tmp <- lapply(object, function(bib) { cat(paste(bib, "\n")) cat("\n\n") }) } ### set package version in BibTeX (quick'n'dirty hack) pkgversions <- function(file) { x <- readLines(file) indx <- grep("VERSION", x) for (i in indx) { xx <- strsplit(x[i], " ")[[1]] xx <- xx[grep("VERSION", xx)] pkg <- gsub("[},]", "", gsub("VERSION", "", xx)) version <- packageDescription(pkg)$Version x[i] <- gsub(paste(pkg, "VERSION", sep = "", collapse = ""), version, x[i]) } class(x) <- "Latex" x } ### set package date in BibTeX (quick'n'dirty hack) pkgyears <- function(file) { x <- readLines(file) indx <- grep("PKGYEAR", x) for (i in indx) { xx <- strsplit(x[i], " ")[[1]] xx <- xx[grep("PKGYEAR", xx)] pkg <- gsub("[{},]", "", gsub("PKGYEAR", "", xx)) year <- format(as.Date(strsplit(packageDescription(pkg)$Built, ";")[[1]][3]),"%Y") x[i] <- gsub(paste(pkg, "PKGYEAR", sep = "", collapse = ""), year, x[i]) } class(x) <- "Latex" x } pkgs <- function() c("scatterplot3d", "alr3", "ape", "coin", "flexmix", "gee", "ipred", "lme4", "mclust", "party", "randomForest", "rmeta", "vcd", "gamair", "multcomp", "sandwich", "mboost") HSAUR3/R/citations.R0000644000175000017500000000121012357775376013712 0ustar nileshnilesh HSAURcite <- function(pkg) { ct <- citation(pkg) attr(ct, "label") <- paste("PKG:", pkg, sep = "", collapse = "") for (n in c("note")) ct[[n]] <- gsub("R", "\\R{}", ct[[n]]) class(ct) <- "HSAURcitation" return(ct) } toBibtex.HSAURcitation <- function (object, ...) { z <- paste("@", attr(object, "entry"), "{", attr(object, "label"), ",", sep = "") if ("author" %in% names(object)) { object$author <- toBibtex(object$author) } for (n in names(object)) z <- c(z, paste(" ", n, " = {", object[[n]], "},", sep = "")) z <- c(z, "}") class(z) <- "Bibtex" z } HSAUR3/inst/0000755000175000017500000000000014133304604012324 5ustar nileshnileshHSAUR3/inst/LaTeXBibTeX/0000755000175000017500000000000014133304614014340 5ustar nileshnileshHSAUR3/inst/LaTeXBibTeX/refstyle.bst0000755000175000017500000006715712357775377016762 0ustar nileshnilesh%% %% This is file `refstyle.bst', %% generated with the docstrip utility. %% %% The original source files were: %% %% merlin.mbs (with options: `,ay,nat,nm-rev,keyxyr,dt-beg,yr-par,note-yr,tit-qq,vnum-x,volp-com,add-pub,pre-pub,isbn,issn,url,url-blk,edby,edbyx,blk-com,pp,ed,xedn') %% ---------------------------------------- %% %% Copyright 1994-1999 Patrick W Daly % =============================================================== % IMPORTANT NOTICE: % This bibliographic style (bst) file has been generated from one or % more master bibliographic style (mbs) files, listed above. % % This generated file can be redistributed and/or modified under the terms % of the LaTeX Project Public License Distributed from CTAN % archives in directory macros/latex/base/lppl.txt; either % version 1 of the License, or any later version. % =============================================================== % Name and version information of the main mbs file: % \ProvidesFile{merlin.mbs}[1999/05/28 3.89 (PWD)] % For use with BibTeX version 0.99a or later %------------------------------------------------------------------- % This bibliography style file is intended for texts in ENGLISH % This is an author-year citation style bibliography. As such, it is % non-standard LaTeX, and requires a special package file to function properly. % Such a package is natbib.sty by Patrick W. Daly % The form of the \bibitem entries is % \bibitem[Jones et al.(1990)]{key}... % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}... % The essential feature is that the label (the part in brackets) consists % of the author names, as they should appear in the citation, with the year % in parentheses following. There must be no space before the opening % parenthesis! % With natbib v5.3, a full list of authors may also follow the year. % In natbib.sty, it is possible to define the type of enclosures that is % really wanted (brackets or parentheses), but in either case, there must % be parentheses in the label. % The \cite command functions as follows: % \citet{key} ==>> Jones et al. (1990) % \citet*{key} ==>> Jones, Baker, and Smith (1990) % \citep{key} ==>> (Jones et al., 1990) % \citep*{key} ==>> (Jones, Baker, and Smith, 1990) % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990) % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32) % \citeauthor{key} ==>> Jones et al. % \citeauthor*{key} ==>> Jones, Baker, and Smith % \citeyear{key} ==>> 1990 %--------------------------------------------------------------------- ENTRY { address author booktitle chapter edition editor howpublished institution isbn issn journal key month note number organization pages publisher school series title type url volume year } {} { label extra.label sort.label short.list } INTEGERS { output.state before.all mid.sentence after.sentence after.block } FUNCTION {init.state.consts} { #0 'before.all := #1 'mid.sentence := #2 'after.sentence := #3 'after.block := } STRINGS { s t } FUNCTION {output.nonnull} { 's := output.state mid.sentence = { ", " * write$ } { output.state after.block = { add.period$ write$ newline$ "\newblock " write$ } { output.state before.all = 'write$ { add.period$ " " * write$ } if$ } if$ mid.sentence 'output.state := } if$ s } FUNCTION {output} { duplicate$ empty$ 'pop$ 'output.nonnull if$ } FUNCTION {output.check} { 't := duplicate$ empty$ { pop$ "empty " t * " in " * cite$ * warning$ } 'output.nonnull if$ } FUNCTION {fin.entry} { add.period$ write$ newline$ } FUNCTION {new.block} { output.state before.all = 'skip$ { after.block 'output.state := } if$ } FUNCTION {new.sentence} { output.state after.block = 'skip$ { output.state before.all = 'skip$ { after.sentence 'output.state := } if$ } if$ } FUNCTION {add.blank} { " " * before.all 'output.state := } FUNCTION {date.block} { skip$ } FUNCTION {not} { { #0 } { #1 } if$ } FUNCTION {and} { 'skip$ { pop$ #0 } if$ } FUNCTION {or} { { pop$ #1 } 'skip$ if$ } FUNCTION {non.stop} { duplicate$ "}" * add.period$ #-1 #1 substring$ "." = } FUNCTION {new.block.checkb} { empty$ swap$ empty$ and 'skip$ 'new.block if$ } FUNCTION {field.or.null} { duplicate$ empty$ { pop$ "" } 'skip$ if$ } FUNCTION {emphasize} { duplicate$ empty$ { pop$ "" } { "{\em " swap$ * "\/}" * } if$ } FUNCTION {capitalize} { "u" change.case$ "t" change.case$ } FUNCTION {space.word} { " " swap$ * " " * } % Here are the language-specific definitions for explicit words. % Each function has a name bbl.xxx where xxx is the English word. % The language selected here is ENGLISH FUNCTION {bbl.and} { "and"} FUNCTION {bbl.etal} { "et~al." } FUNCTION {bbl.editors} { "eds." } FUNCTION {bbl.editor} { "ed." } FUNCTION {bbl.edby} { "edited by" } FUNCTION {bbl.edition} { "edition" } FUNCTION {bbl.volume} { "volume" } FUNCTION {bbl.of} { "of" } FUNCTION {bbl.number} { "number" } FUNCTION {bbl.nr} { "no." } FUNCTION {bbl.in} { "in" } FUNCTION {bbl.pages} { "pp." } FUNCTION {bbl.page} { "p." } FUNCTION {bbl.chapter} { "chapter" } FUNCTION {bbl.techrep} { "Technical Report" } FUNCTION {bbl.mthesis} { "Master's thesis" } FUNCTION {bbl.phdthesis} { "Ph.D. thesis" } MACRO {jan} {"January"} MACRO {feb} {"February"} MACRO {mar} {"March"} MACRO {apr} {"April"} MACRO {may} {"May"} MACRO {jun} {"June"} MACRO {jul} {"July"} MACRO {aug} {"August"} MACRO {sep} {"September"} MACRO {oct} {"October"} MACRO {nov} {"November"} MACRO {dec} {"December"} MACRO {acmcs} {"ACM Computing Surveys"} MACRO {acta} {"Acta Informatica"} MACRO {cacm} {"Communications of the ACM"} MACRO {ibmjrd} {"IBM Journal of Research and Development"} MACRO {ibmsj} {"IBM Systems Journal"} MACRO {ieeese} {"IEEE Transactions on Software Engineering"} MACRO {ieeetc} {"IEEE Transactions on Computers"} MACRO {ieeetcad} {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} MACRO {ipl} {"Information Processing Letters"} MACRO {jacm} {"Journal of the ACM"} MACRO {jcss} {"Journal of Computer and System Sciences"} MACRO {scp} {"Science of Computer Programming"} MACRO {sicomp} {"SIAM Journal on Computing"} MACRO {tocs} {"ACM Transactions on Computer Systems"} MACRO {tods} {"ACM Transactions on Database Systems"} MACRO {tog} {"ACM Transactions on Graphics"} MACRO {toms} {"ACM Transactions on Mathematical Software"} MACRO {toois} {"ACM Transactions on Office Information Systems"} MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} MACRO {tcs} {"Theoretical Computer Science"} FUNCTION {format.url} { url empty$ { "" } { "\urlprefix\url{" url * "}" * } if$ } INTEGERS { nameptr namesleft numnames } FUNCTION {format.names} { 's := "" 't := #1 'nameptr := s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ s nameptr "{ll}" format.name$ duplicate$ "others" = { 't := } { pop$ } if$ t "others" = { " " * bbl.etal * } { bbl.and space.word * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {format.names.ed} { 's := "" 't := #1 'nameptr := s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{f.~}{vv~}{ll}{, jj}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ s nameptr "{ll}" format.name$ duplicate$ "others" = { 't := } { pop$ } if$ t "others" = { " " * bbl.etal * } { bbl.and space.word * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {format.key} { empty$ { key field.or.null } { "" } if$ } FUNCTION {format.authors} { author empty$ { "" } { author format.names } if$ } FUNCTION {format.editors} { editor empty$ { "" } { editor format.names ", " * editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ * } if$ } FUNCTION {format.in.editors} { editor empty$ { "" } { editor format.names.ed } if$ } FUNCTION {format.isbn} { isbn empty$ { "" } { "ISBN " isbn * } if$ } FUNCTION {format.issn} { issn empty$ { "" } { "ISSN " issn * } if$ } FUNCTION {format.note} { note empty$ { "" } { note #1 #1 substring$ duplicate$ "{" = 'skip$ { output.state mid.sentence = { "l" } { "u" } if$ change.case$ } if$ note #2 global.max$ substring$ * } if$ } FUNCTION {format.title} { title empty$ { "" } { title "t" change.case$ "\enquote{" swap$ * non.stop { ",} " * } { "} " * } if$ } if$ } FUNCTION {end.quote.title} { title empty$ 'skip$ { before.all 'output.state := } if$ } FUNCTION {format.full.names} {'s := "" 't := #1 'nameptr := s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv~}{ll}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { s nameptr "{ll}" format.name$ duplicate$ "others" = { 't := } { pop$ } if$ t "others" = { " " * bbl.etal * } { numnames #2 > { "," * } 'skip$ if$ bbl.and space.word * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {author.editor.key.full} { author empty$ { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.full.names } if$ } { author format.full.names } if$ } FUNCTION {author.key.full} { author empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { author format.full.names } if$ } FUNCTION {editor.key.full} { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.full.names } if$ } FUNCTION {make.full.names} { type$ "book" = type$ "inbook" = or 'author.editor.key.full { type$ "proceedings" = 'editor.key.full 'author.key.full if$ } if$ } FUNCTION {output.bibitem} { newline$ "\bibitem[{" write$ label write$ ")" make.full.names duplicate$ short.list = { pop$ } { * } if$ "}]{" * write$ cite$ write$ "}" write$ newline$ "" before.all 'output.state := } FUNCTION {n.dashify} { 't := "" { t empty$ not } { t #1 #1 substring$ "-" = { t #1 #2 substring$ "--" = not { "--" * t #2 global.max$ substring$ 't := } { { t #1 #1 substring$ "-" = } { "-" * t #2 global.max$ substring$ 't := } while$ } if$ } { t #1 #1 substring$ * t #2 global.max$ substring$ 't := } if$ } while$ } FUNCTION {word.in} { bbl.in " " * } FUNCTION {format.date} { year duplicate$ empty$ { "empty year in " cite$ * "; set to ????" * warning$ pop$ "????" } 'skip$ if$ extra.label * before.all 'output.state := " (" swap$ * ")" * } FUNCTION {format.btitle} { title emphasize } FUNCTION {tie.or.space.connect} { duplicate$ text.length$ #3 < { "~" } { " " } if$ swap$ * * } FUNCTION {either.or.check} { empty$ 'pop$ { "can't use both " swap$ * " fields in " * cite$ * warning$ } if$ } FUNCTION {format.bvolume} { volume empty$ { "" } { bbl.volume volume tie.or.space.connect series empty$ 'skip$ { bbl.of space.word * series emphasize * } if$ "volume and number" number either.or.check } if$ } FUNCTION {format.number.series} { volume empty$ { number empty$ { series field.or.null } { output.state mid.sentence = { bbl.number } { bbl.number capitalize } if$ number tie.or.space.connect series empty$ { "there's a number but no series in " cite$ * warning$ } { bbl.in space.word * series * } if$ } if$ } { "" } if$ } FUNCTION {format.edition} { edition empty$ { "" } { output.state mid.sentence = { edition "l" change.case$ " " * bbl.edition * } { edition "t" change.case$ " " * bbl.edition * } if$ } if$ } INTEGERS { multiresult } FUNCTION {multi.page.check} { 't := #0 'multiresult := { multiresult not t empty$ not and } { t #1 #1 substring$ duplicate$ "-" = swap$ duplicate$ "," = swap$ "+" = or or { #1 'multiresult := } { t #2 global.max$ substring$ 't := } if$ } while$ multiresult } FUNCTION {format.pages} { pages empty$ { "" } { pages multi.page.check { bbl.pages pages n.dashify tie.or.space.connect } { bbl.page pages tie.or.space.connect } if$ } if$ } FUNCTION {format.journal.pages} { pages empty$ 'skip$ { duplicate$ empty$ { pop$ format.pages } { ", " * pages n.dashify * } if$ } if$ } FUNCTION {format.vol.num.pages} { volume field.or.null format.journal.pages } FUNCTION {format.chapter.pages} { chapter empty$ 'format.pages { type empty$ { bbl.chapter } { type "l" change.case$ } if$ chapter tie.or.space.connect pages empty$ 'skip$ { ", " * format.pages * } if$ } if$ } FUNCTION {format.in.ed.booktitle} { booktitle empty$ { "" } { editor empty$ { word.in booktitle emphasize * } { word.in booktitle emphasize * ", " * editor num.names$ #1 > { bbl.editors } { bbl.editor } if$ * " " * format.in.editors * } if$ } if$ } FUNCTION {format.thesis.type} { type empty$ 'skip$ { pop$ type "t" change.case$ } if$ } FUNCTION {format.tr.number} { type empty$ { bbl.techrep } 'type if$ number empty$ { "t" change.case$ } { number tie.or.space.connect } if$ } FUNCTION {format.article.crossref} { word.in " \cite{" * crossref * "}" * } FUNCTION {format.book.crossref} { volume empty$ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ word.in } { bbl.volume volume tie.or.space.connect bbl.of space.word * } if$ " \cite{" * crossref * "}" * } FUNCTION {format.incoll.inproc.crossref} { word.in " \cite{" * crossref * "}" * } FUNCTION {format.org.or.pub} { 't := "" address empty$ t empty$ and 'skip$ { address empty$ 'skip$ { address * } if$ t empty$ 'skip$ { address empty$ 'skip$ { ": " * } if$ t * } if$ } if$ } FUNCTION {format.publisher.address} { publisher empty$ { "empty publisher in " cite$ * warning$ "" } { publisher } if$ format.org.or.pub } FUNCTION {format.organization.address} { organization empty$ { "" } { organization } if$ format.org.or.pub } FUNCTION {article} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { journal emphasize "journal" output.check format.vol.num.pages output } { format.article.crossref output.nonnull format.pages output } if$ format.issn output format.url output format.note output fin.entry } FUNCTION {book} { output.bibitem author empty$ { format.editors "author and editor" output.check editor format.key output } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ format.date "year" output.check date.block format.btitle "title" output.check crossref missing$ { format.bvolume output format.number.series output format.publisher.address output } { format.book.crossref output.nonnull } if$ format.edition output format.isbn output format.url output format.note output fin.entry } FUNCTION {booklet} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title howpublished output address output format.isbn output format.url output format.note output fin.entry } FUNCTION {inbook} { output.bibitem author empty$ { format.editors "author and editor" output.check editor format.key output } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ format.date "year" output.check date.block format.btitle "title" output.check crossref missing$ { format.publisher.address output format.bvolume output format.chapter.pages "chapter and pages" output.check format.number.series output } { format.chapter.pages "chapter and pages" output.check format.book.crossref output.nonnull } if$ format.edition output crossref missing$ { format.isbn output } 'skip$ if$ format.url output format.note output fin.entry } FUNCTION {incollection} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { format.in.ed.booktitle "booktitle" output.check format.publisher.address output format.bvolume output format.number.series output format.chapter.pages output format.edition output format.isbn output } { format.incoll.inproc.crossref output.nonnull format.chapter.pages output } if$ format.url output format.note output fin.entry } FUNCTION {inproceedings} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title crossref missing$ { format.in.ed.booktitle "booktitle" output.check publisher empty$ { format.organization.address output } { organization output format.publisher.address output } if$ format.bvolume output format.number.series output format.pages output format.isbn output format.issn output } { format.incoll.inproc.crossref output.nonnull format.pages output } if$ format.url output format.note output fin.entry } FUNCTION {conference} { inproceedings } FUNCTION {manual} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.btitle "title" output.check organization output address output format.edition output format.url output format.note output fin.entry } FUNCTION {mastersthesis} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.btitle "title" output.check bbl.mthesis format.thesis.type output.nonnull school "school" output.check address output format.url output format.note output fin.entry } FUNCTION {misc} { output.bibitem format.authors output author format.key output format.date "year" output.check date.block format.title output end.quote.title howpublished output format.url output format.note output fin.entry } FUNCTION {phdthesis} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.btitle "title" output.check bbl.phdthesis format.thesis.type output.nonnull school "school" output.check address output format.url output format.note output fin.entry } FUNCTION {proceedings} { output.bibitem format.editors output editor format.key output format.date "year" output.check date.block format.btitle "title" output.check format.bvolume output format.number.series output publisher empty$ { format.organization.address output } { organization output format.publisher.address output } if$ format.isbn output format.issn output format.url output format.note output fin.entry } FUNCTION {techreport} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title format.tr.number output.nonnull institution "institution" output.check address output format.url output format.note output fin.entry } FUNCTION {unpublished} { output.bibitem format.authors "author" output.check author format.key output format.date "year" output.check date.block format.title "title" output.check end.quote.title format.url output format.note "note" output.check fin.entry } FUNCTION {default.type} { misc } READ FUNCTION {sortify} { purify$ "l" change.case$ } INTEGERS { len } FUNCTION {chop.word} { 's := 'len := s #1 len substring$ = { s len #1 + global.max$ substring$ } 's if$ } FUNCTION {format.lab.names} { 's := "" 't := s #1 "{vv~}{ll}" format.name$ s num.names$ duplicate$ #2 > { pop$ " " * bbl.etal * } { #2 < 'skip$ { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = { " " * bbl.etal * } { bbl.and space.word * s #2 "{vv~}{ll}" format.name$ * } if$ } if$ } if$ } FUNCTION {author.key.label} { author empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { author format.lab.names } if$ } FUNCTION {author.editor.key.label} { author empty$ { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } { author format.lab.names } if$ } FUNCTION {editor.key.label} { editor empty$ { key empty$ { cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } FUNCTION {calc.short.authors} { type$ "book" = type$ "inbook" = or 'author.editor.key.label { type$ "proceedings" = 'editor.key.label 'author.key.label if$ } if$ 'short.list := } FUNCTION {calc.label} { calc.short.authors short.list "(" * year duplicate$ empty$ short.list key field.or.null = or { pop$ "????" } 'skip$ if$ * 'label := } FUNCTION {sort.format.names} { 's := #1 'nameptr := "" s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" format.name$ 't := nameptr #1 > { " " * namesleft #1 = t "others" = and { "zzzzz" * } { t sortify * } if$ } { t sortify * } if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {sort.format.title} { 't := "A " #2 "An " #3 "The " #4 t chop.word chop.word chop.word sortify #1 global.max$ substring$ } FUNCTION {author.sort} { author empty$ { key empty$ { "to sort, need author or key in " cite$ * warning$ "" } { key sortify } if$ } { author sort.format.names } if$ } FUNCTION {author.editor.sort} { author empty$ { editor empty$ { key empty$ { "to sort, need author, editor, or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } { author sort.format.names } if$ } FUNCTION {editor.sort} { editor empty$ { key empty$ { "to sort, need editor or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } FUNCTION {presort} { calc.label label sortify " " * type$ "book" = type$ "inbook" = or 'author.editor.sort { type$ "proceedings" = 'editor.sort 'author.sort if$ } if$ #1 entry.max$ substring$ 'sort.label := sort.label * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {presort} SORT STRINGS { last.label next.extra } INTEGERS { last.extra.num number.label } FUNCTION {initialize.extra.label.stuff} { #0 int.to.chr$ 'last.label := "" 'next.extra := #0 'last.extra.num := #0 'number.label := } FUNCTION {forward.pass} { last.label label = { last.extra.num #1 + 'last.extra.num := last.extra.num int.to.chr$ 'extra.label := } { "a" chr.to.int$ 'last.extra.num := "" 'extra.label := label 'last.label := } if$ number.label #1 + 'number.label := } FUNCTION {reverse.pass} { next.extra "b" = { "a" 'extra.label := } 'skip$ if$ extra.label 'next.extra := extra.label duplicate$ empty$ 'skip$ { "{\natexlab{" swap$ * "}}" * } if$ 'extra.label := label extra.label * 'label := } EXECUTE {initialize.extra.label.stuff} ITERATE {forward.pass} REVERSE {reverse.pass} FUNCTION {bib.sort.order} { sort.label " " * year field.or.null sortify * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {bib.sort.order} SORT FUNCTION {begin.bib} { preamble$ empty$ 'skip$ { preamble$ write$ newline$ } if$ "\begin{thebibliography}{" number.label int.to.str$ * "}" * write$ newline$ "\newcommand{\enquote}[1]{``#1''}" write$ newline$ "\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi" write$ newline$ "\expandafter\ifx\csname url\endcsname\relax" write$ newline$ " \def\url#1{{\tt #1}}\fi" write$ newline$ "\expandafter\ifx\csname urlprefix\endcsname\relax\def\urlprefix{URL }\fi" write$ newline$ } EXECUTE {begin.bib} EXECUTE {init.state.consts} ITERATE {call.type$} FUNCTION {end.bib} { newline$ "\end{thebibliography}" write$ newline$ } EXECUTE {end.bib} %% End of customized bst file %% %% End of file `jasa.bst'. HSAUR3/inst/LaTeXBibTeX/setup.Rnw0000644000175000017500000000316212627003544016176 0ustar nileshnilesh \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} HSAUR3/inst/LaTeXBibTeX/HSAUR.bib0000644000175000017500000023027112357775377015735 0ustar nileshnilesh> library(utils); library(HSAUR2); HSAUR2:::pkgyears("tmp") > library(utils); library(HSAUR2); HSAUR2:::pkgversions("HSAUR.in") @manual{HSAUR:R, title = {R: A Language and Environment for Statistical Computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:AItR, title = {An Introduction to R}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:RDIE, title = {R Data Import/Export}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:RIA, title = {R Installation and Administration}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @manual{HSAUR:WRE, title = {Writing R Extensions}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org}, } @book{HSAUR:Ripley1996, key = {216}, author = {Ripley, Brian D.}, title = {{Pattern} Recognition and Neural Networks}, year = {1996}, publisher = {Cambridge University Press}, address = {Cambridge, UK}, url = {http://www.stats.ox.ac.uk/pub/PRNN/}, pages = 403 } %% Chapter: Analysing Longitudinal Data @article{HSAUR:WatkinsWilliams1998, author = {E. Watkins and R. Williams}, title = {The efficacy of cognitive behavioural therapy}, journal = {Journal of Counseling and Clinical Psychology}, year = 1998, volume = 27, pages = {31-39} } %% et al? @article{HSAUR:Proudfootetal2003, author = {J. Proudfoot and D. Goldberg and A. Mann and B. S. Everitt and I. Marks and J. A. Gray}, title = {Computerized, interactive, multimedia cognitive-behavioural program for anxiety and depression in general practice}, journal = {Psychological Medicine}, year = 2003, volume = 33, number = 2, pages = {217-227} } %% edition? @manual{HSAUR:Becketal1996, author = {A. Beck and R. Steer and G. Brown}, title = {BDI-II Manual}, year = 1996, edition = {2nd}, organization = {The Psychological Corporation, San Antonio} } @book{HSAUR:Diggleetal2003, author = {P. J. Diggle and P. J. Heagerty and K. Y. Liang and S. L. Zeger}, title = {Analysis of Longitudinal Data}, year = {2003}, publisher = {Oxford University Press}, address = {Oxford, UK} } @book{HSAUR:Longford1993, author = {N. T. Longford}, title = {Random Coefficient Models}, year = {1993}, publisher = {Oxford University Press}, address = {Oxford, UK} } @article{HSAUR:Rubin1976, author = {D. Rubin}, title = {Inference and missing data}, journal = {Biometrika}, year = 1976, volume = 63, pages = {581-592} } @article{HSAUR:MurrayFindlay1988, author = {G. D. Murray and J. G. Findlay}, title = {Correcting for bias caused by dropouts in hypertension trials}, journal = {Statistics in Medicine}, year = 1988, volume = 7, pages = {941-946} } @article{HSAUR:DiggleKenward1994, author = {P. J. Diggle and M. G. Kenward}, title = {Informative dropout in longitudinal data analysis}, journal = {Journal of the Royal Statistical Society, Series C}, year = 1994, volume = 43, pages = {49-93} } @article{HSAUR:Carpenteretal2002, author = {J. Carpenter and S. Pocock and C. J. Lamm}, title = {Coping with missing data in clinical trials: {A} model-based approach applied to asthma trials}, journal = {Statistics in Medicine}, year = 2002, volume = {21}, pages = {1043-1066} } @incollection{HSAUR:Diggle1998, author = {P. J. Diggle}, title = {Dealing with missing values in longitudinal studies}, year = 1998, booktitle = {Statistical Analysis of Medical Data}, editor = {B. S. Everitt and G. Dunn}, publisher = {Arnold}, address = {London, UK} } @book{HSAUR:Everitt2002, author = {B. S. Everitt}, title = {Modern Medical Statistics}, year = 2002, publisher = {Arnold}, address = {London, UK} } @article{HSAUR:Heitjan1997, author = {D. F. Heitjan}, title = {Annotation: {W}hat can be done about missing data? {A}pproaches to imputation}, journal = {American Journal of Public Health}, year = 1997, volume = 87, pages = {548-550} } @book{HSAUR:MayorFrei2003, author = {M. Mayor and P. Frei}, title = {New Worlds in the Cosmos: {T}he Discovery of Exoplanets}, publisher = {Cambridge University Press}, year = 2003, address = {Cambridge, UK} } %%% check volume and pages @article{HSAUR:MayorQueloz1995, author = {M. Mayor and D. Queloz}, title = {A {J}upiter-mass companion to a solar-type star}, journal = {Nature}, year = 1995, volume = {378}, pages = {355} } @article{HSAUR:EverittBullmore1999, author = {B. S. Everitt and E. T. Bullmore}, title = {Mixture model mapping of brain activation in functional magnetic resonance images}, journal = {Human Brain Mapping}, year = 1999, volume = 7, pages = {1-14} } @book{HSAUR:Everittetal2001, author = {B. S. Everitt and S. Landau and M. Leese}, title = {Cluster Analysis}, publisher = {Arnold}, year = 2001, edition = {4th}, address = {London, UK} } @book{HSAUR:Gordon1999, author = {A. Gordon}, title = {Classification}, year = 1999, edition = {2nd}, publisher = {Chapman \& Hall/CRC}, address = {Boca Raton, Florida, USA} } @article{HSAUR:ScottSymons1971, author = {A. J. Scott and M. J. Symons}, title = {Clustering methods based on likelihood ratio criteria}, journal = {Biometrics}, year = 1971, volume = 27, pages = {387-398} } @article{HSAUR:BanfieldRaftery1993, author = {J. D. Banfield and A. E. Raftery}, title = {Model-based {G}aussian and non-{G}aussian clustering}, year = 1993, journal = {Biometrics}, volume = 49, pages = {803-821} } @article{HSAUR:FraleyRaftery1999, author = {G. Fraley and A. E. Raftery}, title = {{MCLUST: S}oftware for model-based cluster analysis}, journal = {Journal of Classification}, year = 1999, volume = 16, pages = {297-306} } @article{HSAUR:FriedmanRubin1967, author = {H. P. Friedman and J. Rubin}, title = {On some invariant criteria for grouping data}, journal = {Journal of the American Statistical Association}, year = 1967, volume = 62, pages = {1159-1178} } @article{HSAUR:Marriott1982, author = {F. H. C. Marriott}, title = {Optimization methods of cluster analysis}, journal = {Biometrika}, year = 1982, volume = 69, pages = {417-421} } @article{HSAUR:Dempsteretal1977, author = {A. P. Dempster and N. M. Laird and D. B. Rubin}, title = {Maximum likelihood from incomplete data via the {EM} algorithm {(C/R: p22-37)}}, journal = {Journal of the Royal Statistical Society, Series B}, year = 1977, volume = 39, pages = {1-22} } @article{HSAUR:DubesJain1979, author = {R. Dubes and A. K. Jain}, title = {Validity studies in clustering methodologies}, journal = {Pattern Recognition}, year = 1979, volume = 8, pages = {247-260} } @article{HSAUR:Tubbetal1980, author = {A. Tubb and N. J. Parker and G. Nickless}, title = {The analysis of {Romano-British} pottery by atomic absorption spectrophotometry}, journal = {Archaeometry}, year = 1980, volume = 22, pages = {153-171} } @article{HSAUR:Alonetal1999, author = {U. Alon and N. Barkai and D. A. Notternam and K. Gish and S. Ybarra and D. Mack and A. J. Levine}, title = {Broad patterns of gene expressions revealed by clustering analysis of tumour and normal colon tissues probed by oligonucleotide arrays}, journal = {Cell Biology}, year = 1999, volume = 99, pages = {6754-6760} } @article{HSAUR:Woodleyetal1977, author = {W. L. Woodley and J. Simpson and R. Biondini and J. Berkeley}, title = {Rainfall results 1970-75: {F}lorida area cumulus experiment}, year = {1977}, journal = {Science}, volume = {195}, pages = {735-742} } @book{HSAUR:EfronTibshirani1993, author = {B. Efron and R. J. Tibshirani}, title = {An Introduction to the Bootstrap}, year = {1993}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:CookWeisberg1982, author = {R. D. Cook and S. Weisberg}, title = {Residuals and Influence in Regression}, year = {1982}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:VenablesRipley2002, author = {William N. Venables and Brian D. Ripley}, title = {Modern Applied Statistics with {S}}, edition = {4th}, publisher = {Springer-Verlag}, address = {New York, USA}, year = 2002, note = {{ISBN} 0-387-95457-0}, url = {http://www.stats.ox.ac.uk/pub/MASS4/} } @book{HSAUR:McLachlanPeel2000, author = {G. McLachlan and D. Peel}, title = {Finite Mixture Models}, year = 2000, publisher = {John Wiley \& Sons}, address = {New York, USA} } @article{HSAUR:Pearson1894, author = {Karl Pearson}, title = {Contributions to the mathematical theory of evolution}, year = 1894, journal = {Philosophical Transactions A}, volume = 185, pages = {71-110} } @book{HSAUR:Scott1992, author = {D. W. Scott}, title = {Multivariate Density Estimation}, year = 1992, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Silverman1986, author = {B. Silverman}, title = {Density Estimation}, year = 1986, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @book{HSAUR:Simonoff1996, author = {J. S. Simonoff}, title = {Smoothing Methods in Statistics}, year = 1996, publisher = {Springer-Verlag}, address = {New York, USA} } @article{HSAUR:VanismaGreve1972, author = {F. Vanisma and J. P. {De Greve}}, title = {Close binary systems before and after mass transfer}, journal = {Astrophysics and Space Science}, year = 1972, volume = 87, pages = {377-401} } @book{HSAUR:WandJones1995, author = {M. P. Wand and M. C. Jones}, title = {Kernel Smoothing}, year = 1995, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Wilkinson1992, author = {L. Wilkinson}, title = {Graphical displays}, journal = {Statistical Methods in Medical Research}, year = 1992, volume = 1, pages = {3-25} } %% An Introduction to R @book{HSAUR:Becker+Chambers+Wilks:1988, author = {Richard A. Becker and John M. Chambers and Allan R. Wilks}, title = {The New {S} Language}, publisher = {Chapman \& Hall}, year = 1988, address = {London, UK}, } @book{HSAUR:Chambers+Hastie:1992, author = {John M. Chambers and Trevor J. Hastie}, title = {Statistical Models in {S}}, publisher = {Chapman \& Hall}, year = 1992, address = {London, UK}, } @book{HSAUR:Chambers:1998, author = {John M. Chambers}, title = {Programming with Data}, publisher = {Springer-Verlag}, year = 1998, address = {New York, USA}, } %% Simple Inference @book{HSAUR:Agresti1996, author = {A. Agresti}, title = {An Introduction to Categorical Data Analysis}, year = 1996, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Everitt1992, author = {Brian S. Everitt}, title = {The Analysis of Contingency Tables}, year = 1992, edition = {2nd}, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Haberman1973, author = {S. J. Haberman}, title = {The analysis of residuals in cross-classified tables}, journal = {Biometrics}, year = 1973, volume = 29, pages = {205-220} } @book{HSAUR:Handetal1994, author = {D. J. Hand and F. Daly and A. D. Lunn and K. J. McConway and E. Ostrowski}, title = {A Handbook of Small Datasets}, year = 1994, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:Mann1981, author = {L. Mann}, title = {The baiting crowd in episodes of threatened suicide}, journal = {Journal of Personality and Social Psychology}, year = 1981, volume = 41, pages = {703-709} } @article{HSAUR:MehtaPatel1983, author = {Cyrus R. Mehta and Nitin R. Patel}, title = {A Network Algorithm for Performing {F}isher's Exact Test in $r \times c $ Contingency Tables}, journal = {Journal of the American Statistical Association}, pages = {427-434}, year = {1983}, month = {June}, volume = {78}, number = {382} } @book{HSAUR:Fisher1935, author = {R. A. Fisher}, title = {The Design of Experiments}, year = 1935, publisher = {Oliver and Boyd}, address = {Edinburgh, UK} } @article{HSAUR:Pitman1937, author = {E. J. G. Pitman}, title = {Significance tests which may be applied to samples from any populations}, journal = {Biometrika}, year = 1937, volume = 29, pages = {322-335} } @book{HSAUR:Barlowetal1972, author = {R. E. Barlow and D. J. Bartholomew and J. M. Bremner and H. D. Brunk}, title = {Statistical Inference under Order Restrictions}, year = 1972, publisher = {John Wiley \& Sons}, address = {New York, USA} } @article{HSAUR:Corbetetal1970, author = {G. B. Corbet and J. Cummins and S. R. Hedges and W. J. Krzanowski}, title = {The taxonomic structure of {B}ritish water voles, genus \textit{Arvicola}}, year = 1970, journal = {Journal of Zoology}, volume = 61, pages = {301-316} } @book{HSAUR:EverittRabeHesketh1997, author = {B. S. Everitt and S. Rabe-Hesketh}, title = {The Analysis of Proximity Data}, year = 1997, publisher = {Arnold}, address = {London, UK} } @book{HSAUR:EverittRabeHesketh2001, author = {B. S. Everitt and S. Rabe-Hesketh}, title = {Analysing Medical Data Using {S-Plus}}, year = 2001, publisher = {Springer-Verlag}, address = {New York, USA} } @book{HSAUR:SkrondalRabeHesketh2004, author = {A. Skrondal and S. Rabe-Hesketh}, year = 2004, title = {Generalized Latent Variable Modeling: {M}ultilevel, Longitudinal and Structural Equation Models}, publisher = {Chapman \& Hall/CRC}, address = {Boca Raton, Florida, USA} } @article{HSAUR:Kruskal1964a, author = {Joseph. B. Kruskal}, title = {Multidimensional scaling by optimizing goodness-of-fit to a nonmetric hypothesis}, journal = {Psychometrika}, year = 1964, volume = 29, pages = {1-27} } @article{HSAUR:Kruskal1964b, author = {Joseph B. Kruskal}, title = {Nonmetric multidimensional scaling: {A} numerical method}, journal = {Psychometrika}, year = 1964, volume = 29, pages = {115-129} } @book{HSAUR:Mardiaetal1979, author = {K. V. Mardia and J. T. Kent and J. M. Bibby}, title = {Multivariate Analysis}, year = 1979, publisher = {Academic Press}, address = {London, UK} } @book{HSAUR:Romesburg1984, author = {H. C. Romesburg}, title = {Cluster Analysis for Researchers}, year = 1984, publisher = {Lifetime Learning Publications}, address = {Belmont, CA} } @article{HSAUR:Shepard1962a, author = {Roger N. Shepard}, title = {The analysis of proximities: {M}ultidimensional scaling with unknown distance function {Part I}}, journal = {Psychometrika}, year = 1962, volume = 27, pages = {125-140} } @article{HSAUR:Shepard1962b, author = {Roger N. Shepard}, title = {The analysis of proximities: {M}ultidimensional scaling with unknown distance function {Part II}}, journal = {Psychometrika}, volume = 27, year = 1962, pages = {219-246} } @article{HSAUR:Sibson1979, author = {R. Sibson}, title = {Studies in the robustness of multidimensional scaling. {P}erturbational analysis of classical scaling}, journal = {Journal of the Royal Statistical Society, Series B}, volume = 41, year = 1979, pages = {217-229} } @article{HSAUR:YoungHouseholder1938, author = {G. Young and A. S. Householder}, title = {Discussion of a set of points in terms of their mutual distances}, year = 1938, journal = {Psychometrika}, volume = 3, pages = {19-22} } ### OUP, New York??? @book{HSAUR:Petitti2000, author = {D. B. Petitti}, title = {Meta-Analysis, Decision Analysis and Cost-Effectiveness Analysis}, year = 2000, publisher = {Oxford University Press}, address = {New York, USA} } @article{HSAUR:DeMets1987, author = {D. L. DeMets}, title = {Methods for combining randomized clinical trials: strengths and limitations}, journal = {Statistics in Medicine}, year = 1987, volume = 6, pages = {341-350} } @article{HSAUR:Bailey1987, author = {K. R. Bailey}, title = {Inter-study differences: how should they influence the interpretation of results?}, journal = {Statistics in Medicine}, year = 1987, volume = 6, pages = {351-360} } @article{HSAUR:SuttonAbrams2001, author = {A. J. Sutton and K. R. Abrams}, title = {Bayesian methods in meta-analysis and evidence synthesis}, year = 2001, journal = {Statistical Methods in Medical Research}, volume = 10, pages = {277-303} } @book{HSAUR:Suttonetal2000, author = {A. J. Sutton and K. R. Abrams and D. R. Jones and T. A. Sheldon}, title = {Methods for Meta-Analysis in Medical Research}, year = 2000, publisher = {John Wiley \& Sons}, address = {Chichester, UK} } @article{HSAUR:Woolf1955, author = {B. Woolf}, title = {On estimating the relationship between blood groups and disease}, journal = {Annals of Human Genetics}, year = 1955, volume = 19, pages = {251-253} } @article{HSAUR:Sterlin1959, author = {T. D. Sterlin}, title = {Publication decisions and their possible effects on inferences drawn from tests of significance-or vice versa}, year = 1959, journal = {Journal of the American Statistical Association}, volume = 54, pages = {30-34} } @article{HSAUR:Greenwald1975, author = {A. G. Greenwald}, title = {Consequences of prejudice against the null hypothesis}, year = 1975, journal = {Psychological Bulletin}, volume = {82}, number = 1, pages = {1-20} } @article{HSAUR:Smith1980, author = {M. L. Smith}, title = {Publication bias and meta-analysis}, year = 1980, journal = {Evaluating Education}, volume = 4, pages = {22-93} } @article{HSAUR:Easterbrooketal1991, author = {P. J. Easterbrook and J. A. Berlin and R. Gopalan and D. R. Matthews}, title = {Publication bias in research}, year = 1991, journal = {Lancet}, volume = 337, pages = {867-872} } @article{HSAUR:DuvalTweedie2000, author = {S. Duval and R. L. Tweedie}, title = {A nonparametric `trim and fill' method of accounting for publication bias in meta-analysis}, year = 2000, journal = {Journal of the American Statistical Association}, volume = 95, pages = {89-98} } @article{HSAUR:Oakes1993, author = {M. 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Cook}, title = {Generalized linear model}, booktitle = {Encyclopedia of Biostatistics}, year = 1998, publisher = {John Wiley \& Sons}, address = {Chichester, UK}, editor = {P. Armitage and T. Colton} } @book{HSAUR:Everitt2001, author = {B. S. Everitt}, title = {Statistics for Psychologists}, year = 2001, publisher = {Lawrence Erlbaum}, address = {Mahwah, New Jersey, USA} } @article{HSAUR:Giardielloetal1993, author = {F. M. Giardiello and S. R. Hamilton and A. J. Krush and S. Piantadosi and L. M. Hylind and P. Celano and S. V. Booker and C. R. Robinson and G. J. A. Offerhaus}, title = {Treatment of colonic and rectal adenomas with sulindac in familial adenomatous polyposis}, year = 1993, journal = {New England Journal of Medicine}, volume = 328, number = 18, pages = {1313-1316} } @article{HSAUR:GreenwoodYule1920, author = {M. Greenwood and G. U. Yule}, title = {An inquiry into the nature of frequency distribution of multiple happenings with particular reference of multiple attacks of disease or of repeated accidents}, year = 1920, journal = {Journal of the Royal Statistical Society}, volume = 83, pages = {255-279} } @book{HSAUR:McCullaghNelder1989, author = {P. McCullagh and J. A. Nelder}, title = {Generalized Linear Models}, year = 1989, publisher = {Chapman \& Hall/CRC}, address = {London, UK} } @article{HSAUR:NelderWedderburn1972, author = {J. A. Nelder and R. W. M. Wedderburn}, title = {Generalized linear models}, year = 1972, journal = {Journal of the Royal Statistical Society, Series A}, volume = 135, pages = {370-384} } @book{HSAUR:Piantadosi1997, author = {S. Piantadosi}, title = {Clinical Trials: A Methodologic Perspective}, year = 1997, publisher = {John Wiley \& Sons}, address = {New York, USA} } @article{HSAUR:Davis1991, author = {C. S. 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Liang}, title = {Longitudinal data analysis for discrete and continuous outcomes}, year = 1986, journal = {Biometrics}, volume = 42, number = 1, pages = {121-130} } @article{HSAUR:Lanzaetal1989, author = {F. L. Lanza and D. Fakouhi and A. Rubin and R. E. Davis and M. F. Rack and C. Nissen and S. Geis}, title = {A double-blind placebo-controlled comparison of the efficacy and safety of 50, 100, and 200 micrograms of misoprostol {QID} in the prevention of {I}buprofen-induced gastric and duodenal mucosal lesions and symptoms}, journal = {American Journal of Gastroenterology}, volume = {84}, number = {6}, pages = {633-636}, year = 1989 } @article{HSAUR:Lanzaetal1988a, author = {F. L. Lanza and R. L. Aspinall and E. A. Swabb and R. E. Davis and M. F. Rack and A. Rubin}, title = {Double-blind, placebo-controlled endoscopic comparison of the mucosal protective effects of misoprostol versus cimetidine on tolmetin-induced mucosal injury to the stomach and duodenum}, journal = {Gastroenterology}, volume = {95}, number = {2}, pages = {289-294}, year = 1988 } @article{HSAUR:Lanzaetal1988b, author = {F. L. Lanza and K. Peace and L. Gustitus and M. F. Rack and B. Dickson}, title = {A blinded endoscopic comparative study of misoprostol versus sucralfate and placebo in the prevention of aspirin-induced gastric and duodenal ulceration}, journal = {American Journal of Gastroenterology}, volume = {83}, number = {2}, pages = {143-146}, year = 1988 } @article{HSAUR:Lanza1987, author = {F. L. Lanza}, title = {A double-blind study of prophylactic effect of misoprostol on lesions of gastric and duodenal mucosa induced by oral administration of tolmetin in healthy subjects}, journal = {British Journal of Clinical Practice}, volume = 40, month = {May suppl}, pages = {91-101}, year = 1987, } @article{HSAUR:WhiteheadJones1994, author = {Anne Whitehead and Nicola M. B. Jones}, title = {A meta-analysis of clinical trials involving different classifications of response into ordered categories}, journal = {Statistics in Medicine}, volume = {13}, pages = {2503-2515}, year = 1994, } @article{HSAUR:Carlinetal2000, author = {John B. Carlin and Louise M. Ryan and Elizabeth A. Harvey and Lewis B. Holmes}, title = {Anticonvulsant Teratogenesis 4: Inter-Rater Agreement in Assessing Minor Physical Features Related to Anticonvulsant Therapy}, journal = {Teratology}, volume = 62, pages = {406-412}, year = 2000 } @book{HSAUR:Edgington1987, author = {Eugene S. Edgington}, title = {Randomization Tests}, publisher = {Marcel Dekker}, year = 1987, address = {New York, USA} } @techreport{HSAUR:TherneauAtkinson1997, author = {Terry M. Therneau and Elizabeth J. Atkinson}, title = {An Introduction to Recursive Partitioning using the rpart Routine}, institution = {Section of Biostatistics, Mayo Clinic}, year = {1997}, address = {Rochester, USA}, number = {61}, url = {http://www.mayo.edu/hsr/techrpt/61.pdf} } @book{HSAUR:Pesarin2001, author = {Fortunato Pesarin}, title = {Multivariate Permutation Tests: With Applications to Biostatistics}, year = {2001}, publisher = {John Wiley \& Sons}, address = {Chichester, UK} } @book{HSAUR:Breimanetal1984, author = {L. Breiman and J. H. Friedman and R. A. Olshen and C. J. Stone}, title = {Classification and Regression Trees}, year = {1984}, publisher = {Wadsworth}, address = {California, USA} } @article{HSAUR:Breiman1996, author = {Leo Breiman}, title = {Bagging Predictors}, journal = {Machine Learning}, pages = {123-140}, year = {1996}, volume = {24}, number = {2} } @article{HSAUR:Mardinetal2003, author = {Christian Y. Mardin and Torsten Hothorn and Andrea Peters and Anselm G J{\"u}nemann and Nhung X Nguyen and Berthold Lausen}, title = {New Glaucoma Classification Method based on standard {HRT} parameters by bagging classification trees}, journal = {Journal of Glaucoma}, pages = {340-346}, year = {2003}, volume = {12}, number = {4} } @article{HSAUR:Breiman2001a, author = {Leo Breiman}, title = {Statistical Modeling: The Two Cultures}, journal = {Statistical Science}, pages = {199-231}, year = {2001}, volume = {16}, number = {3}, note = {with discussion} } @article{HSAUR:Breiman2001b, author = {Leo Breiman}, title = {Random Forests}, journal = {Machine Learning}, pages = {5-32}, year = {2001}, volume = {45}, number = {1} } @article{HSAUR:GarczarekWeihs2003, author = {Ursula Maria Garczarek and Claus Weihs}, title = {Standardizing the comparison of partitions}, journal = {Computational Statistics}, pages = {143-162}, year = {2003}, volume = {18}, number = {1} } @article{HSAUR:Murthy1998, author = {Sreerama K. Murthy}, title = {Automatic Construction of Decision Trees from Data: A Multi-Disciplinary Survey}, journal = {Data Mining and Knowledge Discovery}, pages = {345-389}, year = {1998}, volume = {2} } @incollection{HSAUR:Morrison2005, author = {D. F. Morrison}, title = {Multivariate analysis of variance}, booktitle = {Encyclopedia of Biostatistics}, year = 2005, publisher = {John Wiley \& Sons}, address = {Chichester, UK}, editor = {P. Armitage and T. Colton}, edition = {2nd} } @article{HSAUR:Aitkin1978, author = {M. Aitkin}, title = {The analysis of unbalanced cross-classifications}, journal = {Journal of the Royal Statistical Society, Series A}, year = 1978, volume = 141, pages = {195-223}, note = {with discussion} } @article{HSAUR:Nelder1977, author = {J. A. Nelder}, title = {A reformulation of linear models}, journal = {Journal of the Royal Statistical Society, Series A}, year = 1977, volume = 140, pages = {48-76}, note = {with commentary} } @book{HSAUR:Scheffe1959, author = {H. Scheffe}, title = {The Analysis of Variance}, year = 1959, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Stevens2001, author = {J. Stevens}, title = {Applied Multivariate Statistics for the Social Sciences}, year = 2001, publisher = {Lawrence Erlbaum}, address = {Mahwah, New Jersey, USA}, edition = {4th} } @phdthesis{HSAUR:Quine1975, author = {S. Quine}, title = {Achievement Orientation of Aboriginal and White Adolescents}, year = {1975}, address = {Canberra, Australia}, school = {Australian National University}, type = {Doctoral {D}issertation} } @book{HSAUR:Timm2002, author = {N. H. Timm}, title = {Applied Multivariate Analysis}, year = 2002, publisher = {Springer-Verlag}, address = {New York, USA}, } @book{HSAUR:TherneauGrambsch2000, author = {Terry M. Therneau and Patricia M. Grambsch}, title = {Modeling Survival Data: {E}xtending the Cox Model}, publisher = {Springer-Verlag}, year = {2000}, address = {New York, USA} } @book{HSAUR:Agresti2002, author = {Alan Agresti}, title = {Categorical Data Analysis}, year = 2002, edition = {2nd}, publisher = {John Wiley \& Sons}, address = {Hoboken, New Jersey, USA} } @incollection{HSAUR:Tukey1953, author = {John W. Tukey}, title = {The Problem of Multiple Comparisons (Unpublished Manuscript)}, year = 1953, booktitle = {The Collected Works of John W. Tukey VIII. Multiple Comparisons: 1948-1983}, publisher = {Chapman \& Hall}, address = {New York, USA} } @book{HSAUR:HochbergTamhane1987, author = {Yosef Hochberg and Ajit C. Tamhane}, title = {Multiple Comparison Procedures}, year = 1987, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Everitt1996, author = {Brian S. Everitt}, title = {Making Sense of Statistics in Psychology: A Second-Level Course}, year = 1996, publisher = {Oxford University Press}, address = {Oxford, UK} } @book{HSAUR:Searle1971, author = {S. R. Searle}, title = {Linear Models}, year = 1971, publisher = {John Wiley \& Sons}, address = {New York, USA} } @book{HSAUR:Kraepelin1919, author = {Emil Kraepelin}, title = {Dementia Praecox and Paraphrenia}, year = 1919, publisher = {Livingstone}, address = {Edinburgh, UK} } @article{HSAUR:FraleyRaftery2002, author = {C. Fraley and A. E. 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Goldberg}, year = 1972, title = {The Detection of Psychiatric Illness by Questionnaire}, publisher = {Oxford University Press}, address = {Oxford, UK} } %% PACKAGES @article{PKG:sandwich, title = {Econometric Computing with {HC} and {HAC} Covariance Matrix Estimators}, author = {Achim Zeileis}, journal = {Journal of Statistical Software}, year = {2004}, volume = {11}, number = {10}, pages = {1--17}, url = {http://www.jstatsoft.org/v11/i10/}, } @Manual{PKG:coin, title = {\Rpackage{coin}: Conditional Inference Procedures in a Permutation Test Framework}, author = {Torsten Hothorn and Kurt Hornik and Mark van de Wiel and Achim Zeileis}, year = {2013}, url = {http://CRAN.R-project.org/package=coin}, note = {\rR{} package version 1.0-23} } @Manual{PKG:KernSmooth, title = {\Rpackage{KernSmooth}: Functions for Kernel Smoothing for Wand \& Jones (1995)}, author = {Matt P. Wand and Brian D. Ripley}, year = {2014}, note = {\rR{} package version 2.23-10}, url = {http://CRAN.R-project.org/package=KernSmooth}, } @Manual{PKG:boot, title = {\Rpackage{boot}: Bootstrap \rR{} (\rSPLUS) Functions}, author = {Angelo Canty and Brian D. Ripley}, year = {2014}, url = {http://CRAN.R-project.org/package=boot}, note = {\rR{} package version 1.3-9}, } @Manual{PKG:mclust, title = {\Rpackage{mclust}: Model-based Cluster Analysis}, author = {C. Fraley and A. E. Raftery and Ron Wehrens}, year = {2014}, note = {\rR{} package version 4.3}, url = {http://www.stat.washington.edu/mclust}, } @Manual{PKG:randomForest, title = {\Rpackage{randomForest}: {B}reiman and {C}utler's Random Forests for Classification and Regression}, author = {Leo Breiman and Adele Cutler and Andy Liaw and Matthew Wiener}, year = {2013}, note = {\rR{} package version 4.6-7}, url = {http://stat-www.berkeley.edu/users/breiman/RandomForests}, } @Manual{PKG:rpart, title = {\Rpackage{rpart}: Recursive Partitioning}, author = {Terry M. Therneau and Beth Atkinson and Brian D. Ripley}, year = {2014}, note = {\rR{} package version 4.1-8}, url = {http://mayoresearch.mayo.edu/mayo/research/biostat/splusfunctions.cfm}, } @Manual{PKG:mlbench, title = {\Rpackage{mlbench}: Machine Learning Benchmark Problems}, author = {Friedrich Leisch and Evgenia Dimitriadou}, year = {2013}, url = {http://CRAN.R-project.org/package=mlbench}, note = {\rR{} package version 2.1-1}, } @Manual{PKG:nlme, title = {\Rpackage{nlme}: Linear and Nonlinear Mixed Effects Models}, author = {Jos\'{e} C. Pinheiro and Douglas M. Bates and Saikat DebRoy and Deepayan Sarkar}, year = {2014}, url = {http://CRAN.R-project.org/package=nlme}, note = {\rR{} package version 3.1-113}, } @Manual{PKG:lme4, title = {\Rpackage{lme4}: Linear Mixed-Effects Models Using S4 Classes}, author = {Douglas Bates and Deepayan Sarkar}, year = {2014}, url = {http://CRAN.R-project.org/package=lme4}, note = {\rR{} package version 1.1-5}, } @Manual{PKG:gee, title = {\Rpackage{gee}: Generalized Estimation Equation Solver}, author = {Vincent J. Carey and Thomas Lumley and Brian D. Ripley}, year = {2013}, url = {http://CRAN.R-project.org/package=gee}, note = {\rR{} package version 4.13-18}, } @Manual{PKG:rmeta, title = {\Rpackage{rmeta}: {M}eta-Analysis}, author = {Thomas Lumley}, year = {2013}, url = {http://CRAN.R-project.org/package=rmeta}, note = {\rR{} package version 2.16}, } @Manual{PKG:ape, title = {\Rpackage{ape}: {A}nalyses of Phylogenetics and Evolution}, author = {Emmanuel Paradis and Korbinian Strimmer and Julien Claude and Gangolf Jobb and Rainer Opgen-Rhein and Julien Dutheil and Yvonnick Noel and Ben Bolker}, year = {2014}, url = {http://CRAN.R-project.org/package=ape}, note = {\rR{} package version 3.1-1}, } @Manual{PKG:survival, title = {\Rpackage{survival}: {S}urvival Analysis, Including Penalised Likelihood}, author = {Terry M. Therneau and Thomas Lumley}, year = {2014}, url = {http://CRAN.R-project.org/package=survival}, note = {\rR{} package version 2.37-7}, } @Manual{PKG:mfp, title = {\Rpackage{mfp}: {M}ultivariable Fractional Polynomials}, author = {Gareth Ambler and Axel Benner}, year = {2013}, url = {http://CRAN.R-project.org/package=mfp}, note = {\rR{} package version 1.4.9}, } @Manual{PKG:vcd, title = {\Rpackage{vcd}: {V}isualizing Categorical Data}, author = {David Meyer and Achim Zeileis and Alexandros Karatzoglou and Kurt Hornik}, year = {2013}, url = {http://CRAN.R-project.org/package=vcd}, note = {\rR{} package version 1.3-1}, } @Manual{PKG:leaps, title = {\Rpackage{leaps}: {R}egression Subset Selection}, author = {Thomas Lumley and Alan Miller}, year = {2013}, url = {http://CRAN.R-project.org/package=leaps}, note = {\rR{} package version 2.9}, } @Manual{PKG:party, title = {\Rpackage{party}: {A} Laboratory for Recursive Partytioning}, author = {Torsten Hothorn and Kurt Hornik and Carolin Strobl and Achim Zeileis}, year = {2014}, url = {http://CRAN.R-project.org/package=party}, note = {\rR{} package version 1.0-13} } @Manual{PKG:multcomp, title = {\Rpackage{multcomp}: Simultaneous Inference for General Linear Hypotheses}, author = {Torsten Hothorn and Frank Bretz and Peter Westfall}, year = {2014}, note = {\rR{} package version 1.3-2}, url = {http://CRAN.R-project.org/package=multcomp} } @Manual{PKG:lattice, title = {\Rpackage{lattice}: Lattice Graphics}, author = {Deepayan Sarkar}, year = {2014}, note = {\rR{} package version 0.20-27}, url = {http://CRAN.R-project.org/package=lattice} } @Manual{PKG:partykit, title = {\Rpackage{partykit}: A Toolkit for Recursive Partytioning}, author = {Torsten Hothorn and Achim Zeileis}, year = {2014}, note = {\rR{} package version 0.8-0}, url = {http://R-forge.R-project.org/projects/partykit/} } @Manual{PKG:alr3, title = {\Rpackage{alr3}: Methods and Data to Accompany {Applied Linear Regression 3rd edition}}, author = {Sanford Weisberg}, year = {2013}, note = {\rR{} package version 2.0.5}, url = {http://www.stat.umn.edu/alr}, } @Manual{PKG:mboost, title = {\Rpackage{mboost}: Model-Based Boosting}, author = {Torsten Hothorn and Peter B\"uhlmann and Thomas Kneib and Matthias Schmid and Benjamin Hofner}, year = {2013}, note = {\rR{} package version 2.2-3}, url = {http://CRAN.R-project.org/package=mboost} } @Manual{PKG:meta, title = {\Rpackage{meta}: {M}eta-Analysis}, author = {Guido Schwarzer}, year = {2014}, note = {\rR{} package version 3.2-1}, url = {http://CRAN.R-project.org/package=meta} } @Manual{PKG:rgl, title = {\Rpackage{rgl}: 3D Visualization Device System (OpenGL)}, author = {Daniel Adler and Duncan Murdoch}, year = {2014}, note = {\rR{} package version 0.93.996}, url = {http://rgl.neoscientists.org}, } @Manual{PKG:wordcloud, title = {\Rpackage{wordcloud}: Word Clouds}, author = {Ian Fellows}, year = {2014}, note = {\rR{} package version 2.4}, url = {http://CRAN.R-project.org/package=wordcloud} } @Manual{PKG:quantreg, title = {\Rpackage{quantreg}: {Quantile} Regression}, author = {Roger Koenker}, year = {2013}, url = {http://CRAN.R-project.org/package=quantreg}, note = {\rR{} package version 5.05} } @Manual{PKG:MASS, title = {\Rpackage{MASS}: Support Functions and Datasets for Venables and Ripley's MASS}, author = {Brian D. Ripley}, year = {2014}, url = {http://CRAN.R-project.org/package=MASS}, note = {\rR{} package version 7.3-29} } @Manual{PKG:INLA, title = {\Rpackage{INLA}: Functions Which Allow to Perform Full Bayesian Analysis of Latent Gaussian Models Using Integrated Nested Laplace Approximaxion}, author = {Havard Rue and Sara Martino and Finn Lindgren and Daniel Simpson and Andrea Riebler}, year = {2013}, url = {http://www.r-inla.org/download}, note = {\rR{} package version 0.0-1379661604} } @Manual{PKG:rjags, title = {\Rpackage{rjags}: Bayesian Graphical Models Using {MCMC}}, author = {Martyn Plummer and Alexey Stukalov}, year = {2014}, url = {http://CRAN.R-project.org/package=rjags}, note = {\rR{} package version 3-13} } @Manual{PKG:sp, title = {\Rpackage{sp}: Classes and Methods for Spatial Data}, author = {Edzer Pebesma and Roger Bivand}, year = {2013}, url = {http://CRAN.R-project.org/package=sp}, note = {\rR{} package version 1.0-14} } @Manual{PKG:mice, title = {\Rpackage{mice}: Multivariate Imputation by Chained Equations}, author = {Stef van Buuren and Karin Groothuis-Oudshoorn}, year = {2014}, url = {http://CRAN.R-project.org/package=mice}, note = {\rR{} package version 2.21} } @book{HSAUR:Sarkar2008, title = {Lattice: {M}ultivariate Data Visualization with \rR{}}, author = {Deepayan Sarkar}, year = 2008, publisher = {Springer-Verlag}, address = {New York, USA} } @article{HSAUR:Mazessetal1984, author = {R. B. Mazess and W. W. Peppler and M. Gibbons}, title = {Total Body Composition by Dual Photon Absorptiometry}, year = 1984, journal = {American Journal of Clinical Nutrition}, volume = 40, pages = {834-839} } @book{HSAUR:Rawlingsetal1998, author = {J. O. Rawlings and S. G. Pantula and A. D. Dickey}, title = {Applied Regression Analysis}, year = 1998, publisher = {Springer-Verlag}, address = {New York, USA} } @article{HSAUR:FrisonPocock1992, author = {L. Frison and S. J. Pocock}, year = 1992, title = {Repeated Measures in Clinical Trials: Analysis using Mean Summary Statistics and its Implications for Design}, journal = {Statistics in Medicine}, volume = 11, pages = {1685--1704} } @article{HSAUR:Matthewsetal1990, author = {J. N. S. Matthews and D. G. Altman and M. J. Campbell and P. Royston}, year = 1990, title = {Analysis of Serial Measurements in Medical Research}, journal = {British Medical Journal}, volume = {200}, pages = {230--235} } @article{HSAUR:DeBackeretal1998, author = {M. 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The} Northern {Andes} of {South America}}, journal = {The American Naturalist}, volume = 104, pages = {373--388} } @book{HSAUR:Aitkin1989, author = {M. Aitkin and D. Anderson and B. Francis and J. Hinde}, title = {Statistical Modelling in {GLIM}}, year = 1989, publisher = {Oxford University Press}, address = {New York, USA}, } @incollection{HSAUR:Morabia2013, author = {Alfredo Morabia}, editor = {Wolfgang Ahrens and Iris Pigeot}, booktitle = {Handbook of Epidemiology}, title = {History of Epidemiological Methods and Concepts}, pages = {43--74}, year = {2013}, edition = {2nd}, publisher = {Springer-Verlag}, address = {New York, USA}, } @Article{HSAUR:ZeileisHothornHornik2008, author = {Achim Zeileis and Torsten Hothorn and Kurt Hornik}, title = {Model-based Recursive Partitioning}, journal = {Journal of Computational and Graphical Statistics}, year = {2008}, volume = 17, number = 2, pages = {492--514}, doi = {10.1198/106186008X319331}, } > > HSAUR3/inst/cache/0000755000175000017500000000000012451513136013372 5ustar nileshnileshHSAUR3/inst/cache/DE-bootpara.rda0000644000175000017500000010376212357775376016215 0ustar nileshnileshRDX2 X  bootpara ?\@KOVMl@T(;S names p mu1.2 mu2.1 ?4Fd?֤A8X?։5?[?{͓v?J~L?ׂ?֎i{?.?{θ]?dBj?ګ.?qIz?86?{p?ЉA?Ԛru,?VEX+?HIlD?ʯ=?)A} ??ԫ?9!%ȱ?((~a3?I;E?]?+??Ԣmpd"@?铤9??wל?O՟?U}??p?~bV?CPp?ا2?# ?'M?27m"?Q63(.?5cT?:;2A?6{?ݦ_?L'g?v n?b$v?⬠ \?kP6?ԙ?2?Կ &?#?`?漢^?֨X?؎M?L7+!0?th٘?xT?"3>a?լً?(;P?z?MsΞ?_TD?0SM?ע|d?d!?+?PNHN?֘[iB?+Ii?%ٓny?ֆ&0Br?o@?ԕX? ͩ|?$4b0?=?)D?,ߘ?ӭ|L?%?؅~?Ճd I?hgд?nD??'e4e?ӪQ?2̆?څY]X?> .?v rv?^?ͩƾ?׆0{?ټ9F!?~l^?ٯK?N?[;|?G n?.?֛,!*?8 Os?1i?m'+/??M ?ֿn?>40?vC4?׫\ ?ֲh?+?Ԙĕ~(?٧=I.?C!Z?FXkJ?ڎs= ?l{X?ٝW>K?JmW?Y?bl#.?sۆ?UǨ=?g13?vTg?4Q?/u[?O0?ti\?:=|w~?+Vt?ȟ)?ca?.z\?Ճel?`a|?ԡ-i?MzR?JXr?ɍF?A6fe?&ECS?؂[?՝R.?v6? |Nz?=mc?ۗBz?]?q*+2 ?b?4v?A RT?״K?\C|? |?$MUh?pN?$ϱhPt?:0?#ͣ?XkD??Ƶ¤??$??+@?%%?u?T?xHT,?LV? ++}?YmO&?Ԑ??ֿ4`?]|n١?ٳKqL?YV?+?Z?~wt<(?,vXK?׀?׼c )f?֋L0?裕Z?#4?TO-3i?m?׹zUf??$?ى?ّrY?2iP??ڱy?Q?Մ¼? 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nileshnileshHSAUR3/inst/slides/definitions.tex0000644000175000017500000001012513055275020016644 0ustar nileshnilesh %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@\textit{#1} package}\textit{#1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{`#1'} %%' %%% Math symbols \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\P}{\mathsf{P}} \usepackage{amstext} %%% links \usepackage{hyperref} %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage{rotating} %%% Bibliography \usepackage[round,comma]{natbib} %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.65\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} %%% local definitions \setlength{\parskip}{\parsep} \usepackage[utf8]{inputenc}HSAUR3/inst/slides/Ch_graphical_display.Rnw0000644000175000017500000004050013055275020020370 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 2: Graphical Displays} \end{center} introduces some basic however very useful graphical techniques for extracting information about Malignant Melanoma and Chinese Health and Family Life. } \section{Introduction} \begin{frame} \frametitle{USmelanoma: Malignant Melanoma in the USA} \cite{HSAUR:FisherBelle1993} report mortality rates due to malignant melanoma of the skin for white males during the period 1950--1969, for each state on the US mainland. The include the number of deaths due to malignant melanoma in the corresponding state, the longitude and latitude of the geographic centre of each state, and a binary variable indicating contiguity to an ocean, that is, if the state borders one of the oceans. Questions of interest about these data include: how do the mortality rates compare for ocean and non-ocean states? and how are mortality rates affected by latitude and longitude? \end{frame} \begin{frame} \frametitle{CHFLS: Chinese Health and Family Life Survey} The Chinese Health and Family Life Survey sampled $60$ villages and urban neighbourhoods chosen in such a way as to represent the full geographical and socioeconomic range of contemporary China excluding Hong Kong and Tibet. Eighty-three individuals were chosen at random for each location from official registers of adults aged between $20$ and $64$ years to target a sample of $5000$ individuals in total. Here, we restrict our attention to women with current male partners and the following variables: \end{frame} \begin{frame} \frametitle{CHFLS: Chinese Health and Family Life Survey} \begin{description} \item[\Robject{R\_edu}]: level of education of the responding woman, \item[\Robject{R\_income}]: monthly income (in yuan) of the responding woman, \item[\Robject{R\_health}]: health status of the responding woman in the last year, \item[\Robject{R\_happy}]: how happy was the responding woman in the last year, \item[\Robject{A\_edu}]: level of education of the woman's partner, \item[\Robject{A\_income}]: monthly income (in yuan) of the woman's partner. \end{description} Here, we focus on graphical displays for inspecting the relationship of these health and socioeconomic variables of heterosexual women and their partners. \end{frame} \section{Initial Data Analysis} \begin{frame} \frametitle{Initial Data Analysis} According to \cite{HSAUR:Chambersetal1983}, ``there is no statistical tool that is as powerful as a well chosen graph'': \begin{itemize} \item In comparison with other types of presentation, well-designed charts are more effective in creating interest and in appealing to the attention of the reader. \item Visual relationships as portrayed by charts and graphs are more easily grasped and more easily remembered. \item The use of charts and graphs saves time, since the essential meaning of large measures of statistical data can be visualised at a glance. \item Charts and graphs provide a comprehensive picture of a problem that makes for a more complete and better balanced understanding than could be derived from tabular or textual forms of presentation. \item Charts and graphs can bring out hidden facts and relationships and can stimulate, as well as aid, analytical thinking and investigation. \end{itemize} \end{frame} \begin{frame} \frametitle{A Word of Warning} The following caveat from the late Carl Sagan (in his book \booktitle{Contact}) should be kept in mind: \begin{quote} Humans are good at discerning subtle patterns that are really there, but equally so at imagining them when they are altogether absent. \end{quote} \end{frame} \section{Analysis Using R} \subsection{Malignant Melanoma} \begin{frame}[fragile] \frametitle{Malignant Melanoma: boxplot \& histogram} We might begin to examine the malignant melanoma data by constructing a histogram or boxplot for \stress{all} the mortality rates. Using these relatively simple technique we have to make sure that the $x$-axis is the same in both graphs. This can be done by computing a plausible range of the data, later to be specified in a plot via the \Rcmd{xlim} argument: <>= xr <- range(USmelanoma$mortality) * c(0.9, 1.1) xr @ \end{frame} \begin{frame}[fragile] \small{ \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 2)) par(mar = par("mar") * c(0.8, 1, 1, 1)) boxplot(USmelanoma$mortality, ylim = xr, horizontal = TRUE, xlab = "Mortality") hist(USmelanoma$mortality, xlim = xr, xlab = "", main = "", axes = FALSE, ylab = "") axis(1) @ \end{center} \end{figure} } \end{frame} \begin{frame}[fragile] \frametitle{Malignant Melanoma: Comparing states} Looking at the characteristics of all the mortality rates is a useful beginning but for these data we might be more interested in comparing mortality rates for ocean and non-ocean states. So we might construct two histograms or two boxplots. Such a \stress{parallel boxplot}, visualising the conditional distribution of a numeric variable in groups as given by a categorical variable, are easily computed using the \Rcmd{boxplot} function. \end{frame} \begin{frame}[fragile] \begin{figure} \begin{center} <>= plot(mortality ~ ocean, data = USmelanoma, xlab = "Contiguity to an ocean", ylab = "Mortality") @ \end{center} \end{figure} \end{frame} \begin{frame}[fragile] \frametitle{Malignant Melanoma: density plots} Histograms are generally used for two purposes: counting and displaying the distribution of a variable; according to \cite{HSAUR:Wilkinson1992}, ``they are effective for neither''. Histograms can often be misleading for displaying distributions because of their dependence on the number of classes chosen. An alternative is to formally estimate the density function of a variable and then plot the resulting estimate. \end{frame} \begin{frame}[fragile] \small{ \begin{figure} \begin{center} <>= dyes <- with(USmelanoma, density(mortality[ocean == "yes"])) dno <- with(USmelanoma, density(mortality[ocean == "no"])) plot(dyes, lty = 1, xlim = xr, main = "", ylim = c(0, 0.018)) lines(dno, lty = 2) legend("topleft", lty = 1:2, legend = c("Coastal State", "Land State"), bty = "n") @ \end{center} \end{figure} } \end{frame} \begin{frame}[fragile] \frametitle{Malignant Melanoma: the whole picture} Now we might move on to look at how mortality rates are related to the geographic location of a state as represented by the latitude and longitude of the centre of the state. Here the main graphic will be the scatterplot. The simple $xy$ scatterplot has been in use since at least the eighteenth century and has many virtues -- indeed according to \cite{HSAUR:Tufte1983}: \begin{quote} The relational graphic -- in its barest form the scatterplot and its variants -- is the greatest of all graphical designs. It links at least two variables, encouraging and even imploring the viewer to assess the possible causal relationship between the plotted variables. It confronts causal theories that $x$ causes $y$ with empirical evidence as to the actual relationship between $x$ and $y$. \end{quote} \end{frame} \begin{frame}[fragile] \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) plot(mortality ~ longitude, data = USmelanoma) plot(mortality ~ latitude, data = USmelanoma) @ \end{center} \end{figure} \end{frame} \begin{frame}[fragile] Since mortality rate is clearly related only to latitude we can now produce scatterplots of mortality rate against latitude separately for ocean and non-ocean states. Instead of producing two displays, one can choose different plotting symbols for either states. \end{frame} \begin{frame}[fragile] \begin{figure} \begin{center} <>= plot(mortality ~ latitude, data = USmelanoma, pch = as.integer(USmelanoma$ocean)) legend("topright", legend = c("Land state", "Coast state"), pch = 1:2, bty = "n") @ \end{center} \end{figure} \end{frame} \begin{frame}[fragile] This scatterplot highlights that the mortality is lowest in the northern land states. Coastal states show a higher mortality than land states at roughly the same latitude. The highest mortalities can be observed for the south coastal states with latitude less than $32^\circ$, say, that is <>= subset(USmelanoma, latitude < 32) @ \end{frame} \subsection{Chinese Health and Family Life} \begin{frame}[fragile] \frametitle{Chinese Health and Family Life} One part of the questionnaire the Chinese Health and Family Life Survey focuses on is the self-reported health status. Two questions are interesting for us. The first one is ``Generally speaking, do you consider the condition of your health to be excellent, good, fair, not good, or poor?''. The second question is ``Generally speaking, in the past twelve months, how happy were you?''. The distribution of such variables is commonly visualised using barcharts where for each category the total or relative number of observations is displayed. \end{frame} \begin{frame}[fragile] \begin{figure} <>= barplot(xtabs(~ R_happy, data = CHFLS)) @ \end{figure} \end{frame} \begin{frame}[fragile] \frametitle{Chinese Health and Family Life: Two variables} The visualisation of two categorical variables could be done by conditional barcharts, i.e., barcharts of the first variable within the categories of the second variable. An attractive alternative for displaying such two-way tables are \stress{spineplots} \citep{HSAUR:Friendly1994,HSAUR:HofmannTheus2005,HSAUR:Chenetal2008}. Before constructing such a plot, we produce a two-way table of the health status and self-reported happiness using the \Rcmd{xtabs} function: <>= xtabs(~ R_happy + R_health, data = CHFLS) @ <>= hh <- xtabs(~ R_health + R_happy, data = CHFLS) @ \end{frame} \begin{frame}[fragile] \frametitle{Chinese Health and Family Life: spineplots} A \stress{spineplot} is a group of rectangles, each representing one cell in the two-way contingency table. The area of the rectangle is proportional with the number of observations in the cell. Here, we produce a mosaic plot of health status and happiness: \end{frame} \begin{frame}[fragile] \begin{figure} <>= plot(R_happy ~ R_health, data = CHFLS) @ \end{figure} \end{frame} \begin{frame}[fragile] \frametitle{Chinese Health and Family Life: spinogram} When the association of a categorical and a continuous variable is of interest, say the monthly income and self-reported happiness, we are interested in the conditional distribution of happiness given income. One possibility to produce a more appropriate plot is called \stress{spinogram}. Here, the continuous $x$-variable is categorised first. Within each of these categories, the conditional frequencies of the response variable are given by stacked barcharts, in a way similar to spineplots. \end{frame} \begin{frame}[fragile] \begin{figure} <>= layout(matrix(1:2, ncol = 2)) plot(R_happy ~ log(R_income + 1), data = CHFLS) cdplot(R_happy ~ log(R_income + 1), data = CHFLS) @ \end{figure} \end{frame} \begin{frame}[fragile] \frametitle{Chinese Health and Family Life: conditional plots} For our last example we return to scatterplots for inspecting the association between a woman's monthly income and the income of her partner. In addition, we want to study the relationship between both monthly incomes conditional on the woman's education. Such conditioning plots are called \stress{trellis} plots and are implemented in the package \Rpackage{lattice} \citep{PKG:lattice, HSAUR:Sarkar2008}. \end{frame} \begin{frame}[fragile] \begin{figure} <>= xyplot(jitter(log(A_income + 0.5)) ~ jitter(log(R_income + 0.5)) | R_edu, data = CHFLS) @ <>= library("lattice") lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) print(xyplot(jitter(log(A_income + 0.5)) ~ jitter(log(R_income + 0.5)) | R_edu, data = CHFLS)) @ \end{figure} Four constellations can be identified: both partners have zero income, the partner has no income, the woman has no income or both partners have a positive income. \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} Producing publication-quality graphics is one of the major strengths of the \R{} system and almost anything is possible since graphics are programmable in \R{}. Naturally, this chapter can be only a very brief introduction to some commonly used displays and the reader is referred to specialised books, most important \cite{HSAUR:Murrell2005}, \cite{HSAUR:Sarkar2008}, and \cite{HSAUR:Chenetal2008}. Interactive 3D-graphics are available from package \Rpackage{rgl} \citep{PKG:rgl}. \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The \Robject{household} data are part of a data set collected from a survey of household expenditure and give the expenditure of $20$ single men and $20$ single women on four commodity groups. The units of expenditure are Hong Kong dollars, and the four commodity groups are \begin{description} \item[\Robject{housing}]: housing, including fuel and light, \item[\Robject{food}]: foodstuffs, including alcohol and tobacco, \item[\Robject{goods}]: other goods, including clothing, footwear and durable goods, \item[\Robject{service}]: services, including transport and vehicles. \end{description} The aim of the survey was to investigate how the division of household expenditure between the four commodity groups depends on total expenditure and to find out whether this relationship differs for men and women. Use appropriate graphical methods to answer these questions and state your conclusions. \end{itemize} \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The data set \Robject{USstates} contains values of seven variables for ten states in the US. The seven variables are \begin{description} \item[\Robject{Population}]: population size divided by $1000$, \item[\Robject{Income}]: average per capita income, \item[\Robject{Illiteracy}]: illiteracy rate (\% population), \item[\Robject{Life.Expectancy}]: life expectancy (years), \item[\Robject{Homicide}]: homicide rate (per $1000$), \item[\Robject{Graduates}]: percentage of high school graduates, \item[\Robject{Freezing}]: average number of days per below freezing. \end{description} With these data \begin{enumerate} \item Construct a scatterplot matrix of the data labelling the points by state name (using function \Rcmd{text}). \item Construct a plot of life expectancy and homicide rate conditional on average per capita income. \end{enumerate} \end{itemize} \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Mortality rates per $100,000$ from male suicides for a number of age groups and a number of countries are given in \Robject{suicides2}. Construct side-by-side box plots for the data from different age groups, and comment on what the graphic tells us about the data. \item \cite{HSAUR:FluryRiedwyl1988} report data that give various lengths measurements on $200$ Swiss bank notes. The \Robject{banknote} data are available from package \Rpackage{alr3} \citep{PKG:alr3}. Use whatever graphical techniques you think are appropriate to investigate whether there is any `pattern' or structure in the data. Do you observe something suspicious? \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/beamerthemeHSAUR.sty0000644000175000017500000000267413055275020017443 0ustar nileshnilesh\ProvidesPackageRCS $Header: /home/cvs/CVSroot/RHandbook/HSAUR/slides/beamerthemeHSAUR.sty,v 1.1 2006/05/08 09:16:39 hothorn Exp $ % Copyright 2003 by Till Tantau % % This program can be redistributed and/or modified under the terms % of the GNU Public License, version 2. %%\usepackage[names]{color} \DeclareOptionBeamer{hideothersubsections}{\PassOptionsToPackage{hideothersubsections}{beamerouterthemesidebar}} \DeclareOptionBeamer{hideallsubsections}{\PassOptionsToPackage{hideallsubsections}{beamerouterthemesidebar}} \PassOptionsToPackage{right}{beamerouterthemesidebar} \PassOptionsToPackage{width=2cm}{beamerouterthemesidebar} \DeclareOptionBeamer{width}{\PassOptionsToPackage{width=#1}{beamerouterthemesidebar}} \DeclareOptionBeamer{left}{\PassOptionsToPackage{left}{beamerouterthemesidebar}} \DeclareOptionBeamer{right}{\PassOptionsToPackage{right}{beamerouterthemesidebar}} \ProcessOptionsBeamer \mode \useoutertheme[height=0pt]{sidebar} %\setbeamercolor{structure}{fg=Mahogany} \setbeamercolor{structure}{fg=red!70!green!150} %\setbeamercolor{structure}{bg=red!70!green!50} \setbeamercolor{sidebartab}{fg=white} {\usebeamercolor{structure}} {\usebeamercolor{sidebartab}} \definecolor{lilahell}{rgb}{0.43,0.16,0.41} \definecolor{liladunkel}{rgb}{0.12,0.12,0.13} \setbeamertemplate{sidebar canvas \beamer@sidebarside}[vertical shading][top=lilahell,bottom=lilahell] \insertpagenumber \mode HSAUR3/inst/slides/Ch_introduction_to_R.Rnw0000644000175000017500000006160413055275020020425 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 1: An Introduction to R} \end{center} teaches some \R{} philosophy, explains how to install \R{} and how to make the first steps in \R{}. } \section{What Is R?} %%\R{}?} \frame{ \frametitle{What Is R?} The \R{} system for statistical computing is an environment for data analysis and graphics. The root of \R{} is the \S{} language, developed by John Chambers and colleagues at Bell Laboratories starting in the 1960s. The \S{} language was designed and developed as a programming language for data analysis tasks but in fact it is a full-featured programming language in its current implementations. The development of the \R{} system for statistical computing is heavily influenced by the open source idea: The base distribution of \R{} \index{Base distribution} and a large number of user contributed extensions are available under the terms of the Free Software Foundation's GNU General %%' Public License in source code form. \index{GNU General Public License} } \frame{ The base distribution of \R{} is maintained by a small group of statisticians, the \R{} Development Core Team. A huge amount of additional functionality is implemented in add-on packages \index{Add-on packages} authored and maintained by a large group of volunteers. The main source of information about the \R{} system is the world wide web with the official home page of the \R{} project being \curl{http://www.R-project.org} } \section{Installing R} %%\R{}} \index{Base system|(} \frame{ \frametitle{Installing the Base System} The \R{} system for statistical computing consists of two major parts: the base system and a collection of user contributed add-on packages. A package is a collection of functions, examples and documentation. Both the base system and packages are distributed via the Comprehensive \R{} Archive Network (CRAN) accessible under \curl{http://CRAN.R-project.org} as precompiled binary distribution and in source form. } \subsection{The Base System and the First Steps \label{AItR:Base}} \frame{ \frametitle{First Steps in R} \begin{columns} \begin{column}{3cm} \includegraphics[width = 2.5cm]{graphics/Rlogo} \end{column} \begin{column}{7cm} Depending on the operating system, \R{} can be started either by typing `\texttt{R}' on the shell (Unix systems) or by clicking on the %' \R{} symbol (as shown left) created by the installer (Windows). \end{column} \end{columns} } \begin{frame}[fragile] \frametitle{R as Pocket Calculator} <>= x <- sqrt(25) + 2 @ The assignment operator \Roperator{<-} binds the value of its right hand side to a variable name on the left hand side. The value of the object \Robject{x} can be inspected simply by typing <>= x @ which, implicitly, calls the \Rcmd{print} method: <>= print(x) @ \end{frame} \subsection{Packages} \begin{frame}[fragile] \frametitle{Important Packages} The base distribution already comes with some high-priority add-on packages, namely \begin{center} \texttt{ <>= colwidth <- 4 ip <- installed.packages(priority = "high") pkgs <- unique(ip[,"Package"]) pkgs <- paste("\\Rpackage{", pkgs, "}", sep = "") nrows <- ceiling(length(pkgs) / colwidth) cat(paste(c("\\begin{tabular}{", paste(rep("l", colwidth), collapse=""), "}"), collapse = ""), "\n", file = "tables/rec.tex", append = FALSE) for (i in 1:nrows) { cat(paste(pkgs[(1:colwidth) + (i-1)*colwidth], collapse = " & "), file = "tables/rec.tex", append = TRUE) cat("\\\\ \n", file = "tables/rec.tex", append = TRUE) } cat("\\end{tabular}\n", file = "tables/rec.tex", append = TRUE) rm(ip, nrows) @ \input{tables/rec} } \end{center} The packages listed here %% #Z %% are maintained by members of the \R{} core development team and implement standard statistical functionality, for example linear models, classical tests, a huge collection of high-level plotting functions or tools for survival analysis. \end{frame} <>= cp <- available.packages(contriburl = "http://CRAN.r-project.org/src/contrib") ncp <- sum(!rownames(cp) %in% pkgs) rm(cp, pkgs) @ \begin{frame}[fragile] \frametitle{User-Contributed Packages} Packages not included in the base distribution can be installed directly from the \R{} prompt. Currently, $\Sexpr{ncp}$ user contributed packages covering almost all fields of statistical methodology are available. <>= rm(ncp, colwidth, i) @ A package is installed by supplying the name of the package to the function \Rcmd{install.packages}. For example the \Rpackage{sandwich} package can be downloaded and installed via <>= install.packages("sandwich") @ The package functionality is available after \stress{attaching} the package by <>= library("sandwich") @ A comprehensive list of available packages can be obtained from \curl{http://CRAN.R-project.org/} \end{frame} \section{Help and Documentation \label{AItR:HDN}} \index{Help system|(} \begin{frame}[fragile] \frametitle{Help and Documentation} Three different forms of documentation for the \R{} system for statistical computing may be distinguished: \begin{itemize} \item online help that comes with the base distribution or packages, \item electronic manuals and \item publications work in the form of books etc. \end{itemize} The help system is a collection of manual pages describing each user-visible function and data set that comes with \R{}. \end{frame} \begin{frame}[fragile] \frametitle{Getting Help in R} A manual page is shown in a pager or web browser when the name of the function we would like to get help for is supplied to the \Rcmd{help} function <>= help("mean") @ or, for short, \begin{Verbatim} R> ?mean \end{Verbatim} The function \Rcmd{help.search} is helpful for searching within manual pages. An overview on documented topics in an add-on package is given, for example for the \Rpackage{sandwich} package, by <>= help(package = "sandwich") @ \end{frame} \begin{frame}[fragile] \frametitle{Package Vignettes} Often a package comes along with an additional document describing the package functionality and giving examples. Such a document is called a \Rclass{vignette} and is viewed in a PDF viewer via <>= vignette("sandwich", package = "sandwich") @ All R code contained in a vignette is available from <>= edit(vignette("sandwich")) @ \end{frame} \begin{frame} \frametitle{Written Documentation} For the beginner, at least the first and the second document of the following four manuals are mandatory: \begin{description} \item[An Introduction to R:] A more formal introduction to data analysis with \R{} than this chapter. \item[R Data Import/Export:] A very useful description of how to read and write various external data formats. \item[R Installation and Administration:] Hints for installing \R{} on special platforms. \item[Writing R Extensions:] The authoritative source on how to write \R{} programs and packages. \end{description} \end{frame} \begin{frame} \frametitle{More Documentation on R} Both printed and online publications are available, the most important ones are \booktitle{Modern Applied Statistics with \S{}} \booktitle{Introductory Statistics with \R{}}, \booktitle{\R{} Graphics} and the \R{} Newsletter, freely available from \curl{http://CRAN.R-project.org/doc/Rnews/} In case the electronically available documentation and the answers to frequently asked questions (FAQ), available from \curl{http://CRAN.R-project.org/faqs.html} have been consulted but a problem or question remains unsolved, the \texttt{r-help} email list is the right place to get answers to well-thought-out questions. Read the posting guide before starting to ask! \end{frame} \section{Data Objects in R} %%\R{}} \begin{frame}[fragile] \frametitle{Data Objects: Forbes 2000 List} \index{Forbes 2000 ranking|(} The data handling and manipulation techniques will be illustrated by means of a data set of $2000$ world leading companies, the Forbes 2000 list for the year 2004 collected by \booktitle{Forbes Magazine}. In a first step, we make the data available for computations within \R. The \Rcmd{data} function searches for data objects of the specified name (\Robject{"Forbes2000")} in the package specified via the \Rarg{package} argument and attaches the data object to the global environment: \index{Forbes2000 data@\Robject{Forbes2000} data} <>= data("Forbes2000", package = "HSAUR3") ls() @ \end{frame} \begin{frame}[fragile] \frametitle{Data Objects: Printing} <>= print(Forbes2000) @ <>= print(Forbes2000[1:3,]) cat("...\n") @ will not be particularly helpful. \end{frame} \begin{frame}[fragile] \frametitle{Inspecting Data Objects} Better look at a description of their structure: <>= str(Forbes2000) @ <>= str(Forbes2000, vec.len = 2) @ \end{frame} \begin{frame}[fragile] \frametitle{Data Objects: Forbes 2000} For each observation, the following eight variables are available: \begin{description} \item[\Robject{rank}]: the ranking of the company, \item[\Robject{name}]: the name of the company, \item[\Robject{country}]: where the company is situated, \item[\Robject{category}]: products the company produces, \item[\Robject{sales}]: the amount of sales of the company, US dollars, \item[\Robject{profits}]: the profit of the company, \item[\Robject{assets}]: the assets of the company, \item[\Robject{marketvalue}]: the market value of the company. \end{description} \end{frame} \begin{frame}[fragile] \frametitle{Data Objects: Forbes 2000} A similar but more detailed description is available from the help page for the \Robject{Forbes2000} object: <>= help("Forbes2000") @ or \begin{Verbatim} R> ?Forbes2000 \end{Verbatim} All information provided by \Rcmd{str} can be obtained by specialised functions as well and we will now have a closer look at the most important of these. \end{frame} \begin{frame}[fragile] \frametitle{Everything is an Object!} The \R{} language is an object-oriented programming language, \index{Object-oriented programming language} so every object is an instance of a class: <>= class(Forbes2000) @ The dimensions of a \Rclass{data.frame} can be extracted using the \Rcmd{dim} function <>= dim(Forbes2000) @ or via <>= nrow(Forbes2000) ncol(Forbes2000) @ \end{frame} \begin{frame}[fragile] \frametitle{Data Frames: Assessing Variables} The variable names are accessible from <>= names(Forbes2000) @ The values of single variables can be extracted from the \Robject{Forbes2000} object by their names <>= class(Forbes2000[,"rank"]) @ Brackets \Robject{[]} always indicate a subset \index{Subset} of a larger object. \end{frame} \begin{frame}[fragile] \frametitle{Vectors} The rankings for all $\Sexpr{nrow(Forbes2000)}$ companies are represented in a \Rclass{vector} structure the length of which is given by <>= length(Forbes2000[,"rank"]) @ A \Rclass{vector} is the elementary structure for data handling in \R{} and is a set of simple elements, all being objects of the same class. <>= 1:3 c(1,2,3) seq(from = 1, to = 3, by = 1) @ \end{frame} \begin{frame}[fragile] \frametitle{Nominal Variables: Factors} Nominal measurements are represented by \Rclass{factor} variables in \R, such as the category of the company's business segment %%' <>= class(Forbes2000[,"category"]) @ Objects of class \Rclass{factor} and \Rclass{character} basically differ in the way their values are stored internally. In our case, there are <>= nlevels(Forbes2000[,"category"]) @ different categories: <>= levels(Forbes2000[,"category"]) @ <>= levels(Forbes2000[,"category"])[1:3] cat("...\n") @ \end{frame} \begin{frame}[fragile] \frametitle{Summarizing Factors} As a simple summary statistic, the frequencies of the levels of such a \Rclass{factor} variable can be found from <>= table(Forbes2000[,"category"]) @ <>= table(Forbes2000[,"category"])[1:3] cat("...\n") @ \end{frame} \begin{frame}[fragile] \frametitle{Numeric Variables} The sales, assets, profits and market value variables are of type \Robject{numeric} <>= class(Forbes2000[,"sales"]) @ and simple summary statistics such as the mean, median and range can be found from <>= median(Forbes2000[,"sales"]) mean(Forbes2000[,"sales"]) range(Forbes2000[,"sales"]) @ \end{frame} \begin{frame}[fragile] \frametitle{Summary Statistics} The \Rcmd{summary} method can be applied to a numeric vector to give a set of useful summary statistics namely the minimum, maximum, mean, median and the $25\%$ and $75\%$ quartiles; for example <>= summary(Forbes2000[,"sales"]) @ \end{frame} \section{Data Import and Export} \index{Data import and export|(} \begin{frame}[fragile] \frametitle{Data Import} The most frequent data formats the data analyst is confronted with are \begin{itemize} \item comma separated files, \item \EXCEL{} spreadsheets, \item files in \SPSS{} format and \item a variety of \SQL{} data base engines. \end{itemize} Querying data bases is a non-trivial task and requires additional knowledge about querying languages and we therefore refer to the \booktitle{\R{} Data Import/Export} manual. \end{frame} <>= pkgpath <- system.file(package = "HSAUR3") mywd <- getwd() filep <- file.path(pkgpath, "rawdata") setwd(filep) @ \begin{frame}[fragile] \frametitle{Comma-separated Files} When the variables are separated by commas and each row begins with a name (a text format typically created by \EXCEL{}), we can read in the data as follows using the \Rcmd{read.table} function <>= csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1) @ The function \Rcmd{read.table} by default guesses the class of each variable from the specified file. Files in \SPSS{} format are read in a way similar to reading comma separated files, using the function \Rcmd{read.spss} from package \Rpackage{foreign}. \end{frame} \begin{frame}[fragile] \frametitle{Data Export} A comma separated file readable by \EXCEL{} can be constructed from a \Rclass{data.frame} object via <>= write.table(Forbes2000, file = "Forbes2000.csv", sep = ",", col.names = NA) @ The function \Rcmd{write.csv} is one alternative. Alternatively, when data should be saved for later processing in \R{} only, \R{} objects of arbitrary kind can be stored into an external binary file via <>= save(Forbes2000, file = "Forbes2000.rda") @ <>= setwd(mywd) @ \end{frame} \section{Basic Data Manipulation \label{AItR:BDM}} \begin{frame}[fragile] \frametitle{More on Data Frames} \index{Data manipulation|(} Internally, a \Rclass{data.frame} is a \Rclass{list} of vectors of a common length $n$, the number of rows of the table. Each of those vectors represents the measurements of one variable and we can access such a variable by its name <>= companies <- Forbes2000[,"name"] @ A subset of the elements of the vector \Robject{companies} can be extracted using the \Rcmd{[]} subset operator: <>= companies[1:3] @ \end{frame} \begin{frame}[fragile] \frametitle{Subset Indexing} In contrast to indexing with positive integers, negative indexing returns all elements which are \stress{not} part of the index vector given in brackets. For example, all companies except those with numbers four to two-thousand, i.e., the top three companies, are again <>= companies[-(4:2000)] @ \end{frame} \begin{frame}[fragile] \frametitle{Data Frame Indexing} Because \Rclass{data.frame}s have a concept of rows and columns, we need to separate the subsets corresponding to rows and columns by a comma. The statement <>= Forbes2000[1:3, c("name", "sales", "profits", "assets")] @ extracts four variables for the three largest companies. A single variable can be extracted from a \Rclass{data.frame} by <>= companies <- Forbes2000$name @ \end{frame} \begin{frame}[fragile] \frametitle{Data Frame Ordering} The three top selling companies are to be computed. First, we need to compute the ordering of the companies' sales %%' <>= order_sales <- order(Forbes2000$sales) @ The three companies with the lowest sales are <>= companies[order_sales[1:3]] @ and the three top sellers are <>= Forbes2000[order_sales[c(2000, 1999, 1998)], "name"] @ \end{frame} \begin{frame}[fragile] \frametitle{Data Frame Subsetting} Another way of selecting vector elements is the use of a logical vector being \Robject{TRUE} when the corresponding element is to be selected and \Robject{FALSE} otherwise. The companies with assets of more than $1000$ billion US dollars are <>= Forbes2000[Forbes2000$assets > 1000, c("name", "sales", "profits")] table(Forbes2000$assets > 1000) @ \end{frame} \begin{frame}[fragile] \frametitle{Missing Values} In \R, missing values are treated by a special symbol, \Robject{NA}, indicating \index{NA symbol@\Robject{NA} symbol} that this measurement is not available. \index{Missing values} The observations with profit information missing can be obtained via <>= na_profits <- is.na(Forbes2000$profits) table(na_profits) Forbes2000[na_profits, c("name", "profits")] @ \end{frame} \begin{frame}[fragile] \frametitle{Removing Missing Values} We want to remove all observations with at least one missing value from a \Rclass{data.frame} object. The function \Rcmd{complete.cases} takes a \Rclass{data.frame} and returns a logical vector being \Robject{TRUE} when the corresponding observation does not contain any missing value: <>= table(complete.cases(Forbes2000)) @ \end{frame} \begin{frame}[fragile] \frametitle{Using subset} Subsetting \Rclass{data.frame}s driven by logical expressions may induce a lot of typing which can be avoided. The \Rcmd{subset} function takes a \Rclass{data.frame} as first argument and a logical expression as second argument: <>= UKcomp <- subset(Forbes2000, country == "United Kingdom") dim(UKcomp) @ \end{frame} \section{Simple Summary Statistics} \begin{frame}[fragile] \frametitle{str and summary} Applying the \Rcmd{summary} method to the \Robject{Forbes2000} <>= summary(Forbes2000) @ <>= summary(Forbes2000[,1:3]) @ \end{frame} \begin{frame}[fragile] \frametitle{apply and Friends} The members of the \Rcmd{apply} family help to solve recurring tasks for each element of a \Rclass{data.frame}, \Rclass{matrix}, \Rclass{list} or for each level of a factor. We compare the profits in each of the $\Sexpr{nlevels(Forbes2000$category)}$ categories and first compute the median profit for each category from <>= mprofits <- tapply(Forbes2000$profits, Forbes2000$category, median, na.rm = TRUE) @ \end{frame} \begin{frame}[fragile] \frametitle{Sorting} The three categories with highest median profit are computed from the vector of sorted median profits <>= rev(sort(mprofits))[1:3] @ where \Rcmd{rev} rearranges the vector of median profits \Rcmd{sort}ed from smallest to largest. \end{frame} \subsection{Simple Graphics} \begin{frame}[fragile] \frametitle{Simple Graphics: Histograms} The degree of skewness of a distribution can be investigated by constructing histograms using the \Rcmd{hist} function: <>= layout(matrix(1:2, nrow = 2)) hist(Forbes2000$marketvalue) hist(log(Forbes2000$marketvalue)) @ \end{frame} \begin{frame}[fragile] \begin{center} <>= layout(matrix(1:2, nrow = 2)) hist(Forbes2000$marketvalue) hist(log(Forbes2000$marketvalue)) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Simple Graphics: Scatterplots} In \R, regression relationships are specified by so-called \stress{model formulae} which may look like <>= fm <- marketvalue ~ sales class(fm) @ with the dependent variable on the left hand side and the independent variable on the right hand side. The tilde separates left and right hand side. \end{frame} \begin{frame}[fragile] \frametitle{Simple Graphics: Scatterplots} \begin{center} <>= plot(log(marketvalue) ~ log(sales), data = Forbes2000, pch = ".") @ \end{center} \end{frame} \begin{frame} %%% R CMD build will receive an error from texi2dvi because of pdf version %%% 1.4 used here -- exclude this piece of code \begin{center} <>= pdf("figures/marketvalue-sales.pdf", version = "1.4") plot(log(marketvalue) ~ log(sales), data = Forbes2000, col = rgb(0,0,0,0.1), pch = 16) dev.off() @ \includegraphics{figures/marketvalue-sales} \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Simple Graphics: Boxplots} <>= boxplot(log(marketvalue) ~ country, data = subset(Forbes2000, country %in% c("United Kingdom", "Germany", "India", "Turkey")), ylab = "log(marketvalue)", varwidth = TRUE) @ \end{frame} \begin{frame} \begin{center} <>= tmp <- subset(Forbes2000, country %in% c("United Kingdom", "Germany", "India", "Turkey")) tmp$country <- tmp$country[,drop = TRUE] boxplot(log(marketvalue) ~ country, data = tmp, ylab = "log(marketvalue)", varwidth = TRUE) @ \end{center} \end{frame} \section{Organising an Analysis} \begin{frame}[fragile] \frametitle{Organising an Analysis} <>= file.create("analysis.R") @ ALWAYS maintain your R code for an analysis as a separate text file collecting all steps necessary to perform a certain data analysis task! Such an \R{} transcript file can be read by <>= source("analysis.R", echo = TRUE) @ When all steps of a data analysis, i.e., data preprocessing, transformations, simple summary statistics and plots, model building and inference as well as reporting, are collected in such an \R{} transcript file, the analysis can be reproduced at any time! <>= file.remove("analysis.R") @ \end{frame} \begin{frame}[fragile] \frametitle{Exercises} \begin{itemize} \item Calculate the median profit for the companies in the United States and the median profit for the companies in the UK, France and Germany. \item Find all German companies with negative profit. \item Which business category are most of the companies situated at the Bermuda island working in? \item For the $50$ companies in the Forbes data set with the highest profits, plot sales against assets (or some suitable transformation of each variable), labelling each point with the appropriate country name which may need to be abbreviated (using \Rcmd{abbreviate}) to avoid making the plot look too `messy'. %%' \item Find the average value of sales for the companies in each country in the Forbes data set, and find the number of countries in each country with profits above $5$ billion US dollars. \end{itemize} \end{frame} \end{document} HSAUR3/inst/slides/Ch_analysing_longitudinal_dataII.Rnw0000644000175000017500000002471113055275020022670 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") library("gee") @ \setkeys{Gin}{width=0.95\textheight} \frame{ \begin{center} \Large{Part 12: Analysing Longitudinal Data II} \end{center} focuses on generalised estimation equations for repeated measurements. } \section{Introduction} \begin{frame} \frametitle{Respiratory illness} The \Robject{respiratory} data were collected in a clinical trial comparing two treatments for a respiratory illness \citep{HSAUR:Davis1991}. In each of two centres, eligible patients were randomly assigned to active treatment or placebo. During the treatment, the respiratory status (categorised \Robject{poor} or \Robject{good}) was determined at each of four, monthly visits. The trial recruited \Sexpr{nlevels(respiratory$subject)} participants (54 in the active group, 57 in the placebo group) and there were no missing data for either the responses or the covariates. The question of interest is to assess whether the treatment is effective and to estimate its effect. \end{frame} \section{Generalised Estimating Equations} \begin{frame} \frametitle{Lack of Independence} The assumption of the independence of the repeated measurements in an GLM will lead to estimated standard errors that are too small for the between-subjects covariates (at least when the correlation between the repeated measurements are positive) as a result of assuming that there are more independent data points than are justified. We might begin by asking is there something relatively simple that can be done to `fix-up' these standard errors so that we %' can still apply the \R{} \Rcmd{glm} function to get reasonably satisfactory results on longitudinal data with a non-normal response? Two approaches which can often help to get more suitable estimates of the required standard errors are \stress{bootstrapping} and use of the \stress{robust/sandwich, Huber/White variance estimator}. \end{frame} \begin{frame} \frametitle{Generalised Estimating Equations (GEE)} But perhaps more satisfactory than these methods to simply `fix-up' the standard errors given by the independence model, %' would be an approach that fully utilises information on the data's %' structure, including dependencies over time. A suitable procedure was first suggested by \cite{HSAUR:LiangZeger1986} and is known as \stress{generalised estimating equations} (GEE). \index{Generalised estimating equations (GEE)} In essence GEE is a multivariate extension of the generalised linear model and quasi-likelihood methods. The primary idea behind the GEE approach is that since the parameters specifying the structure of the correlation matrix are rarely of great practical interest, simple structures are used for the within-subject correlations giving rise to the so-called \stress{working correlation matrix}. \end{frame} \begin{frame} \frametitle{Working Correlation Matrices} \cite{HSAUR:LiangZeger1986} show that the estimates of the parameters of most interest, i.e., those that determine the average responses over time, are still valid even when the correlation structure is incorrectly specified, although their standard errors might remain poorly estimated if the working correlation matrix is far from the truth. But as with the independence situation described previously, this potential difficulty can often be handled satisfactorily by again using the \stress{sandwich estimator} to find more reasonable standard errors. Possibilities for the working correlation matrix that are most frequently used in practice are: \end{frame} \begin{frame} \frametitle{Working Correlation Matrices} \begin{itemize} \item An identity matrix: no correlation at all. \item An exchangeable correlation matrix: with a single parameter which gives the correlation of each pair of repeated measures. \item An autoregressive correlation matrix: also with a single parameter but in which $\text{corr}(y_j, y_k) = \vartheta^{|k - j|}, j \not = k$. With $\vartheta$ less than one this gives a pattern in which repeated measures further apart in time are less correlated, than those that are closer to one another. \item An unstructured correlation matrix: with $q(q-1)/2$ parameters in which $\text{corr}(y_j, y_k) = \vartheta_{jk}$ and where $q$ is the number of repeated measures. \end{itemize} \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{Beat the Blues Revisited} <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt" @ <>= osub <- order(as.integer(BtheB_long$subject)) BtheB_long <- BtheB_long[osub,] btb_gee <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "independence") btb_gee1 <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "exchangeable") @ \end{frame} \begin{frame} \frametitle{Beat the Blues Revisited} Note how the na\"{\i}ve and the sandwich or %" robust estimates of the standard errors are considerably different for the independence structure, but quite similar for the exchangeable structure. This simply reflects that using an exchangeable working correlation matrix is more realistic for these data and that the standard errors resulting from this assumption are already quite reasonable without applying the `sandwich' procedure %' to them. And if we compare the results under this assumed structure with those for the random intercept model, we see that they are almost identical, since the random intercept model also implies an exchangeable structure for the correlations of the repeated measurements. \end{frame} \section{Respiratory Illness} \begin{frame}[fragile] \frametitle{Respiratory Illness} The baseline status, i.e., the status for \Robject{month == 0}, will enter the models as an explanatory variable and thus we have to rearrange the \Rclass{data.frame} \Robject{respiratory} in order to create a new variable \Robject{baseline}: <>= data("respiratory", package = "HSAUR3") resp <- subset(respiratory, month > "0") resp$baseline <- rep(subset(respiratory, month == "0")$status, rep(4, 111)) resp$nstat <- as.numeric(resp$status == "good") resp$month <- resp$month[, drop = TRUE] names(resp)[names(resp) == "treatment"] <- "trt" levels(resp$trt)[2] <- "trt" @ \end{frame} \begin{frame}[fragile] \frametitle{Respiratory Illness} <>= resp_glm <- glm(status ~ centre + trt + gender + baseline + age, data = resp, family = "binomial") resp_gee1 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) resp_gee2 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) @ \end{frame} \begin{frame}[fragile] \frametitle{Respiratory Illness} The estimated treatment effect taken from the exchangeable structure GEE model is \Sexpr{round(coef(resp_gee2)["trttrt"], 3)} which, using the robust standard errors, has an associated $95\%$ confidence interval <>= se <- summary(resp_gee2)$coefficients[ "trttrt", "Robust S.E."] coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975) @ These values reflect effects on the log-odds scale, on the exp scale it reads <>= exp(coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975)) @ The odds of achieving a `good' respiratory status with the active treatment is between %' about twice and seven times the corresponding odds for the placebo. \end{frame} \section{Epilepsy} \begin{frame}[fragile] \frametitle{Epilepsy} Moving on to the count data in \Robject{epilepsy}, we begin by calculating the means and variances of the number of seizures for all treatment / period interactions <>= data("epilepsy", package = "HSAUR3") itp <- interaction(epilepsy$treatment, epilepsy$period) tapply(epilepsy$seizure.rate, itp, mean) tapply(epilepsy$seizure.rate, itp, var) @ Overdispersion? \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} The generalised estimation equation approach essentially extends generalised linear models to longitudinal data, and allows for the analysis of such data when the response variable cannot be assumed to be normal distributed. \end{frame} \section*{Exercises} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item For the \Robject{epilepsy} data investigate what Poisson models are most suitable when subject 49 is excluded from the analysis. \item Investigate the use of other correlational structures than the independence and exchangeable structures used in the text, for both the \Robject{respiratory} and the \Robject{epilepsy} data. \item The \Robject{schizophrenia2} data were collected in a follow-up study of women patients with schizophrenia \citep{HSAUR:Davis2002}. The binary response recorded at 0, 2, 6, 8 and 10 months after hospitalisation was thought disorder (absent or present). The single covariate is the factor indicating whether a patient had suffered early or late onset of her condition (age of onset less than 20 years or age of onset 20 years or above). The question of interest is whether the course of the illness differs between patients with early and late onset? Investigate this question using the GEE approach. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/Ch_multiple_linear_regression.Rnw0000644000175000017500000003376713055275020022357 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 6: Multiple Linear Regression} \end{center} focuses on the analysis of cloud seeding experiments. } \begin{frame} \frametitle{clouds: Cloud Seeding} The data were collected in the summer of 1975 from an experiment to investigate the use of massive amounts of silver iodide ($100$ to $1000$ grams per cloud) in cloud seeding to increase rainfall. In the experiment 24 days were judged suitable for seeding on the basis that a measured suitability criterion. On suitable days, a decision was taken at random as to whether to seed or not. \end{frame} \begin{frame} \frametitle{Could Seeding Variables} \begin{description} \item[\Robject{seeding}]: a factor indicating whether seeding action occured (yes or no), \item[\Robject{time}]: number of days after the first day of the experiment, \item[\Robject{cloudcover}]: the percentage cloud cover in the experimental area, measured using radar, \item[\Robject{prewetness}]: the total rainfall in the target area one hour before seeding, \item[\Robject{echomotion}]: a factor showing whether the radar echo was moving or stationary, \item[\Robject{rainfall}]: the amount of rain, \item[\Robject{sne}]: suitability criterion. \end{description} The objective in analysing these data is to see how rainfall is related to the explanatory variables and, in particular, to determine the effectiveness of seeding. \end{frame} \section{Multiple Linear Regression} \begin{frame} \frametitle{Multiple Linear Regression} Assume $y_i$ represents the value of the response variable on the $i$th individual, and that $x_{i1}, x_{i2}, \dots, x_{iq}$ represents the individual's values on $q$ explanatory variables, with $i = 1, \dots, n$. The multiple linear regression model is given by \begin{eqnarray*} y_i = \beta_0 + \beta_1 x_{i1} + \dots + \beta_q x_{iq} + \varepsilon_i. \end{eqnarray*} The residual or error terms $\varepsilon_i$, $i = 1, \dots, n$, are assumed to be independent random variables having a normal distribution with mean zero and constant variance $\sigma^2$. \end{frame} \begin{frame} \frametitle{Multiple Linear Regression} Consequently, the distribution of the random response variable, $y$, is also normal with expected value given by the linear combination of the explanatory variables \begin{eqnarray*} \E(y | x_1, \dots, x_q) = \beta_0 + \beta_1 x_{1} + \dots + \beta_q x_{q} \end{eqnarray*} and with variance $\sigma^2$. The parameters of the model $\beta_k$, $k = 1, \dots, q$, are known as regression coefficients with $\beta_0$ corresponding to the overall mean. The multiple linear regression model can be written most conveniently for all $n$ individuals by using matrices and vectors as \begin{eqnarray*} \y = \X \beta + \varepsilon \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Model Matrix} The \stress{design} or \stress{model matrix} $\X$ \index{Design matrix} \index{Model matrix} consists of the $q$ continuously measured explanatory variables and a column of ones corresponding to the \stress{intercept} term \input{tables/MLR-Xtab} \end{frame} \begin{frame} \frametitle{Nominal Variables} In case one or more of the explanatory variables are nominal or ordinal variables, they are represented by a zero-one dummy coding. Assume that $x_1$ is a factor at $k$ levels, the submatrix of $\X$ corresponding to $x_1$ is a $n \times k$ matrix of zeros and ones, where the $j$th element in the $i$th row is one when $x_{i1}$ is at the $j$th level. \end{frame} \begin{frame}[fragile] \frametitle{Estimation} The least squares estimator of the parameter vector $\beta$ can be calculated by $\hat{\beta} = (\X^\top\X)^{-1} \X^\top \y$ with \begin{eqnarray*} \E(\hat{\beta}) & = & \beta \\ & \text{ and } & \\ \Var(\hat{\beta}) & = & \sigma^2 (\X^\top\X)^{-1} \end{eqnarray*} when the cross-product $\X^\top\X$ is non-singular. \end{frame} \begin{frame} \frametitle{Estimation} If the cross-product $\X^\top\X$ is singular we need to reformulate the model to $\y = \X \C \beta^\star + \varepsilon$ such that $\X^\star = \X \C$ has full rank. The matrix $\C$ is called \stress{contrast matrix} in \S{} and \R{} and the result of the model fit is an estimate $\hat{\beta}^\star$. For the theoretical details we refer to \cite{HSAUR:Searle1971}, the implementation of contrasts in \S{} and \R{} is discussed by \cite{HSAUR:Chambers+Hastie:1992} and \cite{HSAUR:VenablesRipley2002}. \end{frame} \begin{frame}[fragile] \frametitle{Inference} $\hat{y}_i$ is the predicted value of the response variable for the $i$th individual $\hat{y}_i = \hat{\beta}_0 + \hat{\beta}_1 x_{i1} + \dots + \hat{\beta}_q x_{q1}$ and $\bar{y} = \sum_{i = 1}^n y_i / n $ is the mean of the response variable. The mean square ratio \begin{eqnarray*} F = \frac{\sum\limits_{i = 1}^n (\hat{y}_i - \bar{y})^2 / q}{ \sum\limits_{i = 1}^n (\hat{y}_i - y_i)^2 / (n - q - 1)} \sim F_{q, n - q - 1} \end{eqnarray*} provides an $F$-test of the general hypothesis \begin{eqnarray*} H_0: \beta_1 = \dots = \beta_q = 0. \end{eqnarray*} \end{frame} \begin{frame}[fragile] \frametitle{Variance Estimation} An estimate of the variance $\sigma^2$ is \begin{eqnarray*} \hat{\sigma}^2 = \frac{1}{n - q - 1} \sum_{i = 1}^n (y_i - \hat{y_i})^2. \end{eqnarray*} Individual regression coefficients can be assessed by using the ratio $t$-statistics $t_j = \hat{\beta}_j / \sqrt{\Var(\hat{\beta})_{jj}}$, although these ratios should only be used as rough guides to the `significance' %' of the coefficients. The problem of selecting the `best' subset %' of variables to be included in a model is one of the most delicate ones in statistics and we refer to \cite{HSAUR:Miller2002} for the theoretical details and practical limitations. \end{frame} \section{Analysis Using R} \begin{frame} \frametitle{Cloud Seeding} Prior to applying multiple regression to the data it will be useful to look at some graphics to assess their major features. Here we will construct boxplots of the rainfall in each category of the dichotomous explanatory variables and scatterplots of rainfall against each of the continuous explanatory variables. \end{frame} \begin{frame} \begin{center} <>= data("clouds", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) bxpseeding <- boxplot(rainfall ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rainfall ~ echomotion, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") @ \end{center} \end{frame} \begin{frame} \begin{center} <>= layout(matrix(1:4, nrow = 2)) plot(rainfall ~ time, data = clouds) plot(rainfall ~ sne, data = clouds, xlab="S-NE criterion") plot(rainfall ~ cloudcover, data = clouds) plot(rainfall ~ prewetness, data = clouds) @ \end{center} \end{frame} \subsection{Fitting a Linear Model} \begin{frame}[fragile] \frametitle{Fitting a Linear Model} It is sensible to assume that the effect that some of the other explanatory variables is modified by seeding and therefore consider a model that allows interaction terms for \Robject{seeding} with each of the covariates except \Robject{time}. This model can be described by the \Rclass{formula} <>= clouds_formula <- rainfall ~ seeding * (sne + cloudcover + prewetness + echomotion) + time @ and the design matrix $\X^\star$ can be computed via <>= Xstar <- model.matrix(clouds_formula, data = clouds) @ \end{frame} \begin{frame}[fragile] \frametitle{Contrast Matrix} By default, treatment contrasts have been applied to the dummy codings of the factors \Robject{seeding} and \Robject{echomotion} as can be seen from the inspection of the \Robject{contrasts} attribute of the model matrix <>= attr(Xstar, "contrasts") @ \end{frame} \begin{frame}[fragile] \frametitle{Fitting a Linear Model} However, such internals are hidden and performed by high-level model fitting functions such as \Rcmd{lm} which will be used to fit the linear model defined by the \Rclass{formula} \Robject{clouds\_formula}: <>= clouds_lm <- lm(clouds_formula, data = clouds) class(clouds_lm) @ A \Rcmd{summary} method can be used to show the conventional regression analysis output. \end{frame} \begin{frame}[fragile] \frametitle{Inspecting Results} The estimates $\hat{\beta}^\star$ can be assessed via <>= coef(clouds_lm) @ <>= coef(clouds_lm)[1:5] cat("...\n") @ \end{frame} \begin{frame}[fragile] \frametitle{Inspecting Results} The corresponding covariance matrix $\Cov(\hat{\beta}^\star)$ is available via <>= vcov(clouds_lm) @ <>= vcov(clouds_lm)[1:5,1:5] cat("...\n") @ \end{frame} \begin{frame} \frametitle{Inspecting Results} The results of the linear model fit suggest the interaction of seeding with cloud coverage significantly affects rainfall. A suitable graph will help in the interpretation of this result. We can plot the relationship between rainfall and S-Ne criterion for seeding and non-seeding days. \end{frame} \begin{frame} \begin{center} <>= psymb <- as.numeric(clouds$seeding) plot(rainfall ~ sne, data = clouds, pch = psymb) abline(lm(rainfall ~ sne, data = clouds, subset = seeding == "no")) abline(lm(rainfall ~ sne, data = clouds, subset = seeding == "yes"), lty = 2) legend("topright", legend = c("No seeding", "Seeding"), pch = 1:2, lty = 1:2, bty = "n") @ \end{center} \end{frame} \subsection{Regression Diagnostics} \begin{frame} \frametitle{Regression Diagnostics} The possible influence of outliers and the checking of assumptions made in fitting the multiple regression model, i.e., constant variance and normality of error terms, can both be undertaken using a variety of diagnostic tools, of which the simplest and most well known are the estimated residuals, i.e., the differences between the observed values of the response and the fitted values of the response. So, after estimation, the next stage in the analysis should be an examination of such residuals from fitting the chosen model to check on the normality and constant variance assumptions and to identify outliers. \end{frame} \begin{frame} \frametitle{Diagnostic Plots} \begin{itemize} \item A plot of residuals against each explanatory variable in the model. The presence of a non-linear relationship, for example, may suggest that a higher-order term, in the explanatory variable should be considered. \item A plot of residuals against fitted values. If the variance of the residuals appears to increase with predicted value, a transformation of the response variable may be in order. \item A normal probability plot of the residuals. After all the systematic variation has been removed from the data, the residuals should look like a sample from a standard normal distribution. A plot of the ordered residuals against the expected order statistics from a normal distribution provides a graphical check of this assumption. \end{itemize} \end{frame} \begin{frame}[fragile] \frametitle{Residuals and Fitted Values} We need access to the residuals and the fitted values. The residuals can be found by the \Rcmd{residuals} method and the fitted values of the response from the \Rcmd{fitted} method <>= clouds_resid <- residuals(clouds_lm) clouds_fitted <- fitted(clouds_lm) @ \end{frame} \begin{frame} \begin{center} <>= plot(clouds_fitted, clouds_resid, xlab = "Fitted values", ylab = "Residuals", ylim = max(abs(clouds_resid)) * c(-1, 1), type = "n") abline(h = 0, lty = 2) text(clouds_fitted, clouds_resid, labels = rownames(clouds)) @ \end{center} \end{frame} \begin{frame} \begin{center} <>= qqnorm(clouds_resid, ylab = "Residuals") qqline(clouds_resid) @ \end{center} \end{frame} \begin{frame} \frametitle{Cook's Distance} A further diagnostic that is often very useful is an index plot of the Cook's distances for each observation. This statistic %' \index{Cook's distance} %%' is defined as \begin{eqnarray*} D_k = \frac{1}{(q + 1)\hat{\sigma}^2} \sum_{i=1}^n (\hat{y}_{i(k)} - y_i)^2 \end{eqnarray*} where $\hat{y}_{i(k)}$ is the fitted value of the $i$th observation when the $k$th observation is omitted from the model. The values of $D_k$ assess the impact of the $k$th observation on the estimated regression coefficients. Values of $D_k$ greater than one are suggestive that the corresponding observation has undue influence on the estimated regression coefficients. \end{frame} \begin{frame} \begin{center} <>= plot(clouds_lm, which = 4, sub.caption = NULL) @ \end{center} \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Investigate refitting the cloud seeding data after removing any observations which may give cause for concern. \item Show how the analysis of variance for the data \Robject{weightgain} data can be constructed from the results of applying an appropriate multiple linear regression to the data. \item Investigate the use of the \Rcmd{leaps} function from package \Rpackage{leaps} for the selecting the `best' %%' set of variables predicting rainfall in the cloud seeding data. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/HSAUR3_slides_4up.tex0000644000175000017500000000153513055275020017436 0ustar nileshnilesh \documentclass[landscape]{slides} \usepackage{graphicx} \usepackage{color} \usepackage{pdfpages} \pagestyle{empty} \begin{document} \includepdf[pages=1-,nup=4]{Ch_introduction_to_R.pdf} \includepdf[pages=1-,nup=4]{Ch_simple_inference.pdf} \includepdf[pages=1-,nup=4]{Ch_conditional_inference.pdf} \includepdf[pages=1-,nup=4]{Ch_multiple_linear_regression.pdf} \includepdf[pages=1-,nup=4]{Ch_analysis_of_variance.pdf} \includepdf[pages=1-,nup=4]{Ch_logistic_regression_glm.pdf} \includepdf[pages=1-,nup=4]{Ch_density_estimation.pdf} \includepdf[pages=1-,nup=4]{Ch_recursive_partitioning.pdf} \includepdf[pages=1-,nup=4]{Ch_survival_analysis.pdf} \includepdf[pages=1-,nup=4]{Ch_analysing_longitudinal_dataI.pdf} \includepdf[pages=1-,nup=4]{Ch_analysing_longitudinal_dataII.pdf} \includepdf[pages=1-,nup=4]{Ch_cluster_analysis.pdf} \end{document} HSAUR3/inst/slides/Ch_conditional_inference.Rnw0000644000175000017500000003330013055275020021232 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 4: Conditional Inference} \end{center} focuses on conditional statistical test procedures for the Guessing Lengths, Suicides, and Gastrointestinal Damage examples. } <>= nobs <- table(roomwidth$unit) ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - length(unique(x))) library("coin") @ \section{Introduction} \begin{frame} \frametitle{Introduction} There are many experimental designs or studies where the subjects are not a random sample from some well-defined population. For example, in clinical trials the subjects are randomly assigned to certain groups, for example a control and a treatment group, and the analysis needs to take this randomisation into account. In this chapter, we discuss such test procedures usually known as \stress{(re)-randomisation} or \stress{permutation tests} where the distribution of the test statistics under the null hypothesis is determined \stress{conditionally} on the data at hand. \end{frame} \begin{frame} \frametitle{roomwidth: Estimating Room Widths} Shortly after metric units of length were officially introduced in Australia in the 1970s, each of a group of 44 students was asked to guess, to the nearest metre, the width of the lecture hall in which they were sitting. Another group of 69 students in the same room was asked to guess the width in feet, to the nearest foot. But \Sexpr{ties[1]} of the estimated widths (in feet) of \Sexpr{nobs[1]} students and \Sexpr{ties[2]} of the estimated widths (in metres) of \Sexpr{nobs[2]} students are tied. This violates one assumption of the \stress{unconditional} test procedures such as the Wilcoxon Mann-Whitney test, namely that measurements are drawn from a continuous distribution. \end{frame} \begin{frame} \frametitle{suicides: Baiting Behaviour} A study was carried out to investigate the causes of jeering or baiting behaviour by a crowd when a person is threatening to commit suicide by jumping from a high building. A hypothesis is that baiting is more likely to occur in warm weather. 21 accounts of threatened suicide were classified by two factors, the time of year and whether or not baiting occurred. The data come from the northern hemisphere, so June--September are the warm months. \end{frame} \begin{frame} \frametitle{Lanza: Gastrointestinal Damage} The administration of non-steriodal anti-inflammatory drugs for patients suffering from arthritis induced gastrointestinal damage. \cite{HSAUR:Lanza1987} and \cite{HSAUR:Lanzaetal1988a,HSAUR:Lanzaetal1988b,HSAUR:Lanzaetal1989} report the results of placebo-controlled randomised clinical trials investigating the prevention of gastrointestinal damage by the application of Misoprostol. The degree of the damage is determined by endoscopic examinations and the response variable is defined as the classification: \input{tables/Lanza} \end{frame} \section{Conditional Test Procedures} \begin{frame} \frametitle{Conditional Test Procedures} In clinical trials, it is often impossible to draw a random sample from all patients suffering a certain disease. Commonly, volunteers and patients are recruited from hospital staff, relatives or people showing up for some examination. The test procedures applied in this chapter make no assumptions about random sampling or a specific model. \end{frame} \begin{frame} \frametitle{Permutation Tests} Instead, the null distribution of the test statistics is computed conditionally on all random permutations of the data. Therefore, the procedures shown in the sequel are known as \stress{permutation tests} or \stress{(re)-randomisation tests}. For a general introduction we refer to the text books of \cite{HSAUR:Edgington1987} and \cite{HSAUR:Pesarin2001}. \end{frame} \subsection{Testing Independence of Two Variables} \begin{frame} \frametitle{Testing Independence of Two Variables} Based on $n$ pairs of measurements $(x_i, y_i), i = 1, \dots, n$ we want to test the null hypothesis of the independence of $x$ and $y$. We may distinguish three situations: Both variables $x$ and $y$ are continuous (correlation), one is continuous and the other one is a factor (one-way layout, independent two-sample) or both $x$ and $y$ are factors (contingency tables). \end{frame} \begin{frame} \frametitle{Example: Two Independent Samples} One class of test procedures for the above three situations are randomisation and permutation tests whose basic principles have been described by \cite{HSAUR:Fisher1935} and \cite{HSAUR:Pitman1937} and are best illustrated for the case of continuous measurements $y$ in two groups, i.e., the $x$ variable is a factor that can take values $x = 1$ or $x = 2$. The difference of the means of the $y$ values in both groups is an appropriate statistic for the assessment of the association of $y$ and $x$ \begin{eqnarray*} T = \frac{\sum\limits_{i = 1}^n I(x_i = 1) y_i}{\sum\limits_{i = 1}^n I(x_i = 1)} - \frac{\sum\limits_{i = 1}^n I(x_i = 2) y_i}{\sum\limits_{i = 1}^n I(x_i = 2)}. \end{eqnarray*} Clearly, under the null hypothesis of independence of $x$ and $y$ we expect the distribution of $T$ to be centred about zero. \end{frame} \begin{frame} \frametitle{Computing the Null-Distribution} Suppose that the group labels $x = 1$ or $x = 2$ have been assigned to the observational units by randomisation. When the result of the randomisation procedure is independent of the $y$ measurements, we are allowed to fix the $x$ values and shuffle the $y$ values randomly over and over again. Thus, we can compute, or at least approximate, the distribution of the test statistic $T$ under the conditions of the null hypothesis directly from the data $(x_i, y_i), i = 1, \dots, n$ by the so called \stress{randomisation principle}. \end{frame} \begin{frame} \frametitle{Computing the Null-Distribution} The test statistic $T$ is computed for a reasonable number of shuffled $y$ values and we can determine how many of the shuffled differences are at least as large as the test statistic $T$ obtained from the original data. If this proportion is small, smaller than $\alpha = 0.05$ say, we have good evidence that the assumption of independence of $x$ and $y$ is not realistic and we therefore can reject the null hypothesis. The proportion of larger differences is usually referred to as $p$-value. \end{frame} \begin{frame} \frametitle{Categorical Variables} The test statistic can be computed from the corresponding contingency table in which the observations $(x_i, y_i)$ are cross-classified. We can make use of the test statistic \begin{eqnarray*} X^2 = \sum_{j = 1}^r \sum_{k = 1}^c \frac{(n_{jk} - E_{jk})^2}{E_{jk}}. \end{eqnarray*} Alternatively, Fisher's exact test based on the hyper-geometric probability of the observed contingency table can be applied. Here, all possible tables can be ordered with respect to this metric and $p$-values are computed from the fraction of tables more extreme than the observed one. \end{frame} \begin{frame} \frametitle{Correlation} When both the $x$ and the $y$ measurements are numeric, the test statistic can be formulated as the product, i.e., by the sum of all $x_i y_i, i = 1, \dots, n$. Again, we can fix the $x$ values and shuffle the $y$ values in order to approximate the distribution of the test statistic under the laws of the null hypothesis of independence of $x$ and $y$. \end{frame} \section{Analysis Using R} \subsection{Estimating the Width of a Room Revised} \begin{frame}[fragile] \frametitle{roomwidth Revised} First, we convert metres into feet and store the vector of observations in a variable \Robject{y}: <>= convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) feet <- roomwidth$unit == "feet" metre <- !feet y <- roomwidth$width * convert @ The test statistic is simply the difference in means <>= T <- mean(y[feet]) - mean(y[metre]) T @ \end{frame} \begin{frame}[fragile] \frametitle{roomwidth Revised} In order to approximate the conditional distribution of the test statistic $T$ we compute $9999$ test statistics for shuffled $y$ values. A permutation of the $y$ vector can be obtained from the \Rcmd{sample} function. <>= meandiffs <- double(9999) for (i in 1:length(meandiffs)) { sy <- sample(y) meandiffs[i] <- mean(sy[feet]) - mean(sy[metre]) } @ \end{frame} \begin{frame} \begin{center} <>= hist(meandiffs) abline(v = T, lty = 2) abline(v = -T, lty = 2) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Approximate Null-Distribution} Now, the value of the test statistic $T$ for the original unshuffled data can be compared with the distribution of $T$ under the null hypothesis. The $p$-value, i.e., the proportion of test statistics $T$ larger than \Sexpr{-round(T, 3)} or smaller than \Sexpr{round(T, 3)} is <>= greater <- abs(meandiffs) > abs(T) mean(greater) @ with a confidence interval of <>= binom.test(sum(greater), length(greater))$conf.int @ \end{frame} \begin{frame}[fragile] \frametitle{Exact Null-Distribution} The function \Rcmd{independence\_test} \citep[package \Rpackage{coin},][]{PKG:coin,HSAUR:Hothorn:2006:AmStat} can be used to compute the exact $p$-value for two independence samples: <>= library("coin") independence_test(y ~ unit, data = roomwidth, distribution = exact()) @ \end{frame} \begin{frame}[fragile] \frametitle{Exact WMW-Test} The exact conditional Wilcoxon rank sum test applied to the \Robject{roomwidth} data: <>= wilcox_test(y ~ unit, data = roomwidth, distribution = exact()) @ \end{frame} \subsection{Crowds and Threatened Suicide} \begin{frame} \frametitle{Crowds and Threatened Suicide} The data in this case are in the form of a $2 \times 2$ contingency table and it might be thought that the chi-squared test could again be applied to test for the independence of crowd behaviour and time of year. The $\chi^2$-distribution as an approximation to the independence test statistic is bad in this situation since the expected frequencies are rather small. One solution is to use a conditional test procedure such as Fisher's exact test as described %' above. \end{frame} \begin{frame}[fragile] \frametitle{Fisher's Test} We can apply this test procedure using the \R{} function \Rcmd{fisher.test} to the \Rclass{table} \Robject{suicides}: <>= fisher.test(suicides) @ \end{frame} \subsection{Gastrointestinal Damages} \begin{frame}[fragile] \frametitle{Gastrointestinal Damages} Here we are interested in the comparison of two groups of patients, where one group received a placebo and the other one Misoprostol. In the trials shown here, the response variable is measured on an ordered scale. Data from four clinical studies are available and thus the observations are naturally grouped together. From the \Rclass{data.frame} \Robject{Lanza} we can construct a three-way table as follows: <>= xtabs(~ treatment + classification + study, data = Lanza) @ \end{frame} \begin{frame}[fragile] \frametitle{Gastrointestinal Damages} The classifications are defined by the number of haemorrhages or erosions, the midpoint of the interval for each level is a reasonable choice, i.e., $0$, $1$, $6$, $17$ and $30$. The corresponding linear-by-linear association tests extending the general \index{Linear-by-linear association test} Cochran-Mantel-Haenzel statistics \citep[see][for further details]{HSAUR:Agresti2002} are implemented in package \Rpackage{coin}. \index{Cochran-Mantel-Haenzel statistic} \end{frame} \begin{frame}[fragile] \frametitle{First Study Only} For the first study, the null hypothesis of independence of treatment and gastrointestinal damage, i.e., of no treatment effect of Misoprostol, is tested by <>= library("coin") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "I") @ and, by default, the conditional distribution is approximated by the corresponding limiting distribution. \end{frame} \begin{frame}[fragile] \frametitle{All Studies} We can use \Robject{study} as a block variable and perform a global linear-association test investigating the treatment effect of Misoprostol in all four studies: <>= cmh_test(classification ~ treatment | study, scores = list(classification = c(0, 1, 6, 17, 30)), data = Lanza) @ \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Use the \Rcmd{mosaic} and \Rcmd{assoc} functions from the \Rpackage{vcd} package \citep{PKG:vcd} to create a graphical representation of the deviations from independence in the $2 \times 2$ contingency table \Robject{suicides}. \item Generate two groups with measurements following a normal distribution having different means. For multiple replications of this experiment ($1000$, say), compare the $p$-values of the Wilcoxon Mann-Whitney rank sum test and a permutation test (using \Rcmd{independence\_test}). Where do the differences come from? \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/Ch_cluster_analysis.Rnw0000644000175000017500000003276513055275020020313 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") library("mclust") library("mvtnorm") mai <- par("mai") options(SweaveHooks = list(rmai = function() { par(mai = mai * c(1,1,1,2))})) @ \frame{ \begin{center} \Large{Part 16: Cluster Analysis} \end{center} focuses on finding homogeneous groups of observations. } \section{Introduction} \begin{frame} \frametitle{Exoplanets classification} Exoplanets are planets outside the Solar System. Since 1995 over a hundred exoplanets have been discovered, nearly all being detected indirectly, using the gravitational influence they exert on their associated central stars. From the properties of the exoplanets found up to now it appears that the theory of planetary development constructed for the planets of the Solar System may need to be reformulated. The exoplanets are not at all like the nine local planets that we know so well. A first step in the process of understanding the exoplanets might be to try to classify them with respect to their known properties. The data gives the mass (in Jupiter mass), the period (in earth days) and the eccentricity (\Robject{eccent}) of the exoplanets discovered up until October 2002. \end{frame} \section{Cluster Analysis} \begin{frame} \frametitle{Cluster analysis} Cluster analysis refers to methods for uncovering or discovering groups or clusters of observations that are homogeneous and separated from other groups, for example in medicine (microarray data) or marketing (groups of customers). Clustering techniques essentially try to formalise what human observers do so well in two or three dimensions. Consider, for example, the following scatterplot. We concentrate on two types of clustering procedures: $k$-means type and classification maximum likelihood methods. \end{frame} \begin{frame} \frametitle{Cluster analysis} \begin{center} <>= dat <- rbind(rmvnorm(25, mean = c(3,3)), rmvnorm(20, mean = c(10, 8)), rmvnorm(10, mean = c(20, 1))) plot(abs(dat), xlab = expression(x[1]), ylab = expression(x[2])) @ \end{center} \end{frame} \subsection{$k$-Means Clustering} \begin{frame} \frametitle{$k$-means clustering} The $k$-means clustering technique seeks to partition a set of data into a specified number of groups, $k$, by minimising some numerical criterion, low values of which are considered indicative of a `good' solution. The most commonly %%' used approach, for example, is to try to find the partition of the $n$ individuals into $k$ groups, which minimises the within-group sum of squares over all variables. The problem then appears relatively simple; namely, consider every possible partition of the $n$ individuals into $k$ groups, and select the one with the lowest within-group sum of squares. \end{frame} \begin{frame} \frametitle{$k$-means clustering} Unfortunately, the problem in practice is not so straightforward. The numbers involved are so vast that complete enumeration of \stress{every} possible partition remains impossible even with the fastest computer: \begin{center} \begin{tabular}{rrl} $n$ & $k$ & Number of possible partitions \\ \hline $15$ & $3$ & $2,375,101$ \\ $20$ & $4$ & $45,232,115,901$ \\ $25$ & $8$ & $690,223,721,118,368,580$ \\ $100$ & $5$ & $10^{68}$ \\ \end{tabular} \end{center} \end{frame} \begin{frame} \frametitle{Heuristical approach} \begin{enumerate} \item Find some initial partition of the individuals into the required number of groups. \item Calculate the change in the clustering criterion produced by `moving' each individual from its own to another cluster. %%' \item Make the change that leads to the greatest improvement in the value of the clustering criterion. \item Repeat steps 2 and 3 until no move of an individual causes the clustering criterion to improve. \end{enumerate} When variables are on very different scales (as they are for the exoplanets data) some form of standardization will be needed before applying $k$-means clustering. Note: $k$ has to be fixed in advance and can hardly be estimated. \end{frame} \subsection{Model-based Clustering} \begin{frame} \frametitle{Model-based Clustering} It is assumed that the population from which the observations arise consists of $c$ subpopulations each corresponding to a cluster, and that the density of a $q$-dimensional observation $\x^\top = (x_1, \dots, x_q)$ from the $j$th subpopulation is $f_j(\x, \vartheta_j), j = 1, \dots, c$, for some unknown vector of parameters, $\vartheta_j$. We also introduce a vector $\gamma = (\gamma_1, \dots, \gamma_n)$, where $\gamma_i = j$ of $\x_i$ is from the $j$ subpopulation. The $\gamma_i$ label the subpopulation for each observation $i = 1, \dots, n$. The clustering problem now becomes that of choosing $\vartheta = (\vartheta_1, \dots, \vartheta_c)$ and $\gamma$ to maximise the likelihood function associated with such assumptions. \end{frame} \subsection{Classification Maximum Likelihood} \begin{frame} \frametitle{Classification Maximum Likelihood} $\gamma = (\gamma_1, \dots, \gamma_n)$ gives the labels of the subpopulation to which the observation belongs: so $\gamma_i = j$ if $\x_i$ is from the $j$th population. The clustering problem becomes that of choosing $\vartheta = (\vartheta_1, \dots, \vartheta_c)$ and $\gamma$ to maximise the likelihood \begin{eqnarray*} L(\vartheta, \gamma) = \prod_{i = 1}^n f_{\gamma_i}(\x_i, \vartheta_{\gamma_i}). \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Normal Distribution} If $f_j(\x, \vartheta_j)$ is taken as the multivariate normal density with mean vector $\mu_j$ and covariance matrix $\Sigma_j$, this likelihood has the form \begin{eqnarray*} L(\vartheta, \gamma) = \prod_{j = 1}^c \prod_{i: \gamma_i = j} |\Sigma_j|^{-1/2} \exp\left(-\frac{1}{2} (\x_i - \mu_j)^\top \Sigma_j^{-1} (\x_i - \mu_j)\right). \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Normal Distribution} The maximum likelihood estimator of $\mu_j$ is \begin{eqnarray*} \hat{\mu}_j = n_j^{-1} \sum_{i: \gamma_i = j} \x_i \end{eqnarray*} where the number of observations in each subpopulation is $n_j = \sum_{i = 1}^n I(\gamma_i = j)$. Replacing $\mu_j$ in the likelihood yields the following log-likelihood \begin{eqnarray*} l(\vartheta, \gamma) = -\frac{1}{2} \sum_{j = 1}^c \text{trace}(\W_j \Sigma_j^{-1} + n \log |\Sigma_j|) \end{eqnarray*} where $\W_j$ is the $q \times q$ matrix of sums of squares and cross-products of the variables for subpopulation $j$. \end{frame} \begin{frame} \frametitle{Normal Distribution} If the covariance matrix $\Sigma_j$ is $\sigma^2$ times the identity matrix for all populations $j = 1, \dots, c$, then the likelihood is maximised by choosing $\gamma$ to minimise trace$(\W)$, where \begin{eqnarray*} \W = \sum_{j = 1}^c \W_j, \end{eqnarray*} i.e., minimisation of the written group sum of squares. Use of this criterion in a cluster analysis will lend to produce spherical clusters of largely equal sizes. \end{frame} \begin{frame} \frametitle{Normal Distribution} If $\Sigma_j = \Sigma$ for $j = 1, \dots, c$, then the likelihood is maximised by choosing $\gamma$ to minimise $|\W|$. Use of this criterion in a cluster analysis will lend to produce clusters with the same elliptical slope. If $\Sigma_j$ is not constrained, the likelihood is maximised by choosing $\gamma$ to minimise $\sum_{j = 1}^c n_j \log | \W_j | / n_j$. \end{frame} \begin{frame} \frametitle{Determining $c$} Model selection is a combination of choosing the appropriate clustering model and the optimal number of clusters. A Bayesian approach is used \citep[see][]{HSAUR:FraleyRaftery1999}, using what is known as the \stress{Bayesian Information Criterion} (BIC). \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{Analysis Using R} \begin{center} <>= data("planets", package = "HSAUR3") library("scatterplot3d") scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen), type = "h", angle = 55, pch = 16, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, scale.y = 0.7) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{$k$-means} <>= rge <- apply(planets, 2, max) - apply(planets, 2, min) planet.dat <- sweep(planets, 2, rge, FUN = "/") n <- nrow(planet.dat) wss <- rep(0, 10) wss[1] <- (n - 1) * sum(apply(planet.dat, 2, var)) for (i in 2:10) wss[i] <- sum(kmeans(planet.dat, centers = i)$withinss) plot(1:10, wss, type = "b", xlab = "Number of groups", ylab = "Within groups sum of squares") @ \end{frame} \begin{frame}[fragile] \frametitle{$k$-means} \begin{center} <>= plot(1:10, wss, type = "b", xlab = "Number of groups", ylab = "Within groups sum of squares") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{$k$-means: three clusters} <>= planet_kmeans3 <- kmeans(planet.dat, centers = 3) table(planet_kmeans3$cluster) @ The centers of the clusters for the untransformed data can be computed using a small convenience function <>= ccent <- function(cl) { f <- function(i) colMeans(planets[cl == i,]) x <- sapply(sort(unique(cl)), f) colnames(x) <- sort(unique(cl)) return(x) } ccent(planet_kmeans3$cluster) @ \end{frame} \begin{frame}[fragile] \frametitle{$k$-means: five clusters} <>= planet_kmeans5 <- kmeans(planet.dat, centers = 5) table(planet_kmeans5$cluster) ccent(planet_kmeans5$cluster) @ \end{frame} \subsection{Model-based Clustering in R} \begin{frame}[fragile] \frametitle{Model-based Clustering} <>= library("mclust") planet_mclust <- Mclust(planet.dat) plot(planet_mclust, planet.dat, what = "BIC", col = "black", ylab = "-BIC", ylim = c(0, 350)) @ \end{frame} \begin{frame}[fragile] \frametitle{Model-based Clustering} \begin{center} <>= plot(planet_mclust, planet.dat, what = "BIC", col = "black", ylab = "-BIC", ylim = c(0, 350)) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Model-based Clustering} Different shape of clusters possible: \begin{enumerate} \item Spherical, equal volume, \item Spherical, unequal volume, \item Diagonal equal volume, equal shape, \item Diagonal varying volume, varying shape, \item Ellipsoidal, equal volume, shape and orientation, \item Ellipsoidal, varying volume, shape and orientation. \end{enumerate} The BIC selects model $4$ (diagonal varying volume and varying shape) with three clusters as the best solution: <>= print(planet_mclust) @ \end{frame} \begin{frame}[fragile] \frametitle{Visualizing Results} \begin{center} <>= clPairs(planet.dat, classification = planet_mclust$classification, symbols = 1:3, col = "black") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Visualizing Results} \begin{center} <>= scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen), type = "h", angle = 55, scale.y = 0.7, pch = planet_mclust$classification, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Clusters} <>= table(planet_mclust$classification) ccent(planet_mclust$classification) @ \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} Cluster analysis techniques provide a rich source of possible strategies for exploring complex multivariate data. But the use of cluster analysis in practice does not involve simply the application of one particular technique to the data under investigation, but rather necessitates a series of steps, each of which may be dependent on the results of the preceding one. The final, extremely important, stage concerns the evaluation of the clustering solutions obtained. Are the clusters `real' or merely artefacts of the algorithms? Do other solutions %%' exist that are better in some sense? Can the clusters be given a convincing interpretation? \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The \Robject{pottery}-data give the chemical composition of $48$ specimens of Romano-British pottery, determined by atomic absorption spectrophotometry, for nine oxides. Analyse the pottery data using \Rcmd{Mclust}. To what model in \Rcmd{Mclust} does the $k$-mean approach approximate? \item Construct a three-dimensional drop-line scatterplot of the planets data in which the points are labelled with a suitable cluster label. \item Write a general \R{} function that will display a particular partition from the $k$-means cluster method on both a scatterplot matrix of the original data and a scatterplot or scatterplot matrix of a selected number of principal components of the data. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/graphics/0000755000175000017500000000000012451513136015412 5ustar nileshnileshHSAUR3/inst/slides/graphics/Rlogo.jpg0000644000175000017500000001577312357775376017240 0ustar nileshnileshJFIFvvExifMM*C  !"$"$C" S  !1AQ"2Raq#356BVu$SWr¢%&7CETbcst$!123ARq ?pAAsS*bie,%)ܝ>868⒄$(:-.Y&^ߖt9r)]cquv+Wu'mJ B[ $l6+Ehr&N>.U=!>z?-,d2>HVqO++  ^=1L`;@ܴt~L9p{8.vR%a0q \~ST1qN90|c0q[GOW),eAjt㌔/a}_(O&E9ܓÎ W$s4Hovx-ܻ훈FJM,A|. +Db)rY[EHPI\m=]m'U[*ڜYSx\@8)YQ, U.Ի3_Ԕ2sD%E[ !\(<"/q!AAEjemq#ꃩ X߄|YKeJZ G#=g8#tLfupGY 3w;W—aO>&&HGqS-*}<5RjXjȶ|~J^*&dM~VKؽQ{L3"bNϧ?9cp?4=F*qVJ[q@szt#VE*зFp 5 ?$|ηccc ZP)$5U/ˉ4DR}xZegpPp RWP|z`NY -p!=] [LIeR9NqDK{O2t Ϛ7;BR<Ӎ88q)PEƾB#T*5kRђVfnmrU’G qڲ{2d^j_B+J??l^UqcG[kyy~?tG#D}M}(dj5Ghp&1PzQ^^j_Ad+E~Zr? t+R.$({ jvS&}.\$fS4=wRGTN $''CQ% \58OUovx=G#DFX Y$M!XtT)TCe[fN4۝.g|z@#b]`nzVz 22q3JTTZoAB8R(g g8> 88wr\ͱPBFT |HTYW Ug6 i}k?)sjjߐmc '?$B_7;:sS6n&ʡ;ҮeI)@zdܓ-zfJ\'e,yߊVܾ Tȵ)l)'ڣ0&֧9UCImm)6 X*u'F6,VɫEA )"麮d{_teeMR-mE7YfeyqǭrL\3zJR鮶4[)cBkIj}}LTSa$=g5ni:j6Ku}eJWh; Js !P[Q7](OzYE֜@h (˭R' I1%zy30~U PA340]۞7;䐤|'9I=p7W|Lb M%n9*T H;b)KMye =+ssC92(SZs:Hü800qA CNZX34BezKjRÒ g.3K̺BAG\~"馢ܺq4)vDH[ N[;I#9=x#MٷwI %E ]oa$LM;-PbwS-PbwS=7fLG=FN^~MYq#%i34LrqVJ$׍FN&d/Qh\ңzdeQJ}6=1Wv%&[+U C+u%' 1v+.]sisjX30x~"BVEJSƃ)q)p8Z}xP;s!a%'e(M gJ'N: _cGsnE'Its!9ܓ-MlI[Id%(*=dhJJ2̳hP`Cu&F$L%qy9sG>RohI"sP.knAs>r1FJbJsYzNӕur"j6 C~iT{#m_VM!Y  ( |j] Z~Y Q-PxIN@{Iò*KK2 2M6 `$mzAA3LW4qO ^}"zOaS2nIO+(qRAcr7Qt۽ɞ }Ɉ3j$aY)Une8o1W^6c3.-RfO Zs&)u60*A(q |*u3WH=Q!r`W|K5VpHN\|RsA8s)y/1i%j1΍/tfqI Df!׎PŽKT֝Aa@@@@hkOBf*Q8aQ+ڷJe%{-Lp֏ܥÜn 1m-F[KOKͰ Iv7vw9p%^4݈W2?lFVr^ӈIɼ_!;4vw9Ȼ;NĿL=( ԉ[Ffe6uANQ%ff]wN$) I؈D"ʹSjPІm F2v3{, ( *$HSAUR3/inst/slides/graphics/HSAUR.jpg0000644000175000017500000010037012357775376017024 0ustar nileshnileshJFIFvvCreated with GIMPC       C " \  !1TU"AQSaq2R#B &3bru67ds$%5Vc8CDv4EtJ !1AQ"aq2R#BSr35bcs$4TC ?я,:Zoh_}KRxi}㥦L#4E/7O,:Zoh_}D2>KRxi}㥦L#4E/7O,:Zoh_}D2>KRxi}㥦L#4E/7O,:Zoh_}DȎQ\R,:Zoh_}ks#{v]a-phe-\p;6|;]-BCs'jM++WUHQFM7=ll:<ή9Xv/Qj+_k9r_[g]DM\E}gOS"}gj/3=_zg{/OHDu8zB'{V">M\E}gOS"}gj/3=_zg{/OHDu8zB'{V">M\E}gOS"}gj/3=_zg{/OHDu8zB'{Zni[(Fu ފFjD쮊JRTJU˂u;C׽K;×[An xO xsNJ Zrҽ?o⯐Ci6ޓ--~(vJ07Ù7mʉ|R?U}mFt4tI@<D}d! -)%)=@WsV;ź~Nv)gB[o"dh=)JV$)DJRDUoIe`R)_Mv^.]9OFu|?ܺv7;ѬϮ]M-ǮD$?PRxg68)JRNULF1q?Knq>#l6DQD!FF=ve!1Ksy[+o<*lxs{G]ŧ+o<*mis{G&+o<*mis{G&+o<*mis{G&+o<*mis{G&+o<*mis{G&+o<*mis{G&+o<*mis{G/ (͉Y)XEKKmLZ"C BR}A fMfpY74d9N YӶ~0p5?*=Z\x X\X-r't2>=ulv(Gceu<([c/;泦8_ų ZC]Igzƫ?K]%mjh8VeH JTJ#nN)k`|)DJRD)DJRD)DT]^rz1Kt^sAOggKǘiǏ1ԟEc<'SR?DQ1:}EJp Te>mi$r㖣?mmO&l4cFqO|) (r+ZW߳Md3gb>3kfQ$ŵ-MǙDiǏ1i+@ 1+V5.gO+g>&6\I̸HV^nP^ (XkGh_0o76qTN}{N?+{T"yNDu66~gyT4'DO>ScmM58:ۮ -%? ]kwgEyVp`\t^@-yBA[3mF+4>u!ĭr[Z6;A~#YoiAV$_m]aF_J' Uxߣ_bь\x, "+Ax-N{Ŗ  ꟣ΈI)WW"k ʳK!ȓ]f;쨥ƝYJG3c=ջҽLMcݠ+ĝG|u<S7씫4= a.Vbk| ܴf ^#ʵ1rom ɬd:͕>QO<']^v OH;rVv4f6q Pk^Wlmp;Fn~CYGE03*h23l6 (Eq]yCk!$gvV.GXT1.: ߯܃Sc&2]m>L! 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Ten rats are randomised to each of the four treatments and the weight gain in grams recorded. The question of interest is how diet affects weight gain. \end{frame} \begin{frame} \frametitle{foster: Feeding Rats} The data from a foster feeding experiment with rat mothers and litters of four different genotypes: A, B, I and J. The measurement is the litter weight (in grams) after a trial feeding period. Here the investigator's interest lies %' in uncovering the effect of genotype of mother and litter on litter weight. \end{frame} \begin{frame} \frametitle{skulls: Egyptian Skulls} The data give four measurements made on Egyptian skulls from five epochs. The data has been collected with a view to deciding if there are any differences between the skulls from the five epochs. The measurements are: \begin{description} \item[\Robject{mb}]: maximum breadths of the skull, \item[\Robject{bh}]: basibregmatic heights of the skull, \item[\Robject{bl}]: basialiveolar length of the skull, and \item[\Robject{nh}]: nasal heights of the skull. \end{description} Non-constant measurements of the skulls over time would indicate interbreeding with immigrant populations. \end{frame} \section{Analysis of Variance} \begin{frame} \frametitle{Analysis of Variance} For each of the data sets described previously, the question of interest involves assessing whether certain populations differ in mean value for a single variable or for a set of four variables (\Robject{skulls} data). In the first two cases we shall use \stress{analysis of variance} (ANOVA) and in the last \stress{multivariate analysis of variance} (MANOVA) method for the analysis of this data. \end{frame} \begin{frame} \frametitle{Factorial Designs} Both the \Robject{weightgain} and \Robject{foster} data sets are examples of \stress{factorial designs}, with the factors in the first data set being amount of protein with two levels, and source of protein also with two levels. In the second the factors are the genotype of the mother and the genotype of the litter, both with four levels. The analysis of each data set can be based on the same model but the two data sets differ in that the first is \stress{balanced}, i.e., there are the same number of observations in each cell, whereas the second is \stress{unbalanced} having different numbers of observations in the 16 cells of the design. \end{frame} \begin{frame} \frametitle{ANOVA Model} The model used in the analysis of each is \begin{eqnarray*} y_{ijk} = \mu + \gamma_i + \beta_j + (\gamma\beta)_{ij} + \varepsilon_{ijk} \end{eqnarray*} where $y_{ijk}$ represents the $k$th measurement made in cell $(i,j)$ of the factorial design, $\mu$ is the overall mean, $\gamma_i$ is the main effect of the first factor, $\beta_j$ is the main effect of the second factor, $(\gamma\beta)_{ij}$ is the interaction effect of the two factors and \index{Interaction} $\varepsilon_{ijk}$ is the residual or error term assumed to have a normal distribution with mean zero and variance $\sigma^2$. \end{frame} \begin{frame}[fragile] \frametitle{Formula Specification in R} In \R{}, the model is specified by a model \Rclass{formula}. The \stress{two-way layout with interactions} specified above reads <>= y ~ a + b + a:b @ where the variable \Robject{a} is the first and the variable \Robject{b} is the second \Rclass{factor}. The interaction term $(\gamma\beta)_{ij}$ is denoted by \Robject{a:b}. \end{frame} \begin{frame} \frametitle{Estimation and Inference} The model as specified above is overparameterised, i.e., there are infinitively many solutions to the corresponding estimation equations, and so the parameters have to be constrained in some way, commonly by requiring them to sum to zero. The model given above leads to a partition of the variation in the observations into parts due to main effects and interaction plus an error term that enables a series of $F$-tests. The assumptions made in deriving the $F$-tests are: \begin{itemize} \item The observations are independent of each other, \item The observations in each cell arise from a population having a normal distribution, and \item The observations in each cell are from populations having the same variance. \end{itemize} \end{frame} \begin{frame} \frametitle{MANOVA} The linear model used in this case is \begin{eqnarray*} y_{ijh} = \mu_h + \gamma_{jh} + \varepsilon_{ijh} \end{eqnarray*} where $\mu_h$ is the overall mean for variable $h$, $\gamma_{jh}$ is the effect of the $j$th level of the single factor on the $h$th variable, and $\varepsilon_{ijh}$ is a random error term. The vector $\varepsilon^\top_{ij} = (\varepsilon_{ij1}, \varepsilon_{ij2}, \dots, \varepsilon_{ijq})$ where $q$ is the number of response variables (four in the skull example) is assumed to have a multivariate normal distribution with null mean vector and covariance matrix, $\Sigma$, assumed to be the same in each level of the grouping factor. The hypothesis of interest is that the population mean vectors for the different levels of the grouping factor are the same. \end{frame} \begin{frame} \frametitle{MANOVA Inference} A number of different test statistics are available which may give different results when applied to the same data set, although the final conclusion is often the same. The principal test statistics for the multivariate analysis of variance are \begin{itemize} \item Hotelling-Lawley trace, \item Wilks' ratio of determinants \item Roy's greatest root, \item Pillai trace. \end{itemize} \end{frame} \section{Analysis Using R} \subsection{Weight Gain in Rats} \begin{frame}[fragile] \frametitle{Weight Gain in Rats} We should try to summarise the main features of the data first. The following \R{} code produces the required summary statistics <>= tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), mean) tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), sd) @ \end{frame} \begin{frame} \begin{center} <>= plot.design(weightgain) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{ANOVA} To apply analysis of variance to the data we can use the \Rcmd{aov} function in \R{} and then the \Rcmd{summary} method to give us the analysis of variance table: <>= summary(wg_aov <- aov(weightgain ~ source * type, data = weightgain)) @ \end{frame} \begin{frame}[fragile] \frametitle{ANOVA} The analysis of variance table shows that the main effect of type is highly significant. The main effect of source is not significant. But interpretation of both these main effects is complicated by the type $\times$ source interaction which approaches significance at the $5$\% level. To try to understand this interaction effect it will be useful to plot the mean weight gain for low- and high-protein diets for each level of source of protein, beef and cereal. \end{frame} \begin{frame} \begin{center} <>= interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain, legend = FALSE) legend(1.5, 95, legend = levels(weightgain$source), title = "weightgain$source", lty = 1:2, bty = "n") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{ANOVA Results} The estimates of the intercept and the main and interaction effects can be extracted from the model fit by <>= coef(wg_aov) @ Note that the model was fitted with the restrictions $\gamma_1 = 0$ (corresponding to \Rlevel{Beef}) and $\beta_1 = 0$ (corresponding to \Rlevel{High}) because treatment contrasts were used as default as can be seen from <>= options("contrasts") @ Thus, the coefficient for \Robject{source} of $\Sexpr{coef(wg_aov)[2]}$ can be interpreted as an estimate of the difference $\gamma_2 - \gamma_1$. \end{frame} \subsection{Foster Feeding of Rats of Different Genotype} \begin{frame} \frametitle{Foster Feeding} \begin{center} <>= plot.design(foster) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Unbalanced ANOVA} We can now apply analysis of variance using the \Rcmd{aov} function, but there is a complication caused by the unbalanced nature of the data. Here where there are unequal numbers of observations in the $16$ cells of the two-way layout, it is no longer possible to partition the variation in the data into \stress{non-overlapping} or \stress{orthogonal} sums of squares representing main effects and interactions. In an unbalanced two-way layout with factors $A$ and $B$ there is a proportion of the variance of the response variable that can be attributed to either $A$ or $B$. \end{frame} \begin{frame}[fragile] \frametitle{ANOVA Results} We can derive the two analyses of variance tables for the foster feeding example by applying the \R{} code <>= summary(aov(weight ~ litgen * motgen, data = foster)) @ \end{frame} \begin{frame}[fragile] \frametitle{ANOVA Results} and <>= summary(aov(weight ~ motgen * litgen, data = foster)) @ \end{frame} \begin{frame} \frametitle{Multiple Comparisons} We can investigate the effect of genotype B on litter weight in more detail by the use of \stress{multiple comparison procedures}. Such procedures allow a comparison of all pairs of levels of a factor whilst maintaining the nominal significance level at its selected value and producing adjusted confidence intervals for mean differences. One such procedure is called \stress{Tukey honest significant differences} \index{Tukey honest significant differences} suggested by \cite{HSAUR:Tukey1953}, see \cite{HSAUR:HochbergTamhane1987} also. \end{frame} \begin{frame}[fragile] \frametitle{All-Pair Differences} Here, we are interested in simultaneous confidence intervals for the weight differences between all four genotypes of the mother: <>= TukeyHSD(aov(weight ~ litgen * motgen, data = foster), "motgen") @ \end{frame} \begin{frame} \begin{center} <>= foster_aov <- aov(weight ~ litgen * motgen, data = foster) plot(TukeyHSD(foster_aov, "motgen")) @ \end{center} \end{frame} \subsection{Water Hardness and Mortality} \begin{frame} \frametitle{Water Hardness and Mortality} The water hardness and mortality data for $61$ large towns in England and Wales was analysed in Part~2 and here we will extend the analysis by an assessment of the differences of both hardness and mortality in the North or South. The hypothesis that the two-dimensional mean-vector of water hardness and mortality is the same for cities in the North and the South can be tested by \stress{Hotelling-Lawley} test in a multivariate analysis of variance framework. The \R{} function \Rcmd{manova} can be used to fit such a model and the corresponding \Rcmd{summary} method performs the test specified by the \Rcmd{test} argument. \end{frame} \begin{frame}[fragile] <>= summary(manova(cbind(hardness, mortality) ~ location, data = water), test = "Hotelling-Lawley") @ \end{frame} \begin{frame}[fragile] Looking at the sample means <>= tapply(water$hardness, water$location, mean) tapply(water$mortality, water$location, mean) @ we see large differences in the two regions both in water hardness and mortality, where low mortality is associated with hard water in the South and high mortality with soft water in the North. \end{frame} \subsection{Male Egyptian Skulls} \begin{frame}[fragile] \frametitle{Male Egyptian Skulls} We can begin by looking at a table of mean values for the four measurements within each of the five epochs: <>= means <- aggregate(skulls[,c("mb", "bh", "bl", "nh")], list(epoch = skulls$epoch), mean) means @ \end{frame} \begin{frame} \begin{center} <>= pairs(means[,-1], panel = function(x, y) { text(x, y, abbreviate(levels(skulls$epoch))) }) @ \end{center} \end{frame} \begin{frame}[fragile] There appear to be quite large differences between the epoch means, at least on some of the four measurements. We can now test for a difference more formally by using MANOVA with the following \R{} code to apply each of the four possible test criteria mentioned earlier; <>= skulls_manova <- manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls) sapply(c("Pillai", "Wilks", "Hotelling-Lawley", "Roy"), function(test) summary(skulls_manova, test = test)$stats[1,6]) @ \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Examine the residuals ($\text{observed value} - \text{fitted value}$) from fitting a main effects only model to the \Robject{weightgain} data. What conclusions do you draw? \item The data \Robject{students} arise from a large study of risk taking. Students were randomly assigned to three different treatments labelled AA, C and NC. Students were administered two parallel forms of a test called `low' and `high'. Carry out a test of the equality of the bivariate means of each treatment population. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/title_UZH.tex0000644000175000017500000000150713055275020016204 0ustar nileshnilesh\title{Introduction to Data Analysis with \textsf{R}} \author[T. Hothorn]{Torsten Hothorn} \institute{ Universit\"at Z\"urich \\ \texttt{Torsten.Hothorn@R-project.org} } \date{} \begin{document} \frame{\titlepage} \setbeamertemplate{footline}[page number] \begin{frame}[fragile] \begin{columns} \begin{column}{3.5cm} \includegraphics[width = 3cm]{graphics/HSAUR} \end{column} \begin{column}{7.5cm} This course material is based on \booktitle{A Handbook of Statistical Analysis Using \R{}} (3rd edition) published by CRC press. The \R{} package \Rpackage{HSAUR3} contains all data sets, examples and \R{} code and is available from \curl{http://CRAN.R-project.org/package=HSAUR3} \end{column} \end{columns} \end{frame} HSAUR3/inst/slides/HSAUR_title.Rnw0000644000175000017500000000027713055275020016371 0ustar nileshnilesh \documentclass{beamer} \input{definitions} \usetheme{boxes} \setbeamercovered{transparent} <>= title <- "title_UZH.tex" writeLines(readLines(title)) @ HSAUR3/inst/slides/tables/0000755000175000017500000000000013055275242015070 5ustar nileshnileshHSAUR3/inst/slides/tables/MLR-Xtab.tex0000644000175000017500000000047313055275242017144 0ustar nileshnilesh\begin{eqnarray*} \X = \left( \begin{array}{ccccc} 1 & x_{11} & x_{12} & \dots & x_{1q} \\ 1 & x_{21} & x_{22} & \dots & x_{2q} \\ \vdots & \vdots & \vdots & \ddots & \vdots \\ 1 & x_{n1} & x_{n2} & \dots & x_{nq} \\ \end{array} \right). \end{eqnarray*} HSAUR3/inst/slides/tables/PCA_tab.tex0000644000175000017500000000056013055275242017044 0ustar nileshnilesh \begin{center} \begin{longtable}{cccccc} \caption{Correlations for calculus measurements for the six anterior mandibular teeth.} \\ \hline 1.00 & & & & & \\ 0.54 & 1.00 & & & & \\ 0.34 & 0.65 & 1.00 & & & \\ 0.37 & 0.65 & 0.84 & 1.00 & & \\ 0.36 & 0.59 & 0.67 & 0.80 & 1.00 & \\ 0.62 & 0.49 & 0.43 & 0.42 & 0.55 & 1.00 \\ \hline \end{longtable} \end{center} HSAUR3/inst/slides/tables/CA_perm.tex0000644000175000017500000000057613055275242017130 0ustar nileshnilesh \begin{center} \begin{longtable}{rrl} \caption{Number of possible partitions depending on the sample size $n$ and number of clusters $k$. \label{CA:perm}} \\ $n$ & $k$ & Number of possible partitions \\ \hline $15$ & $3$ & $2,375,101$ \\ $20$ & $4$ & $45,232,115,901$ \\ $25$ & $8$ & $690,223,721,118,368,580$ \\ $100$ & $5$ & $10^{68}$ \\ \end{longtable} \end{center} HSAUR3/inst/slides/tables/CI_rtimesc.tex0000644000175000017500000000123413055275242017633 0ustar nileshnilesh \begin{center} \begin{longtable}{cc|ccc|c} \caption{The general $r \times c$ table. \label{SI:rtimesc}} \\ & & & $y$ & & \\\ & & $1$ & $\dots$ & $c$ & \\ \hline & $1$ & $n_{11}$ & $\dots$ & $n_{1c}$ & $n_{1 \cdot}$ \\\ & $2$ & $n_{21}$ & $\dots$ & $n_{2c}$ & $n_{2 \cdot}$ \\\ $x$ & $\vdots$ & $\vdots$ & $\dots$ & $\vdots$ & $\vdots$ \\\ & $r$ & $n_{r1}$ & $\dots$ & $n_{rc}$ & $n_{r \cdot}$ \\ \hline & & $n_{\cdot 1}$ & $\dots$ & $n_{\cdot c}$ & $n$ \\\ \end{longtable} \end{center}HSAUR3/inst/slides/tables/rec.tex0000644000175000017500000000120613055275242016362 0ustar nileshnilesh\begin{tabular}{llll} \Rpackage{boot} & \Rpackage{lattice} & \Rpackage{Matrix} & \Rpackage{mgcv}\\ \Rpackage{rpart} & \Rpackage{survival} & \Rpackage{base} & \Rpackage{class}\\ \Rpackage{cluster} & \Rpackage{codetools} & \Rpackage{compiler} & \Rpackage{datasets}\\ \Rpackage{foreign} & \Rpackage{graphics} & \Rpackage{grDevices} & \Rpackage{grid}\\ \Rpackage{KernSmooth} & \Rpackage{MASS} & \Rpackage{methods} & \Rpackage{nlme}\\ \Rpackage{nnet} & \Rpackage{parallel} & \Rpackage{spatial} & \Rpackage{splines}\\ \Rpackage{stats} & \Rpackage{stats4} & \Rpackage{tcltk} & \Rpackage{tools}\\ \Rpackage{utils} & NA & NA & NA\\ \end{tabular} HSAUR3/inst/slides/tables/SI_rtimesc.tex0000644000175000017500000000113013055275242017646 0ustar nileshnilesh \begin{center} \begin{tabular}{cc|ccc|c} & & & $y$ & & \\\ & & $1$ & $\dots$ & $c$ & \\ \hline & $1$ & $n_{11}$ & $\dots$ & $n_{1c}$ & $n_{1 \cdot}$ \\\ & $2$ & $n_{21}$ & $\dots$ & $n_{2c}$ & $n_{2 \cdot}$ \\\ $x$ & $\vdots$ & $\vdots$ & $\dots$ & $\vdots$ & $\vdots$ \\\ & $r$ & $n_{r1}$ & $\dots$ & $n_{rc}$ & $n_{r \cdot}$ \\ \hline & & $n_{\cdot 1}$ & $\dots$ & $n_{\cdot c}$ & $n$ \\\ \end{tabular} \end{center}HSAUR3/inst/slides/tables/SI_mcnemar.tex0000644000175000017500000000030413055275242017624 0ustar nileshnilesh \begin{center} \begin{tabular}{cccc} & & \multicolumn{2}{c}{Sample 1} \\ & & present & absent \\ Sample 2 & present & $a$ & $b$ \\ & absent & $c$ & $d$ \\ \end{tabular} \end{center} HSAUR3/inst/slides/tables/Lanza.tex0000644000175000017500000000052313055275242016657 0ustar nileshnilesh \begin{center} \begin{tabular}{ll} Classification & Endoscopy Examination \\ \hline 1 & No visible lesions \\ 2 & One haemorrhage or erosion \\ 3 & 2-10 haemorrhages or erosions \\ 4 & 11-25 haemorrhages or erosions \\ 5 & More than 25 haemorrhages or erosions \\ & or an invasive ulcer of any size\\ \hline \end{tabular} \end{center} HSAUR3/inst/slides/tables/MLR-ANOVA-tab.tex0000644000175000017500000000067713055275242017664 0ustar nileshnilesh \begin{center} \begin{longtable}{lccc} \caption{Analysis of variance table for the multiple linear regression model. \label{MLR-ANOVA-tab}} \\ Source of variation & Sum of squares & Degrees of freedom \\ \hline Regression & $\sum\limits_{i = 1}^n (\hat{y}_i - \bar{y})^2$ & $q$ \\ Residual & $\sum\limits_{i = 1}^n (\hat{y}_i - y_i)^2$ & $n - q - 1$ \\ Total & $\sum\limits_{i = 1}^n (y_i - \bar{y})^2$ & $n - 1$ \\ \end{longtable} \end{center} HSAUR3/inst/slides/tables/exMDS.tex0000644000175000017500000000044313055275242016573 0ustar nileshnilesh\begin{eqnarray*} s_{ij} = \left\{ \begin{array}{lcl} 9 & \text{if} & i = j \\ 8 & \text{if} & 1 \le | i - j | \le 3 \\ 7 & \text{if} & 4 \le | i - j | \le 6 \\ & \cdots & \\ 1 & \text{if} & 22 \le | i - j | \le 24 \\ 0 & \text{if} & | i - j | \ge 25 \\ \end{array} \right. \end{eqnarray*} HSAUR3/inst/slides/Ch_density_estimation.Rnw0000644000175000017500000004500013055275020020624 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 8: Density Estimation} \end{center} focuses on estimating uni- and multivariate densities. } <>= x <- library("KernSmooth") x <- library("flexmix") x <- library("boot") data("CYGOB1", package = "HSAUR3") @ \section{Introduction} \begin{frame} \frametitle{Erupting Geysers} Old Faithful is the most popular attraction of Yellowstone National Park, although it is not the largest or grandest geyser in the park. Old Faithful can vary in height from 100--180 feet with an average near 130--140 feet. Eruptions normally last between $1.5$ to $5$ minutes. From August 1 to August 15, 1985, Old Faithful was observed and the waiting times between successive eruptions noted. There were $300$ eruptions observed, so $299$ waiting times were (in minutes) recorded. \end{frame} \begin{frame} \frametitle{Star Clusters} The Hertzsprung-Russell (H-R) diagram forms the basis of the theory of stellar evolution. The diagram is essentially a plot of the energy output of stars plotted against their surface temperature. Data from the H-R diagram of Star Cluster CYG OB1, calibrated according to \cite{HSAUR:VanismaGreve1972} are given in \Robject{CYGOB1}. \end{frame} \section{Density Estimation} \begin{frame} \frametitle{Density Estimation} The goal of density estimation is to approximate the probability density function of a random variable (univariate or multivariate) given a sample of observations of the variable. Univariate histograms are a simple example of a density estimate; they are often used for two purposes, counting and displaying the distribution of a variable, but according to \cite{HSAUR:Wilkinson1992}, they are effective for neither. For bivariate data, two-dimensional histograms can be constructed, but for small and moderate sized data sets that is not of any real use for estimating the bivariate density function, simply because most of the `boxes' in the histogram %' will contain too few observations, or if the number of boxes is reduced the resulting histogram will be too coarse a representation of the density function. \end{frame} \begin{frame} \frametitle{Density Estimation} If we are willing to assume a particular form for the variable's %' distribution, for example, Gaussian, density estimation would be reduced to estimating the parameters of the assumed distribution. More commonly, however, we wish to allow the data to speak for themselves and so one of a variety of non-parametric estimation procedures that are now available might be used. One of the most popular class of procedures is the kernel density estimators, which we now briefly describe for univariate and bivariate data. \end{frame} \subsection{Kernel Density Estimators} \begin{frame} \frametitle{Kernel Density Estimators} From the definition of a probability density, if the random $X$ has a density $f$, \begin{eqnarray*} f(x) = \lim_{h \rightarrow 0} \frac{1}{2h} \P(x - h < X < x + h). \end{eqnarray*} For any given $h$ a na{\"\i}ve estimator is \begin{eqnarray*} \hat{f}(x) = \frac{1}{2hn} \sum_{i = 1}^n I(x_i \in (x - h, x + h)), \end{eqnarray*} i.e., the number of $x_1, \dots, x_n$ falling in the interval $(x - h, x + h)$ divided by $2hn$. \end{frame} \begin{frame} \frametitle{Kernel Density Estimators} If we introduce a weight function $W$ given by \begin{eqnarray*} W(x) = \left\{\begin{array}{lcl} \frac{1}{2} & & |x| < 1 \\\\ %end 0 & & \text{else} \end{array} \right . \end{eqnarray*} then the na{\"\i}ve estimator can be rewritten as %" \begin{eqnarray*} \hat{f}(x) = \frac{1}{n} \sum_{i = 1}^n \frac{1}{h} W\left(\frac{x - x_i}{h}\right). \end{eqnarray*} but is unfortunately not continuous function. \end{frame} \begin{frame} \frametitle{Kernel Density Estimators} Better: \begin{eqnarray*} \hat{f}(x) = \frac{1}{hn} \sum_{i = 1}^n K\left(\frac{x - x_i}{h}\right) \end{eqnarray*} where $K$ is known as the \stress{kernel function} and $h$ as the \stress{bandwidth} or \stress{smoothing parameter}. The kernel function must satisfy the condition \begin{eqnarray*} \int_{-\infty}^\infty K(x)dx = 1. \end{eqnarray*} Usually, but not always, the kernel function will be a symmetric density function for example, the normal. \end{frame} \begin{frame} \frametitle{Kernel Functions} \begin{description} \item[rectangular:] \begin{eqnarray*} K(x) = \left\{\begin{array}{lcl} \frac{1}{2} & & |x| < 1 \\\\ %end 0 & & \text{else} \end{array} \right . \end{eqnarray*} \item[triangular:] \begin{eqnarray*} K(x) = \left\{\begin{array}{lcl} 1 - |x| & & |x| < 1 \\\\ %end 0 & & \text{else} \end{array} \right . \end{eqnarray*} \item[Gaussian:] \begin{eqnarray*} K(x) = \frac{1}{\sqrt{2 \pi}} e^{-\frac{1}{2}x^2} \end{eqnarray*} \end{description} \end{frame} \begin{frame}[fragile] \frametitle{Kernel Functions} \begin{center} <>= rec <- function(x) (abs(x) < 1) * 0.5 tri <- function(x) (abs(x) < 1) * (1 - abs(x)) gauss <- function(x) 1/sqrt(2*pi) * exp(-(x^2)/2) x <- seq(from = -3, to = 3, by = 0.001) plot(x, rec(x), type = "l", ylim = c(0,1), lty = 1, ylab = expression(K(x))) lines(x, tri(x), lty = 2) lines(x, gauss(x), lty = 3) legend(-3, 0.8, legend = c("Rectangular", "Triangular", "Gaussian"), lty = 1:3, title = "kernel functions", bty = "n") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Kernel Functions} The kernel estimator $\hat{f}$ is a sum of `bumps' placed at the observations. %' The kernel function determines the shape of the bumps while the window width $h$ determines their width. We look at the individual bumps $n^{-1}h^{-1} K((x - x_i) / h)$, as well as the estimate $\hat{f}$ obtained by adding them up for an artificial set of data points <>= x <- c(0, 1, 1.1, 1.5, 1.9, 2.8, 2.9, 3.5) n <- length(x) xgrid <- seq(from = min(x) - 1, to = max(x) + 1, by = 0.01) h <- 0.4 bumps <- sapply(x, function(a) gauss((xgrid - a)/h)/(n * h)) @ \end{frame} \begin{frame}[fragile] \frametitle{Kernel Functions} \small \begin{center} <>= plot(xgrid, rowSums(bumps), type = "l", xlab = "x", ylab = expression(hat(f)(x)), lwd = 2) rug(x, lwd = 2) out <- apply(bumps, 2, function(b) lines(xgrid, b)) @ \end{center} \normalsize \end{frame} \subsection{Bivariate Density Estimation} \begin{frame} \frametitle{Bivariate Density Estimation} The kernel density estimator considered as a sum of `bumps' %' centred at the observations has a simple extension to two dimensions (and similarly for more than two dimensions). The bivariate estimator for data $(x_1, y_1)$, $(x_2, y_2)$, $\dots$, $(x_n, y_n)$ is defined as \begin{eqnarray*} \hat{f}(x, y) = \frac{1}{nh_xh_y} \sum_{i = 1}^n K\left(\frac{x - x_i}{h_x}, \frac{y - y_i}{h_y}\right). \end{eqnarray*} In this estimator each coordinate direction has its own smoothing parameter $h_x$ and $h_y$. An alternative is to scale the data equally for both dimensions and use a single smoothing parameter. \end{frame} \begin{frame} \frametitle{Bivariate Kernels} \begin{description} \item[Bivariate Normal kernel:] \begin{eqnarray*} K(x, y) = \frac{1}{2 \pi}e^{-\frac{1}{2} (x^2 + y^2)}. \end{eqnarray*} \item[Bivariate Epanechnikov kernel:] \begin{eqnarray*} K(x, y) = \left\{\begin{array}{lcl} \frac{2}{\pi}(1 - x^2 - y^2) & & x^2 + y^2 < 1 \\\\ %end 0 & & \text{else} \end{array} \right. \end{eqnarray*} \end{description} \end{frame} \begin{frame}[fragile] \frametitle{Epanechnikov} \begin{center} <>= epa <- function(x, y) ((x^2 + y^2) < 1) * 2/pi * (1 - x^2 - y^2) x <- seq(from = -1.1, to = 1.1, by = 0.05) epavals <- sapply(x, function(a) epa(a, x)) persp(x = x, y = x, z = epavals, xlab = "x", ylab = "y", zlab = expression(K(x, y)), theta = -35, axes = TRUE, box = TRUE) @ \end{center} \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{Old Faithful} \begin{center} <>= data("faithful", package = "datasets") x <- faithful$waiting layout(matrix(1:3, ncol = 3)) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Gaussian kernel", border = "gray") lines(density(x, width = 12), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Rectangular kernel", border = "gray") lines(density(x, width = 12, window = "rectangular"), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Triangular kernel", border = "gray") lines(density(x, width = 12, window = "triangular"), lwd = 2) rug(x) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Star Clusters} \small \begin{center} <>= CYGOB1d <- bkde2D(CYGOB1, bandwidth = sapply(CYGOB1, dpik)) contour(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity") @ \end{center} \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Star Clusters} \begin{center} <>= persp(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity", zlab = "estimated density", theta = -35, axes = TRUE, box = TRUE) @ \end{center} \end{frame} \subsection{A Parametric Density Estimate for the Old Faithful Data} \begin{frame} \frametitle{Parametric Old Faithful} Two-component normal mixture distribution \begin{eqnarray*} f(x) = p \phi(x, \mu_1, \sigma_1^2) + (1 - p) \phi(x, \mu_2, \sigma^2_2) \end{eqnarray*} where $\phi(x, \mu, \sigma^2)$ denotes the normal density. This distribution had five parameters to estimate, the mixing proportion, $p$, and the mean and variance of each component normal distribution. Pearson 100 years ago heroically attempted this by the method of moments, which required solving a polynomial equation of the 9$^{\text{th}}$ degree. Nowadays the preferred estimation approach is maximum likelihood. \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} <>= logL <- function(param, x) { d1 <- dnorm(x, mean = param[2], sd = param[3]) d2 <- dnorm(x, mean = param[4], sd = param[5]) -sum(log(param[1] * d1 + (1 - param[1]) * d2)) } startparam <- c(p = 0.5, mu1 = 50, sd1 = 3, mu2 = 80, sd2 = 3) opp <- optim(startparam, logL, x = faithful$waiting, method = "L-BFGS-B", lower = c(0.01, rep(1, 4)), upper = c(0.99, rep(200, 4))) opp @ \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} <>= print(opp[names(opp) != "message"]) @ \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} Optimising the appropriate likelihood `by hand' %' is not very convenient. In fact, (at least) two packages offer high-level functionality for estimating mixture models. The first one is package \Rpackage{mclust} \citep{PKG:mclust} implementing the methodology described in \cite{HSAUR:FraleyRaftery2002}. Here, a Bayesian information criterion (BIC) is applied to choose the form of the mixture model: <>= library("mclust") @ <>= library("mclust") mc <- Mclust(faithful$waiting) mc @ \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} The estimated means are <>= mc$parameters$mean @ with estimated standard deviation (found to be equal within both groups) <>= sqrt(mc$parameters$variance$sigmasq) @ The proportion is $\hat{p} = \Sexpr{round(mc$parameters$pro[1], 2)}$. \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} The second package is called \Rpackage{flexmix}: <>= library("flexmix") fl <- flexmix(waiting ~ 1, data = faithful, k = 2) @ with $\hat{p} = \Sexpr{round(fl@prior, 2)}$ and estimated parameters <>= parameters(fl, component = 1) parameters(fl, component = 2) @ \end{frame} \begin{frame}[fragile] \frametitle{Maximum Likelihood Estimation} \small \begin{center} <>= opar <- as.list(opp$par) rx <- seq(from = 40, to = 110, by = 0.1) d1 <- dnorm(rx, mean = opar$mu1, sd = opar$sd1) d2 <- dnorm(rx, mean = opar$mu2, sd = opar$sd2) f <- opar$p * d1 + (1 - opar$p) * d2 hist(x, probability = TRUE, xlab = "Waiting times (in min.)", border = "gray", xlim = range(rx), ylim = c(0, 0.06), main = "") lines(rx, f, lwd = 2) lines(rx, dnorm(rx, mean = mean(x), sd = sd(x)), lty = 2, lwd = 2) legend(50, 0.06, lty = 1:2, bty = "n", legend = c("Fitted two-component mixture density", "Fitted single normal density")) @ \end{center} \normalsize \end{frame} \section{Bootstrap} \begin{frame}[fragile] \frametitle{The Bootstrap} We can get standard errors for the five parameter estimates by using a bootstrap approach \citep[see][]{HSAUR:EfronTibshirani1993}. First, we define a function that, for a bootstrap sample \Robject{indx}, fits a two-component mixture model and returns $\hat{p}$ and the estimated means <>= library("boot") fit <- function(x, indx) { a <- Mclust(x[indx], minG = 2, maxG = 2)$parameters if (a$pro[1] < 0.5) return(c(p = a$pro[1], mu1 = a$mean[1], mu2 = a$mean[2])) return(c(p = 1 - a$pro[1], mu1 = a$mean[2], mu2 = a$mean[1])) } @ \end{frame} \begin{frame}[fragile] \frametitle{The Bootstrap} The function \Rcmd{fit} can now be fed into the \Rcmd{boot} function \citep{PKG:boot} for bootstrapping (here $1000$ bootstrap samples are drawn) \begin{Schunk} \begin{Sinput} R> bootpara <- boot(faithful$waiting, fit, R = 1000) \end{Sinput} \end{Schunk} <>= bootparafile <- system.file("cache", "DE-bootpara.rda", package = "HSAUR3") if (file.exists(bootparafile)) { load(bootparafile) } else { bootpara <- boot(faithful$waiting, fit, R = 1000) } @ Variability of our estimates $\hat{p}$ (BCa confidence intervals): <>= boot.ci(bootpara, type = "bca", index = 1) @ \end{frame} \begin{frame}[fragile] \frametitle{The Bootstrap} We see that there is a reasonable variability in the mixture model, however, the means in the two components are rather stable, as can be seen from <>= boot.ci(bootpara, type = "bca", index = 2) @ for $\hat{\mu}_1$ \end{frame} \begin{frame}[fragile] \frametitle{The Bootstrap} and for $\hat{\mu}_2$ from <>= boot.ci(bootpara, type = "bca", index = 3) @ \end{frame} \begin{frame}[fragile] \frametitle{The Bootstrap} Bootstrap-distribution of $\hat{\mu}_1$ and $\hat{\mu}_2$ with BCa confidence intervals: <>= bootplot <- function(b, index, main = "") { dens <- density(b$t[,index]) ci <- boot.ci(b, type = "bca", index = index)$bca[4:5] est <- b$t0[index] plot(dens, main = main) y <- max(dens$y) / 10 segments(ci[1], y, ci[2], y, lty = 2) points(ci[1], y, pch = "(") points(ci[2], y, pch = ")") points(est, y, pch = 19) } @ \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) bootplot(bootpara, 2, main = expression(mu[1])) bootplot(bootpara, 3, main = expression(mu[2])) @ \end{center} \end{figure} \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} Histograms and scatterplots are frequently used to give graphical representations of univariate and bivariate data. But both can often be improved and made more helpful by adding some form of density estimate. For scatterplots in particular adding a contour plot of the estimated bivariate density can be particularly useful in aiding in the identification of clusters, gaps and outliers. \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The \Robject{galaxies} data are the velocities of $82$ galaxies from six well-separated conic sections of space \citep{HSAUR:Postmanetal1986,HSAUR:Roeder1990}. The data are intended to shed light on whether or not the observable universe contains superclusters of galaxies surrounded by large voids. The evidence for the existence of superclusters would be the multimodality of the distribution of velocities. Construct a histogram of the data and add a variety of kernel estimates of the density function. What do you conclude about the possible existence of superclusters of galaxies? \item The \Robject{birthdeathrates} data give the birth and death rates for 69 countries \citep[from][]{HSAUR:Hartigan1975}. Produce a scatterplot of the data that shows a contour plot of the estimated bivariate density. Does the plot give you any interesting insights into the possible structure of the data? \end{itemize} \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item A sex difference in the age of onset of schizophrenia was noted by \cite{HSAUR:Kraepelin1919}. Subsequent epidemiological studies of the disorder have consistently shown an earlier onset in men than in women. One model that has been suggested to explain this observed difference is known as the \stress{subtype model} which postulates two types of schizophrenia, one characterised by early onset, typical symptoms and poor premorbid competence, and the other by late onset, atypical symptoms and good premorbid competence. The early onset type is assumed to be largely a disorder of men and the late onset largely a disorder of women. By fitting finite mixtures of normal densities separately to the onset data for men and women given in \Robject{schizophrenia} see if you can produce some evidence for or against the subtype model. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/Ch_simple_inference.Rnw0000644000175000017500000003264213055275020020230 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 3: Simple Inference} \end{center} focuses on classical statistical test procedures for the Guessing Lengths, Wave Energy, Water Hardness, Piston Rings, and Rearrests of Juveniles examples. } \section{Introduction} <>= library("vcd") @ \begin{frame} \frametitle{roomwidth: Estimating Room Widths} Shortly after metric units of length were officially introduced in Australia in the 1970s, each of a group of 44 students was asked to guess, to the nearest metre, the width of the lecture hall in which they were sitting. Another group of 69 students in the same room was asked to guess the width in feet, to the nearest foot. The main question is whether estimation in feet and in metres gives different results. \end{frame} \begin{frame} \frametitle{waves: Bending Stress} In a design study for a device to generate electricity from wave power at sea, experiments were carried out on scale models in a wave tank to establish how the choice of mooring method for the system affected the bending stress produced in part of the device. The wave tank could simulate a wide range of sea states and the model system was subjected to the same sample of sea states with each of two mooring methods, one of which was considerably cheaper than the other. The question of interest is whether bending stress differs for the two mooring methods. \end{frame} \begin{frame} \frametitle{water: Mortality and Water Hardness} The data were collected in an investigation of environmental causes of disease. They show the annual mortality per 100,000 for males, averaged over the years 1958--1964, and the calcium concentration (in parts per million) in the drinking water for 61 large towns in England and Wales. The higher the calcium concentration, the harder the water. Towns at least as far north as Derby are identified in the table. Here there are several questions that might be of interest including: are mortality and water hardness related, and do either or both variables differ between northern and southern towns? \end{frame} \begin{frame} \frametitle{pistonrings: Piston-ring Failures} The two-way contingency table shows the number of piston-ring failures in each of three legs of four steam-driven compressors located in the same building. The compressors have identical design and are oriented in the same way. The question of interest is whether the two categorical variables (compressor and leg) are independent. \end{frame} \begin{frame} \frametitle{rearrests: Rearrests of Juveniles} The data arise from a sample of juveniles convicted of felony in Florida in 1987. Matched pairs were formed using criteria such as age and the number of previous offences. For each pair, one subject was handled in the juvenile court and the other was transferred to the adult court. Whether or not the juvenile was rearrested by the end of 1988 was then noted. Here the question of interest is whether the true proportions rearrested were identical for the adult and juvenile court assignments? \end{frame} \section{Statistical Tests} \begin{frame} \frametitle{Statistical Tests} Inference is the process of \begin{itemize} \item drawing conclusions about a population \item on the basis of measurements or observations \item made on a random (!) sample of individuals from the population. \end{itemize} In the following, we shall illustrate the application of the most common statistical tests to the examples shown before. \end{frame} \subsection{Comparing Normal Populations: Student's $t$-Tests} %' \begin{frame} \frametitle{Comparing Normal Populations} The independent samples $t$-test is used to test the null hypothesis that the means of two populations are the same: $H_0: \mu_1 = \mu_2$. The variable to be compared is assumed to have a normal distribution with the same standard deviation in both populations. Test statistic: \begin{eqnarray*} t = \frac{\bar{y}_1 - \bar{y}_2}{s \sqrt{1 / n_1 + 1 / n_2}} \sim t_{n_1 + n_2 - 2} \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Unequal Variances} If the two populations are suspected of having different variances (boxes in boxplots differ significantly), a modified form of the $t$ statistic, known as the Welch test, may be used: \begin{eqnarray*} t = \frac{\bar{y}_1 - \bar{y}_2}{\sqrt{s_1^2 / n_1 + s_2^2 / n_2}} \sim t_\nu. \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Paired Observations} A paired $t$-test is used to compare the means of two populations when samples from the populations are available, in which each individual in one sample is paired with an individual in the other sample or each individual in the sample is observed twice. If the values of the variable of interest, $y$, for the members of the $i$th pair in groups $1$ and $2$ are denoted as $y_{1i}$ and $y_{2i}$, then the differences $d_i = y_{1i} - y_{2i}$ are assumed to have a normal distribution with mean $\mu$ and the null hypothesis here is that the mean difference is zero, i.e., $H_0: \mu = 0$. The paired $t$-statistic is \begin{eqnarray*} t = \frac{\bar{d}}{s / \sqrt{n}} \sim t_{n-1}. \end{eqnarray*} \end{frame} \subsection{Non-parametric Analogues of Independent Samples and Paired $t$-Tests} \begin{frame} \frametitle{Wilcoxon-Mann-Whitney Test} For two independent groups, the Wilcoxon Mann-Whitney rank sum test applies the $t$-statistic to the joint ranks of all measurements in both groups instead of the original measurements. The null hypothesis to be tested is that the two populations being compared have identical distributions. \end{frame} \begin{frame} \frametitle{Wilcoxon-Signed-Rank Test} The Wilcoxon signed-rank statistic is based on the ranks of the absolute differences $|d_i|$. The statistic is defined as the sum of the ranks associated with positive difference $d_i > 0$. It should be noted that this test is only valid when the differences $d_i$ are symmetrically distributed. \end{frame} \subsection{Testing Independence in Contingency Tables} \begin{frame} \frametitle{Contingency Tables} When a sample of $n$ observations in two nominal (categorical) variables are available, they can be arranged into a cross-classification \input{tables/SI_rtimesc} \end{frame} \begin{frame} \frametitle{$\chi^2$-Test} Under the null hypothesis of independence of the row variable $x$ and the column variable $y$, estimated expected values $E_{jk}$ for cell $(j, k)$ can be computed from the corresponding margin totals $E_{jk} = n_{j\cdot} n_{\cdot k} / n$. The test statistic is \begin{eqnarray*} X^2 = \sum_{j = 1}^r \sum_{k = 1}^c \frac{(n_{jk} - E_{jk})^2}{E_{jk}} \sim \chi^2_{(r-1)(c-1)} \end{eqnarray*} \end{frame} \subsection{McNemar's Test} %' \begin{frame} \frametitle{McNemar's Test} Often categorical data arise from \stress{paired} observations, for example, cases matched with controls on variables such as sex, age and so on, or observations made on the same subjects on two occasions: \input{tables/SI_mcnemar} Under the hypothesis that the two populations do not differ in their probability of having the characteristic present, the test statistic \begin{eqnarray*} X^2 = \frac{ (c - b)^2}{c + b} \sim \chi^2_1. \end{eqnarray*} \end{frame} \section{Analysis Using R} \subsection{Estimating the Width of a Room} \begin{frame}[fragile] \frametitle{Estimating the Width of a Room} The first step should be to convert the metre estimates into feet: <>= convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) @ Now, we get the usual summary statistics by <>= tapply(roomwidth$width * convert, roomwidth$unit, summary) @ \end{frame} \begin{frame}[fragile] \frametitle{Boxplots} \begin{center} <>= layout(matrix(c(1,2,1,3), nrow = 2, ncol = 2, byrow = FALSE)) boxplot(I(width * convert) ~ unit, data = roomwidth, ylab = "Estimated width (feet)", var.width = TRUE, names = c("Estimates in feet", "Estimates in metres (converted to feet)")) feet <- roomwidth$unit == "feet" qqnorm(roomwidth$width[feet], ylab = "Estimated width (feet)") qqline(roomwidth$width[feet]) qqnorm(roomwidth$width[!feet], ylab = "Estimated width (metres)") qqline(roomwidth$width[!feet]) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Test for Differences} The two-sample test problem is specified by a \Rclass{formula} and the $t$-test reads <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) @ \end{frame} \begin{frame}[fragile] \frametitle{Test for Differences} The Welch-test can be computed via <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = FALSE) @ \end{frame} \begin{frame}[fragile] \frametitle{Test for Differences} The Wilcoxon Mann-Whitney test as one alternative test procedure: <>= wilcox.test(I(width * convert) ~ unit, data = roomwidth, conf.int = TRUE) @ \end{frame} \subsection{Wave Energy Device Mooring} \begin{frame}[fragile] \frametitle{Wave Energy Device Mooring} The \Robject{waves} data set requires the use of a matched pairs $t$-test. This test assumes that the differences between the matched observations have a normal distribution so we can begin by checking this assumption by constructing a boxplot and a normal probability plot \end{frame} \begin{frame} \begin{center} <>= mooringdiff <- waves$method1 - waves$method2 layout(matrix(1:2, ncol = 2)) boxplot(mooringdiff, ylab = "Differences (Newton metres)", main = "Boxplot") abline(h = 0, lty = 2) qqnorm(mooringdiff, ylab = "Differences (Newton metres)") qqline(mooringdiff) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Test for Zero Mean} The paired-$t$-test is performed via <>= t.test(mooringdiff) @ \end{frame} \begin{frame}[fragile] \frametitle{Test for Zero Median} <>= wilcox.test(mooringdiff) @ \end{frame} \subsection{Mortality and Water Hardness} \begin{frame}[fragile] \frametitle{Mortality and Water Hardness} We will construct a scatterplot of the data enhanced somewhat by the addition of information about the marginal distributions of water hardness (calcium concentration) and mortality, and by adding the estimated linear regression fit for mortality on hardness. The scatterplot shows that as hardness increases mortality decreases, and the histogram for the water hardness shows it has a rather skewed distribution. \end{frame} \begin{frame} \begin{center} <>= nf <- layout(matrix(c(2, 0, 1, 3), 2, 2, byrow = TRUE), c(2, 1), c(1, 2), TRUE) psymb <- as.numeric(water$location) plot(mortality ~ hardness, data = water, pch = psymb) abline(lm(mortality ~ hardness, data = water)) legend("topright", legend = levels(water$location), pch = c(1,2), bty = "n") hist(water$hardness) boxplot(water$mortality) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Testing Correlation} We can both calculate the Pearson's correlation coefficient %' between the two variables and test whether it differs significantly for zero by using <>= cor.test(~ mortality + hardness, data = water) @ \end{frame} \subsection{Piston-ring Failures} \begin{frame}[fragile] \frametitle{Piston-ring Failures} The first step in the analysis of the \Robject{pistonrings} data is to apply the chi-squared test for independence. This we can do in \R{} using <>= chisq.test(pistonrings) @ \end{frame} \begin{frame}[fragile] \frametitle{Inspection Deviations} Rather than looking at the simple differences of observed and expected values for each cell it is preferable to consider a \stress{standardised residual}: <>= chisq.test(pistonrings)$residuals @ \end{frame} \begin{frame} \begin{center} <>= library("vcd") assoc(pistonrings) @ \end{center} \end{frame} \subsection{Rearrests of Juveniles} \begin{frame}[fragile] \frametitle{Rearrests of Juveniles} In \Robject{rearrests} the counts in the four cells refer to the matched pairs of subjects; for example, in $\Sexpr{rearrests[1,1]}$ pairs both members of the pair were rearrested. Here, we use McNemar's test: <>= mcnemar.test(rearrests, correct = FALSE) binom.test(rearrests[2], n = sum(rearrests[c(2,3)]))$p.value @ \end{frame} \section*{Exercises} \begin{frame}[fragile] \frametitle{Exercises} \begin{itemize} \item After the students had made the estimates of the width of the lecture hall the room width was accurately measured and found to be $13.1$ metres ($43.0$ feet). Use this additional information to determine which of the two types of estimates was more precise. \item For the mortality and water hardness data calculate the correlation between the two variables in each region, north and south. \item For the data in table \Robject{rearrests} estimate the difference between the probability of being rearrested after being tried in an adult court and in a juvenile court, and find a $95\%$ confidence interval for the population difference. \end{itemize} \end{frame} \end{document} HSAUR3/inst/slides/Ch_logistic_regression_glm.Rnw0000644000175000017500000003716713055275020021644 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 7: Logistic Regression and \\ Generalised Linear Models} \end{center} explains how to fit regression models to binary response variables and to counts. } \section{Introduction} \begin{frame} \frametitle{Introduction} Ordinary linear regression models assume the response variable to be (approximately) normal distributed. However, many experiments require an assessment of the relationship between covariates and a binary response variable, i.e., a variable measured at only two levels, or counts. Generalised linear models provide a framework for the estimation of regression models with non-normal response variables. The regression relationship between the covariates and the response is modelled by a linear combination of the covariates. \end{frame} \begin{frame} \frametitle{plasma: Erythrocyte sedimentation rate (ESR)} The erythrocyte sedimentation rate (ESR) is the rate at which red blood cells (erythrocytes) settle out of suspension in blood plasma, when measured under standard conditions. If the ESR increases when the level of certain proteins in the blood plasma rise in association with conditions such as rheumatic diseases, chronic infections and malignant diseases, its determination might be useful in screening blood samples taken from people suspected of suffering from one of the conditions mentioned. The absolute value of the ESR is not of great importance, rather it is whether it is less than 20mm/hr since lower values indicate a `healthy' individual. The question of interest is whether there is any association between the probability of an ESR reading greater than 20mm/hr and the levels of the two plasma proteins. If there is not then the determination of ESR would not be useful for diagnostic purposes. \end{frame} \begin{frame} \frametitle{womensrols: Women's role in society} In a survey carried out in 1974/1975 each respondent was asked if he or she agreed or disagreed with the statement `Women should take care of running their homes and leave running the country up to men'. The questions here are whether the responses of men and women differ and how years of education affects the response. \end{frame} \begin{frame} \frametitle{polyps: Colonic polyps} The data stem from an placebo-controlled trial of a non-steroidal anti-inflammatory drug in the treatment of familial andenomatous polyposis (FAP). The trial was halted after a planned interim analysis had suggested compelling evidence in favour of the treatment. The data give the number of colonic polyps after a $12$-month treatment period. The question of interest is whether the number of polyps is related to treatment and/or age of patients. \end{frame} \section{Logistic Regression and Generalised Linear Models} \begin{frame} \frametitle{Logistic Regression} The ordinary multiple regression model is described as $y \sim \N(\mu, \sigma^2)$ where $\mu = \beta_0 + \beta_1 x_1 + \dots + \beta_q x_q$. This makes it clear that this model is suitable for continuous response variables with, conditional on the values of the explanatory variables, a normal distribution with constant variance. So clearly the model would not be suitable for applying to the erythrocyte sedimentation rate since the response variable is binary. \end{frame} \begin{frame} \frametitle{Logistic Regression} For modelling the expected value of the response directly as a linear function of explanatory variables, a suitable transformation is modelled. In this case the most suitable transformation is the \stress{logistic} or \stress{logit} function of $\pi = P(y = 1)$ leading to the model \begin{eqnarray*} \text{logit}(\pi) = \log\left(\frac{\pi}{1 - \pi}\right) = \beta_0 + \beta_1 x_1 + \dots + \beta_q x_q. \end{eqnarray*} The logit of a probability is simply the log of the odds of the response taking the value one. \end{frame} \begin{frame} \frametitle{Logistic Regression} The logit function can take any real value, but the associated probability always lies in the required $[0,1]$ interval. In a logistic regression model, the parameter $\beta_j$ associated with explanatory variable $x_j$ is such that $\exp(\beta_j)$ is the odds that the response variable takes the value one when $x_j$ increases by one, conditional on the other explanatory variables remaining constant. The parameters of the logistic regression model (the vector of regression coefficients $\beta$) are estimated by maximum likelihood. \end{frame} \begin{frame} \frametitle{The Generalised Linear Model (GLM)} Essentially GLMs consist of three main features; \begin{enumerate} \item An \stress{error distribution} giving the distribution of the response around its mean. \item A \stress{link function}, $g$, that shows how the linear function of the explanatory variables is related to the expected value of the response \begin{eqnarray*} g(\mu) = \beta_0 + \beta_1 x_1 + \dots + \beta_q x_q. \end{eqnarray*} \item The \stress{variance function} that captures how the variance of the response variable depends on the mean. \end{enumerate} Estimation of the parameters in a GLM is usually achieved through a maximum likelihood approach. \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Plot} At first, we will look at conditional density plots of the response variable given the two explanatory variables describing how the conditional distribution of the categorical variable ESR changes over the numerical variables fibrinogen and gamma globulin. It appears that higher levels of each protein are associated with ESR values above $20$ mm/hr. \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Plot} \begin{center} <>= layout(matrix(1:2, ncol = 2)) cdplot(ESR ~ fibrinogen, data = plasma) cdplot(ESR ~ globulin, data = plasma) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: GLM} We can now fit a logistic regression model to the data using the \Rcmd{glm} function. We start with a model that includes only a single explanatory variable, \Robject{fibrinogen}. The code to fit the model is <>= plasma_glm_1 <- glm(ESR ~ fibrinogen, data = plasma, family = binomial()) @ \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Summary} \small <>= summary(plasma_glm_1) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Estimation} From the summary we see that the regression coefficient for fibrinogen is significant at the $5\%$ level. An increase of one unit in this variable increases the log-odds in favour of an ESR value greater than $20$ by an estimated $\Sexpr{round(coef(plasma_glm_1)["fibrinogen"], 2)}$ with 95\% confidence interval <>= confint(plasma_glm_1)["fibrinogen",] @ \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: GLM} Nevertheless it seems likely that increased values of fibrinogen lead to a greater probability of an ESR value greater than $20$. We can now fit a logistic regression model that includes both explanatory variables using the code <>= plasma_glm_2 <- glm(ESR ~ fibrinogen + globulin, data = plasma, family = binomial()) @ \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Summary} \small <>= summary(plasma_glm_2) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Model Comparison} <>= anova(plasma_glm_1, plasma_glm_2, test = "Chisq") @ \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Prediction} The estimated conditional probability of a ESR value larger $20$ for all observations can be computed by <>= prob <- predict(plasma_glm_1, type = "response") @ \end{frame} \begin{frame}[fragile] \frametitle{ESR and Plasma Proteins: Plot} %%\setkeys{Gin}{width = 0.5\textwidth} \tiny \begin{center} <>= plot(globulin ~ fibrinogen, data = plasma, xlim=c(2,6), ylim=c(25,50), pch = ".") symbols(plasma$fibrinogen, plasma$globulin, circles = prob, add = TRUE) @ \end{center} \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: GLM} %' We first fit a model that includes the two explanatory variables using the code <>= fm <- cbind(agree,disagree) ~ gender + education womensrole_glm_1 <- glm(fm, data = womensrole, family = binomial()) @ \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Summary} %' \small <>= summary(womensrole_glm_1) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Plot} We now are going to construct a plot comparing the observed proportions of agreeing with those fitted by our fitted model. Because we will reuse this plot for another fitted object later on, we define a function which plots years of education against some fitted probabilities, e.g., \tiny <>= role.fitted1 <- predict(womensrole_glm_1, type = "response") myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Plot} \begin{center} <>= myplot(role.fitted1) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Interactions} %' An interaction term for gender and education can be included into the logistic regression model via <>= fm <- cbind(agree,disagree) ~ gender * education womensrole_glm_2 <- glm(fm, data = womensrole, family = binomial()) @ \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Interactions} %' \small <>= summary(womensrole_glm_2) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Women's Role in Society: Plot} \begin{center} <>= myplot(predict(womensrole_glm_2, type = "response")) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Poisson GLM} We will apply a GLM with a log link function, ensuring that fitted values are positive, and a Poisson error distribution, i.e., \begin{eqnarray*} \P(y) = \frac{e^{-\lambda}\lambda^y}{y!}. \end{eqnarray*} This type of GLM is often known as \stress{Poisson regression}. \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Poisson GLM} <>= polyps_glm_1 <- glm(number ~ treat + age, data = polyps, family = poisson()) @ (The default link function when the Poisson family is requested is the log function.) \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Summary} \small <>= summary(polyps_glm_1) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Overdispersion} We see that the regression coefficients for both age and treatment are highly significant. But there is a problem with the model, but before we can deal with it we need a short digression to describe in more detail the third component of GLMs mentioned in the previous section, namely their variance functions, $V(\mu)$. Both the Poisson and binomial distributions have variance functions that are completely determined by the mean. The phenomenon of greater variability than expected under the model is observed is called \stress{overdispersion}. \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Quasi-Likelihood} We can deal with overdispersion by using a procedure known as \stress{quasi-likelihood}, which allows the estimation of model parameters without fully knowing the error distribution of the response variable. <>= polyps_glm_2 <- glm(number ~ treat + age, data = polyps, family = quasipoisson()) @ \end{frame} \begin{frame}[fragile] \frametitle{Colonic Polyps: Summary} \small <>= summary(polyps_glm_2) @ \normalsize \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} Generalised linear models provide a very powerful and flexible framework for the application of regression models to a variety of non-normal response variables, for example, logistic regression to binary responses and Poisson regression to count data. \end{frame} \section{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Construct a perspective plot of the fitted values from a logistic regression model fitted to the \Robject{plasma} data in which both fibrinogen and gamma globulin are included as explanatory variables. \item \cite{HSAUR:Collett2003} argues that two outliers need to be removed from the \Robject{plasma} data. Try to identify those two unusual observations by means of a scatterplot. \item The \Robject{bladdercancer} data arise from $31$ male patients who have been treated for superficial bladder cancer \citep[see][]{HSAUR:Seeber1998}, and give the number of recurrent tumours during a particular time after the removal of the primary tumour, along with the size of the original tumour (whether smaller or larger than $3$ cm). Use Poisson regression to estimate the effect of size of tumour on the number of recurrent tumours. \end{itemize} \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The \Robject{leuk} data show the survival times from diagnosis of patients suffering from leukemia and the values of two explanatory variables, the white blood cell count (\Robject{wbc}) and the presence or absence of a morphological characteristic of the white blood cells (\Robject{ag}) \citep[the data are available in package \Rpackage{MASS},][]{HSAUR:VenablesRipley2002}. Define a binary outcome variable according to whether or not patients lived for at least 24 weeks after diagnosis and then fit a logistic regression model to the data. It may be advisable to transform the very large white blood counts to avoid regression coefficients very close to 0 (and odds ratios very close to 1). And a model that contains only the two explanatory variables may not be adequate for these data. Construct some graphics useful in the interpretation of the final model you fit. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/setup.R0000644000175000017500000000060013055275020015067 0ustar nileshnilesh rm(list = ls()) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", width = 55, # digits = 4, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) HSAUR3/inst/slides/Ch_analysing_longitudinal_dataI.Rnw0000644000175000017500000003410313055275020022553 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \setkeys{Gin}{width=0.95\textheight} \frame{ \begin{center} \Large{Part 11: Analysing Longitudinal Data I} \end{center} focuses on mixed effects models for repeated measurements. } \section{Introduction} <>= library("Matrix") library("lme4") @ \begin{frame} \frametitle{Beat the Blues} Depression is a major public health problem across the world. Antidepressants are the front line treatment, but many patients either do not respond to them, or do not like taking them. The main alternative is psychotherapy, and the modern `talking treatments' such as \stress{cognitive behavioural therapy} (CBT) %%' have been shown to be as effective as drugs, and probably more so when it comes to relapse. The data to be used in this chapter arise from a clinical trial of an interactive, multimedia program known as `Beat the Blues' %%' designed to deliver cognitive behavioural therapy to depressed patients via a computer terminal. In a randomised controlled trial of the program, patients with depression recruited in primary care were randomised to either the Beating the Blues program, or to `Treatment as Usual' (TAU). \end{frame} \begin{frame} \frametitle{Beat the Blues} Here, we concentrate on the \stress{Beck Depression Inventory II} (BDI). Measurements on this variable were made on the following five occasions: \begin{itemize} \item Prior to treatment, \item Two months after treatment began and \item At one, three and six months follow-up, i.e., at three, five and eight months after treatment. %%%better: At two, four and six months follow-up, i.e. at four, six and eight %%%months after treatment \end{itemize} There is interest here in assessing the effect of taking antidepressant drugs (\Robject{drug}, yes or no) and length of the current episode of depression (\Robject{length}, less or more than six months). \end{frame} \section{Analysing Longitudinal Data} \begin{frame} \frametitle{Analysing Longitudinal Data} Because several observations of the response variable are made on the same individual, it is likely that the measurements will be correlated rather than independent, even after conditioning on the explanatory variables. Consequently repeated measures data require special methods of analysis and models for such data need to include parameters linking the explanatory variables to the repeated measurements, parameters analogous to those in the usual multiple regression model and, in addition parameters that account for the correlational structure of the repeated measurements. In this chapter: linear mixed effects models. Next chapter: generalised estimating equations. \end{frame} \section{Linear Mixed Effects Models} \begin{frame} \frametitle{Linear Mixed Effects Models} Linear mixed effects models for repeated measures data formalise the sensible idea that an individual's pattern of responses is %%' likely to depend on many characteristics of that individual, including some that are unobserved. These unobserved variables are then included in the model as random variables, i.e., random effects. The essential feature of such models is that correlation amongst the repeated measurements on the same unit arises from shared, unobserved variables. Conditional on the values of the random effects, the repeated measurements are assumed to be independent, the so-called \stress{local independence} assumption. \end{frame} \begin{frame} \frametitle{Random Intercept Model} Let $y_{ij}$ represent the observation made at time $t_j$ on individual $i$. A possible model for the observation $y_{ij}$ might be \begin{eqnarray*} y_{ij} = \beta_0 + \beta_1 t_j + u_i + \varepsilon_{ij}. \end{eqnarray*} Here the total residual that would be present in the usual linear regression model has been partitioned into a subject-specific random component $u_i$ which is constant over time plus a residual $\varepsilon_{ij}$ which varies randomly over time. $\E(u_i) = 0$ and $\Var(u) = \sigma^2_u$, $\E(\varepsilon_{ij}) = 0$ with $\Var(\varepsilon_{ij}) = \sigma^2$; $u_i$ and $\varepsilon_{ij}$ independent of each other and of time $t_j$. \begin{eqnarray*} \Var(y_{ij}) = \Var(u_i + \varepsilon_{ij}) = \sigma^2_u + \sigma^2 \end{eqnarray*} ``variance components'' \end{frame} \begin{frame} \frametitle{Random Intercept Model} The covariance between the total residuals at two time points $j$ and $k$ in the same individual is $\Cov(u_i + \varepsilon_{ij}, u_i + \varepsilon_{ik}) = \sigma^2_u$. Note that these covariances are induced by the shared random intercept; for individuals with $u_i > 0$, the total residuals will tend to be greater than the mean, for individuals with $u_i < 0$ they will tend to be less than the mean. \begin{eqnarray*} \Cor(u_i + \varepsilon_{ij}, u_i + \varepsilon_{ik}) = \frac{\sigma^2_u}{\sigma^2_u + \sigma^2}. \end{eqnarray*} This is an \stress{intra-class correlation} interpreted as the proportion of the total residual variance that is due to residual variability between subjects. \end{frame} \begin{frame} \frametitle{Random Intercept and Slope Model} In this model there are two types of random effects, the first modelling heterogeneity in intercepts, $u_i$, and the second modelling heterogeneity in slopes, $v_i$: \begin{eqnarray*} y_{ij} = \beta_0 + \beta_1 t_j + u_i + v_i t_j + \varepsilon_{ij} \end{eqnarray*} The two random effects are assumed to have a bivariate normal distribution with zero means for both variables and variances $\sigma^2_u$ and $\sigma^2_v$ with covariance $\sigma_{uv}$: \begin{eqnarray*} \Var(u_i + v_i t_j + \varepsilon_{ij}) = \sigma^2_u + 2 \sigma_{uv} t_j + \sigma^2_v t_j^2 + \sigma^2 \end{eqnarray*} which is no longer constant for different values of $t_j$. \end{frame} \begin{frame} \frametitle{Random Intercept and Slope Model} \begin{eqnarray*} \Cov(u_i + v_i t_j + \varepsilon_{ij}, u_i + v_i t_{k} + \varepsilon_{ik}) = \sigma^2_u + \sigma_{uv} (t_j - t_{k}) + \sigma^2_v t_jt_{k} \end{eqnarray*} is not constrained to be the same for all pairs $t_j$ and $t_{k}$. \end{frame} \begin{frame} \frametitle{Mixed Effects Models} Linear mixed-effects models can be estimated by maximum likelihood. However, this method tends to underestimate the variance components. A modified version of maximum likelihood, known as \stress{restricted maximum likelihood} is therefore often recommended; this provides consistent estimates of the variance components. Competing linear mixed-effects models can be compared using a likelihood ratio test. If however the models have been estimated by restricted maximum likelihood this test can only be used if both models have the same set of fixed effects. \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{Beat the Blues} \begin{center} <>= data("BtheB", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) ylim <- range(BtheB[,grep("bdi", names(BtheB))], na.rm = TRUE) tau <- subset(BtheB, treatment == "TAU")[, grep("bdi", names(BtheB))] boxplot(tau, main = "Treated as usual", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 4, 6, 8), ylim = ylim) btheb <- subset(BtheB, treatment == "BtheB")[, grep("bdi", names(BtheB))] boxplot(btheb, main = "Beat the Blues", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 4, 6, 8), ylim = ylim) @ \end{center} \end{frame} \begin{frame} \frametitle{Beat the Blues} Fit model to the data including the baseline BDI values (\Robject{pre.bdi}), \Robject{treatment} group, \Robject{drug} and \Robject{length} as fixed effect covariates. First, a rearrangement of the data is necessary from the `wide form' in which they appear in the \Robject{BtheB} data frame %%' into the `long form' in which each separate repeated measurement %%' and associated covariate values appear as a separate row in a \Rclass{data.frame}. \end{frame} \begin{frame}[fragile] \frametitle{Beat the Blues} <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt" @ The resulting \Rclass{data.frame} \Robject{BtheB\_long} contains a number of missing values! \end{frame} \begin{frame}[fragile] \frametitle{Random Intercept and Slope} <>= library("lme4") BtheB_lmer1 <- lmer(bdi ~ bdi.pre + time + trt + drug + length + (1 | subject), data = BtheB_long, method = "ML", na.action = na.omit) BtheB_lmer2 <- lmer(bdi ~ bdi.pre + time + trt + drug + length + (time | subject), data = BtheB_long, method = "ML", na.action = na.omit) anova(BtheB_lmer1, BtheB_lmer2) @ \end{frame} \begin{frame} \frametitle{Model Checking} We can check the assumptions of the final model fitted to the \Robject{BtheB} data, i.e., the normality of the random effect terms and the residuals, by first using the \Rcmd{ranef} method to \stress{predict} the former and the \Rcmd{residuals} method to calculate the differences between the observed data values and the fitted values, and then using normal probability plots on each. There appear to be no large departures from linearity in either plot. \end{frame} \begin{frame}[fragile] \frametitle{Model Checking} \begin{center} <>= layout(matrix(1:2, ncol = 2)) qint <- ranef(BtheB_lmer1)$subject[["(Intercept)"]] qres <- residuals(BtheB_lmer1) qqnorm(qint, ylab = "Estimated random intercepts", xlim = c(-3, 3), ylim = c(-20, 20), main = "Random intercepts") qqline(qint) qqnorm(qres, xlim = c(-3, 3), ylim = c(-20, 20), ylab = "Estimated residuals", main = "Residuals") qqline(qres) @ \end{center} \end{frame} \section{Prediction of Random Effects} \begin{frame} \frametitle{Prediction of Random Effects} The random effects are not estimated as part of the model. However, having estimated the model, we can \stress{predict} the values of the random effects. According to Bayes' Theorem, the \stress{posterior %' probability} of the random effects is given by \begin{eqnarray*} \P(u | y, x) = f(y | u, x) g(u) \end{eqnarray*} where $f(y | u, x)$ is the conditional density of the responses given the random effects and covariates (a product of normal densities) and $g(u)$ is the \stress{prior} density of the random effects (multivariate normal). The means of this posterior distribution can be used as estimates of the random effects and are known as \stress{empirical Bayes estimates}. \end{frame} \section{The Problem of Dropouts} \begin{frame} \frametitle{The Problem of Dropouts} \begin{itemize} \item[Dropout completely at random (DCAR)] here the probability that a patient drops out does not depend on either the observed or missing values of the response. \item[\stress{Dropout at random} (DAR)] The dropout at random mechanism occurs when the probability of dropping out depends on the outcome measures that have been observed in the past, but given this information is conditionally independent of all the future (unrecorded) values of the outcome variable following dropout. \item[\stress{Non-ignorable} dropout] The final type of dropout mechanism is one where the probability of dropping out depends on the unrecorded missing values -- observations are likely to be missing when the outcome values that would have been observed had the patient not dropped out, are systematically higher or lower than usual. \end{itemize} \end{frame} \begin{frame} \frametitle{The Problem of Dropouts} Under what type of dropout mechanism are the mixed effects models considered in this chapter valid? The good news is that such models can be shown to give valid results under the relatively weak assumption that the dropout mechanism is DAR. When the missing values are thought to be informative, any analysis is potentially problematical. \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} Mixed effects models allow the correlations between the repeated measurements to be accounted for so that correct inferences can be drawn about the effects of covariates of interest on the repeated response values. In this chapter we have concentrated on responses that are continuous and conditional on the explanatory variables and random effects have a normal distribution. But random effects models can also be applied to non-normal responses, for example binary variables. \end{frame} \section*{Exercises} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Use the \Rcmd{lm} function to fit a model to the Beat the Blues data that assumes that the repeated measurements are independent. Compare the results to those from fitting the random intercept model \Robject{BtheB\_lmer1}. \item Investigate whether there is any evidence of an interaction between treatment and time for the Beat the Blues data. \item Construct a plot of the mean profiles of both groups in the Beat the Blues data, showing also standard deviation bars at each time point. \end{itemize} \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item The \Robject{phosphate} data show the plasma inorganic phosphate levels for $33$ subjects, $20$ of whom are controls and $13$ of whom have been classified as obese \citep{HSAUR:Davis2002}. Produce separate plots of the profiles of the individuals in each group, and guided by these plots fit what you think might be sensible linear mixed effects models. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \end{frame} \end{document} HSAUR3/inst/slides/Ch_survival_analysis.Rnw0000644000175000017500000003442413055275020020477 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") @ \frame{ \begin{center} \Large{Part 10: Survival Analysis} \end{center} explains how to fit regression models to response variables which are only incompletely available. } \section{Introduction} \begin{frame} \frametitle{Introduction} \cite{HSAUR:Granaetal2002} report results of a non-randomised clinical trial investigating a novel radioimmunotherapy in malignant glioma patients. The overall survival, i.e., the time from the beginning of the therapy to the disease-caused death of the patient, is compared for two groups of patients. Since only some patients die by others survive, the time to death is not completely observed. Only the time the patient is still alive is known. Such a time measurement is called \stress{censored}. The main interest is to investigate whether the patients treated with the novel radioimmunothery survive for a longer time. \end{frame} \begin{frame} \frametitle{Introduction} The effects of hormonal treatment with Tamoxifen in women suffering from node-positive breast cancer were investigated in a randomised clinical trial as reported by \cite{HSAUR:Schumacher1994}. Complete data of seven prognostic factors of $686$ women are available for prognostic modelling. Observed hypothetical prognostic factors are age, menopausal status, tumor size, tumor grade, number of positive lymph nodes, progesterone receptor, estrogen receptor and the information of whether or not a hormonal therapy was applied. We are interested in an assessment of the impact of the covariates on the survival time of the patients. \end{frame} \section{Survival Analysis} \begin{frame} \frametitle{Survival Analysis} In many medical studies, the main outcome variable is the time to the occurrence of a particular event. Such observations are generally referred to by the generic term \stress{survival data}. Such data generally require special techniques for analysis for two main reasons: \begin{enumerate} \item Survival data are generally not symmetrically distributed. \item At the completion of the study, some patients may not have reached the endpoint of interest (death, relapse, etc.). Consequently, the exact survival times are not known. All that is known is that the survival times are greater than the amount of time the individual has been in the study. The survival times of these individuals are said to be \stress{censored} (precisely, they are right-censored). \end{enumerate} \end{frame} \begin{frame} \frametitle{Survival and Hazard Function} Of central importance in the analysis of survival time data are two functions used to describe their distribution, namely the \stress{survival} (or \stress{survivor}) \stress{function} and the \stress{hazard function}. The survivor function, $S(t)$, is defined as the probability that the survival time, $T$, is greater than or equal to some time $t$, i.e., \begin{eqnarray*} S(t) = \P(T \ge t) \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Estimation} When there are no censored observations in the sample of survival times, a non-parametric survivor function can be estimated simply as \begin{eqnarray*} \hat{S}(t) = \frac{\text{number of individuals with survival times} \ge t} {n} \end{eqnarray*} where $n$ is the total number of observations. This simple method used to estimate the survivor function when there are no censored observations cannot now be used for survival times when censored observations are present. In the presence of censoring, the survivor function is typically estimated using the \stress{Kaplan-Meier} estimator \citep{HSAUR:KaplanMeier1958}. \end{frame} \begin{frame} \frametitle{Kaplan-Meier Estimator} This involves first ordering the survival times from the smallest to the largest such that $t_{(1)} \le t_{(2)} \le \dots \le t_{(n)}$, where $t_{(j)}$ is the $j$th largest unique survival time. The Kaplan-Meier estimate of the survival function is obtained as \begin{eqnarray*} \hat{S}(t) = \prod_{j: t_{(j)} \le t} \left( 1 - \frac{d_j}{r_j} \right) \end{eqnarray*} where $r_j$ is the number of individuals at risk just before $t_{(j)}$ (including those censored at $t_{(j)}$), and $d_j$ is the number of individuals who experience the event of interest (death, etc.) at time $t_{(j)}$. \end{frame} \begin{frame} \frametitle{Comparing Survival Functions} A formal test of the equality of the survival curves for the two groups can be made using the \stress{log-rank test}. First, the expected number of deaths is computed for each unique death time, or \stress{failure time} in the data set, assuming that the chances of dying, given that subjects are at risk, are the same for both groups. The total number of expected deaths is then computed for each group by adding the expected number of deaths for each failure time. The test then compares the observed number of deaths in each group with the expected number of deaths using a chi-squared test. \end{frame} \begin{frame} \frametitle{Hazard Functions} The hazard function, $h(t)$, is defined as the probability that an individual experiences the event in a small time interval, $s$, given that the individual has survived up to the beginning of the interval, when the size of the time interval approaches zero; \begin{eqnarray*} h(t) = \lim_{s \rightarrow 0} \frac{\P(t \le T \le t + s | T \ge t)}{s} \end{eqnarray*} where $T$ is the individual's survival time. For example, the probability of dying at age $100$ is very small because most people die before that age; in contrast, the probability of a person dying at age $100$ who has reached that age is much greater. \end{frame} \begin{frame} \frametitle{Hazard and Survival Function} The hazard function and survivor function are related by the formula \begin{eqnarray*} S(t) = \exp(-H(t)) \end{eqnarray*} where $H(t)$ is known as the \stress{integrated hazard} or \stress{cumulative hazard}, and is defined as follows: \begin{eqnarray*} H(t) = \int_0^t h(u) du, \end{eqnarray*} \end{frame} \begin{frame} \frametitle{Shapes of Hazard Functions} In practice the hazard function may increase, decrease, remain constant or have a more complex shape. The hazard function for death in human beings, for example, has the `bath tub' shape: \begin{center} <>= hazard <- function(x, alpha = 5, theta = 0.1, sigma = 100) (alpha*theta*(1 - exp(-(x/sigma)^alpha))^(theta - 1)* exp(-(x/sigma)^alpha)*(x/sigma)^(alpha-1))/(sigma* (1 - (1 - exp(-(x/sigma)^alpha))^theta)) x <- seq(from = 0.1, to = 100, by = 0.1) h <- hazard(x, alpha = 5, theta = 0.1, sigma = 100) plot(x, h, type = "l", xlab = "Time", ylab = "Hazard", ylim = c(0, max(h))) @ \end{center} \end{frame} \begin{frame} \frametitle{Cox' Proportional Hazards Model} Modelling the hazard function directly as a linear function of explanatory variables is not appropriate since $h(t)$ is restricted to being positive, however \begin{eqnarray*} h(t) = h_0(t) \exp(\beta_1 x_1 + \dots + \beta_q x_q). \end{eqnarray*} is appropriate. Written in this way we see that the model forces the hazard ratio between two individuals to be constant over time since \begin{eqnarray*} \frac{h(t | \x_1)}{h(t | \x_2)} = \frac{\exp(\beta^\top \x_1)}{\exp(\beta^\top \x_2)} \end{eqnarray*} where $\x_1$ and $\x_2$ are vectors of covariate values for two individuals. \end{frame} \begin{frame} \frametitle{Interpreting Cox' Model} In the Cox model, the baseline hazard describes the common shape of the survival time distribution for all individuals, while the \stress{relative risk function}, $\exp(\beta^\top \x)$, gives the level of each individual's hazard. The interpretation %%' of the parameter $\beta_j$ is that $\exp(\beta_j)$ gives the relative risk change associated with an increase of one unit in covariate $x_j$, all other explanatory variables remaining constant. The parameters in a Cox model can be estimated by maximising what is known as a \stress{partial likelihood}. \end{frame} \section{Analysis Using R} \begin{frame}[fragile] \frametitle{Analysis Using R: Glioma Data} \small \begin{center} <>= data("glioma", package = "coin") library("survival") layout(matrix(1:2, ncol = 2)) g3 <- subset(glioma, histology == "Grade3") plot(survfit(Surv(time, event) ~ group, data = g3), main = "Grade III Glioma", lty = c(2, 1), ylab = "Probability", xlab = "Survival Time in Month", legend.bty = "n", legend.text = c("Control", "Treated") ) g4 <- subset(glioma, histology == "GBM") plot(survfit(Surv(time, event) ~ group, data = g4), main = "Grade IV Glioma", ylab = "Probability", lty = c(2, 1), xlab = "Survival Time in Month", xlim = c(0, max(glioma$time) * 1.05)) @ \end{center} \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Analysis Using R: Glioma Data} \begin{center} <>= data("glioma", package = "coin") library("survival") layout(matrix(1:2, ncol = 2)) g3 <- subset(glioma, histology == "Grade3") plot(survfit(Surv(time, event) ~ group, data = g3), main = "Grade III Glioma", lty = c(2, 1), ylab = "Probability", xlab = "Survival Time in Month", legend.bty = "n", legend.text = c("Control", "Treated") ) g4 <- subset(glioma, histology == "GBM") plot(survfit(Surv(time, event) ~ group, data = g4), main = "Grade IV Glioma", ylab = "Probability", lty = c(2, 1), xlab = "Survival Time in Month", xlim = c(0, max(glioma$time) * 1.05)) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Comparing Groups} The figure leads to the impression that patients treated with the novel radioimmunotherapy survive longer, regardless of the tumor type. In order to assess if this informal finding is reliable, we may perform a log-rank test via <>= survdiff(Surv(time, event) ~ group, data = g3) @ which indicates that the survival times are indeed different in both groups. \end{frame} \begin{frame}[fragile] \frametitle{Permutation Testing} However, the number of patients is rather limited and so it might be dangerous to rely on asymptotic tests. Conditioning on the data and computing the distribution of the test statistics without additional assumptions is one alternative: <>= library("coin") surv_test(Surv(time, event) ~ group, data = g3, distribution = exact()) @ \end{frame} \begin{frame}[fragile] \frametitle{Breast Cancer Survival} \begin{center} <>= data("GBSG2", package = "TH.data") plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2), lty = 1:2, mark.time = FALSE, ylab = "Probability", xlab = "Survival Time in Days") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Breast Cancer Survival} \begin{center} <>= data("GBSG2", package = "TH.data") plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2), lty = 1:2, mark.time = FALSE, ylab = "Probability", xlab = "Survival Time in Days") legend(250, 0.2, legend = c("yes", "no"), lty = c(2, 1), title = "Hormonal Therapy", bty = "n") @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Fitting Cox' Model} The response variable is coded as a \Rclass{Surv} object and Cox' model can be fitted using: <>= GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2) summary(GBSG2_coxph) @ \end{frame} \begin{frame}[fragile] \frametitle{Fitting Cox' Model} The response variable is coded as a \Rclass{Surv} object and Cox' model can be fitted using: \small <>= GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2) summary(GBSG2_coxph) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Confidence Intervals} Since we are especially interested in the relative risk for patients who underwent a hormonal therapy, we can compute an estimate of the relative risk and a corresponding confidence interval via <>= ci <- confint(GBSG2_coxph) exp(cbind(coef(GBSG2_coxph), ci))["horThyes",] @ This result implies that patients treated with a hormonal therapy had a lower risk and thus survived longer compared to women who were not treated this way. \end{frame} \begin{frame}[fragile] \frametitle{Survival Trees} A simple prognostic tree model with only a few terminal nodes might be helpful for relating the risk to certain subgroups of patients: \small <>= library("partykit") ctree(Surv(time, cens) ~ ., data = GBSG2) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Visualizing Survival Trees} \begin{center} <>= plot(ctree(Surv(time, cens) ~ ., data = GBSG2)) @ \end{center} \end{frame} \section{Summary} \begin{frame} \frametitle{Summary} The analysis of life-time data is complicated by the fact that the time to some event is not observable for all observations due to censoring. Survival times are analysed by some estimates of the survival function, for example by a non-parametric Kaplan-Meier estimate or by semi-parametric proportional hazards regression models. \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Try to reproduce the analysis presented by \cite{HSAUR:SauerbreiRoyston1999}, i.e., fit a multivariable fractional polynomial to the \Robject{GBSG2} data (using package \Rpackage{mfp})! \item The \Robject{mastectomy} data are the survival times (in months) after mastectomy of women with breast cancer. The cancers are classified as having metastised or not based on a histochemical marker. Plot the survivor functions of each group, estimated using the Kaplan-Meier estimate, on the same graph and comment on the differences. Use a log-rank test to compare the survival experience of each group more formally. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \normalsize \end{frame} \end{document} HSAUR3/inst/slides/Ch_recursive_partitioning.Rnw0000644000175000017500000003234613055275020021520 0ustar nileshnilesh \input{HSAUR_title} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= source("setup.R") library("randomForest") library("partykit") @ \frame{ \begin{center} \Large{Part 9: Recursive Partitioning} \end{center} explains how to fit regression models via simple recursive partitioning methods. } \section{Introduction} \begin{frame} \frametitle{Introduction} The Forbes 2000 list of the world's biggest industrial companies was %%' introduced in detail in Part~1. Here, our interest is to construct a model explaining the profit of a company based on assets, sales and the market value. The second set of data involves the investigation reported in \cite{HSAUR:Mardinetal2003} of whether laser scanner images of the eye background can be used to classify a patient's eye as suffering %' from glaucoma or not. Glaucoma is a neuro-degenerative disease of the optic nerve and is one of the major reasons for blindness in elderly people. \end{frame} \begin{frame} \frametitle{Glaucoma Data} For $196$ people, $98$ patients suffering glaucoma and $98$ controls which have been matched by age and sex, $62$ numeric variables derived from the laser scanning images are available. The data are available as \Robject{GlaucomaM} \index{GlaucomaM data@\Robject{GlaucomaM} data} from package \Rpackage{TH.data}. The variables describe the morphology of the optic nerve head, i.e., measures of volumes and areas in certain regions of the eye background. Those regions have been manually outlined by a physician. Our aim is to construct a prediction model which is able to decide whether an eye is affected by glaucomateous changes based on the laser image data. \end{frame} \begin{frame} \frametitle{Candidate Models} Both sets of data described above could be analysed using the regression models described in Parts~5 and 6, i.e., regression models for numeric and binary response variables based on a linear combination of the covariates. But here we shall employ an alternative approach known as \stress{recursive partitioning}, where the resulting models are usually called \stress{regression or classification trees}. \end{frame} \begin{frame} \frametitle{Recursive Partitioning} This method was originally invented to deal with possible non-linear relationships between covariates and response. The basic idea is to partition the covariate space and to compute simple statistics of the dependent variable, like the mean or median, inside each cell. There exist many algorithms for the construction of classification or regression trees but the majority of algorithms follow a simple general rule: First partition the observations by univariate splits in a recursive way and second fit a constant model in each cell of the resulting partition. \end{frame} \begin{frame} \frametitle{Recursive Partitioning} For the first step, one selects a covariate $x_j$ from the $q$ available covariates $x_1, \dots, x_q$ and estimates a split point which separates the response values $y_i$ into two groups. For an ordered covariate $x_j$ a split point is a number $\xi$ dividing the observations into two groups. The first group consists of all observations with $x_j \le \xi$ and the second group contains the observations satisfying $x_j > \xi$. Once that the splits $\xi$ or $A$ for some selected covariate $x_j$ have been estimated, one applies the procedure sketched above for all observations in the first group and, recursively, splits this set of observations further. The same happens for all observations in the second group. The recursion is stopped when some stopping criterion is fulfilled. \end{frame} \begin{frame} \frametitle{Ensemble Methods} When the underlying relationship between covariate and response is smooth, such a split point estimate will be affected by high variability. This problem is addressed by so called \stress{ensemble methods}. Here, multiple trees are grown on perturbed instances of the data set and their predictions are averaged. The simplest representative of such a procedure is called \stress{bagging} \citep{HSAUR:Breiman1996}. \end{frame} \begin{frame} \frametitle{Bagging} We draw $B$ bootstrap samples from the original data set, i.e., we draw $n$ out of $n$ observations with replacement from our $n$ original observations. For each of those bootstrap samples we grow a very large tree. When we are interested in the prediction for a new observation, we pass this observation through all $B$ trees and average their predictions. It has been shown that the goodness of the predictions for future cases can be improved dramatically by this or similar simple procedures. More details can be found in \cite{HSAUR:Buehlmann2004}. \end{frame} \section{Analysis using R} \begin{frame}[fragile] \frametitle{Analysis using R: Forbes 2000} The \Rcmd{rpart} function from \Rpackage{rpart} can be used to grow a regression tree. The response variable and the covariates are defined by a model formula in the same way as for \Rcmd{lm}, say. By default, a large initial tree is grown. <>= library("rpart") data("Forbes2000", package = "HSAUR3") Forbes2000 <- subset(Forbes2000, !is.na(profits)) fm <- profits ~ assets + marketvalue + sales forbes_rpart <- rpart(fm, data = Forbes2000) @ \end{frame} \begin{frame}[fragile] \frametitle{Plot Tree} \begin{center} <>= plot(as.party(forbes_rpart)) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Inspect Tree Complexity} <>= print(forbes_rpart$cptable) opt <- which.min(forbes_rpart$cptable[,"xerror"]) cp <- forbes_rpart$cptable[opt, "CP"] forbes_prune <- prune(forbes_rpart, cp = cp) @ \end{frame} \begin{frame}[fragile] \frametitle{Plot Pruned Tree} \small \begin{center} <>= plot(as.party(forbes_prune)) @ \end{center} \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Glaucoma Data} Here, we are primarily interested in the construction of a predictor. The relationship between the $62$ covariates and the glaucoma status itself is not very interesting. We start with a large initial tree and prune back branches according to the cross-validation criterion. \small <>= set.seed(290875) @ <>= data("GlaucomaM", package = "TH.data") glaucoma_rpart <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 100)) glaucoma_rpart$cptable opt <- which.min(glaucoma_rpart$cptable[,"xerror"]) cp <- glaucoma_rpart$cptable[opt, "CP"] glaucoma_prune <- prune(glaucoma_rpart, cp = cp) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Pruned Tree for Glaucoma Data} \small \begin{center} <>= plot(as.party(glaucoma_prune)) @ \end{center} \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Problem: Instability} <>= nsplitopt <- vector(mode = "integer", length = 25) for (i in 1:length(nsplitopt)) { cp <- rpart(Class ~ ., data = GlaucomaM)$cptable nsplitopt[i] <- cp[which.min(cp[,"xerror"]), "nsplit"] } table(nsplitopt) @ \end{frame} \begin{frame}[fragile] \frametitle{Bagging: Grow a Forest} <>= trees <- vector(mode = "list", length = 25) n <- nrow(GlaucomaM) bootsamples <- rmultinom(length(trees), n, rep(1, n)/n) mod <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 0)) for (i in 1:length(trees)) trees[[i]] <- update(mod, weights = bootsamples[,i]) @ \end{frame} \begin{frame}[fragile] \frametitle{Bagging: Prediction} Estimate the conditional probability of suffering from glaucoma given the covariates for each observation in the original data set by <>= classprob <- matrix(0, nrow = n, ncol = length(trees)) for (i in 1:length(trees)) { classprob[,i] <- predict(trees[[i]], newdata = GlaucomaM)[,1] classprob[bootsamples[,i] > 0,i] <- NA } @ \end{frame} \begin{frame}[fragile] \frametitle{Estimate Misclassification Error} \small <>= avg <- rowMeans(classprob, na.rm = TRUE) predictions <- factor(ifelse(avg > 0.5, "glaucoma", "normal")) predtab <- table(predictions, GlaucomaM$Class) predtab @ \normalsize An honest estimate of the probability of a glaucoma prediction when the patient is actually suffering from glaucoma is \small <>= round(predtab[1,1] / colSums(predtab)[1] * 100) @ \normalsize per cent. \end{frame} \begin{frame}[fragile] \frametitle{Visualizing a Forest of Trees} \small <>= library("lattice") gdata <- data.frame(avg = rep(avg, 2), class = rep(as.numeric(GlaucomaM$Class), 2), obs = c(GlaucomaM[["varg"]], GlaucomaM[["vari"]]), var = factor(c(rep("varg", nrow(GlaucomaM)), rep("vari", nrow(GlaucomaM))))) panelf <- function(x, y) { panel.xyplot(x, y, pch = gdata$class) panel.abline(h = 0.5, lty = 2) } print(xyplot(avg ~ obs | var, data = gdata, panel = panelf, scales = "free", xlab = "", ylab = "Estimated Class Probability Glaucoma")) @ \normalsize \end{frame} \begin{frame}[fragile] \frametitle{Visualizing a Forest of Trees} \begin{center} <>= library("lattice") gdata <- data.frame(avg = rep(avg, 2), class = rep(as.numeric(GlaucomaM$Class), 2), obs = c(GlaucomaM[["varg"]], GlaucomaM[["vari"]]), var = factor(c(rep("varg", nrow(GlaucomaM)), rep("vari", nrow(GlaucomaM))))) panelf <- function(x, y) { panel.xyplot(x, y, pch = gdata$class) panel.abline(h = 0.5, lty = 2) } print(xyplot(avg ~ obs | var, data = gdata, panel = panelf, scales = "free", xlab = "", ylab = "Estimated Class Probability Glaucoma")) @ \end{center} \end{frame} \begin{frame}[fragile] \frametitle{Random Forest} The \stress{bagging} procedure is a special case of a more general approach called \stress{random forest} \citep{HSAUR:Breiman2001b}. The package \Rpackage{randomForest} \citep{PKG:randomForest} can be used to compute such ensembles via <>= library("randomForest") rf <- randomForest(Class ~ ., data = GlaucomaM) @ and we obtain out-of-bag estimates for the prediction error via <>= table(predict(rf), GlaucomaM$Class) @ \end{frame} \begin{frame}[fragile] \frametitle{Unbiased Trees} Another approach to recursive partitioning, making a connection to classical statistical test problems. In each node of those trees, a significance test on independence between any of the covariates and the response is performed and a split is established when the $p$-value is smaller than a pre-specified nominal level $\alpha$. This approach has the advantage that one does not need to prune back large initial trees since we have a statistically motivated stopping criterion -- the $p$-value -- at hand. Such \stress{conditional inference trees} are implemented in the \Rpackage{partykit} package \citep{HSAUR:Hothorn:2006:JCGS}. \end{frame} \begin{frame}[fragile] \frametitle{Unbiased Trees} For the glaucoma data, such a conditional inference tree can be computed using <>= glaucoma_ctree <- ctree(Class ~ ., data = GlaucomaM) @ A convenient display is available. \end{frame} \begin{frame}[fragile] \frametitle{Classification Tree for Glaucoma Data} \begin{center} <>= plot(glaucoma_ctree) @ \end{center} \end{frame} \begin{frame} \frametitle{Summary} Recursive partitioning procedures are rather simple non-parametric tools for regression modelling. The main structures of regression relationship can be visualised in a straightforward way. However, one should bear in mind that the nature of those models is very simple and can only serve as a rough approximation to reality. When multiple simple models are averaged, powerful predictors can be constructed. \end{frame} \begin{frame} \frametitle{Exercises} \begin{itemize} \item Construct a classification tree for the Boston Housing data which are available as \Rclass{data.frame} \Robject{BostonHousing} from package \Rpackage{mlbench}. Compare the predictions of the tree with the predictions obtained from \Rcmd{randomForest}. Which method is more accurate? \item For each possible cutpoint in \Robject{varg} of the glaucoma data, compute the test statistic of the chi-square test of independence and plot them against the values of \Robject{varg}. Is a simple cutpoint for this variable appropriate for discriminating between healthy and glaucomateous eyes? \item Compare the tree models fitted to the glaucoma data with a logistic regression model. \end{itemize} \end{frame} \begin{frame} \frametitle{References} \tiny <>= src <- system.file(package = "HSAUR3") style <- file.path(src, "LaTeXBibTeX", "refstyle") bst <- file.path(src, "LaTeXBibTeX", "HSAUR") cat(paste("\\bibliographystyle{", style, "}", sep = ""), "\n \n") cat(paste("\\bibliography{", bst, "}", sep = ""), "\n \n") @ \normalsize \end{frame} \end{document} HSAUR3/inst/doc/0000755000175000017500000000000014133304604013071 5ustar nileshnileshHSAUR3/inst/doc/Ch_analysing_longitudinal_dataII.pdf0000644000175000017500000027023014133304605022154 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3039 /Filter /FlateDecode /N 54 /First 423 >> stream xZYw~߮sD soI<*;3DBY߯A!CUU1L0T2L$X)Xg=a|%#d Ѯ5F0aH>bXCtfʧ)m)T&e:4x&eFH􏘑X_z[%4~C^T,h1B/@a&mQHSt(#Ô`dQ:bQ)"T0epO^ Bb)A3M,F2 6xMXLn1af5=??AR㸌cCƏf$͒)5 ξ%o$f^)6gM^ITXV;I .Ll'.C(Gg7Erwɷ/y1 Cx6J0ߛ}&Qޕ,hNg$ml'r7[lu,b%h(,|9iv !1^ϲėKAnٛoo'N4{s=wZKsgXW%Q!\gHnN=}-YVc"?#qP0biݯb^q1?LB%eE>:MJ̏w^k)_jna"1$ϟ[^*w)/>"it `uX6LhnJ64J/j !?Ϯr6NQvH"0g|NfL?x3?̋[͏gXY̒bzH7]:Iz}SqJ$W|o_7-!?g=%Q>3> SvOox_9Wl~o8M~3xs0i>?gPfX^)&1d~%/o$嗜WJ~#1hVj m26N' W ;oeŃtJx`򗟖9,N&tjx~w n]4 :mftQ1$K:F}zXL6d21lpګ o)iG/Y/Çpb + r wflʀ,23gBZOÏ `<*&%'Cӵm+Zr;ZZhx[j:R_—몪B #A 4t>߾5/=*HAń!Ny1 C1mB> TTL^jj B?O.7O,Z_}//p:B6 C{A[O}7"@`p!pMHF ϡmb2k| aG` :`㵛ϧ=Qq$Ԩ>p_lo@FHX: ΀8-w!8s/-`MɟxRyW)(LV HO&U ;=,m/vB^*ϵRodnmkݴ>~8bѽ{ag5iKѫ0t8!- :$>j#6H\uL]SDwZ.42w(Rs#%g+C0m[uuoZ;9M)`G㜶ur+U5Ci[!’$Ѳ/Igogp鋃vUOOS=wﺚ뭌_6?2!Z b9Y5P<ҴL' O˸E<2gˈ7'OX)]$i[q͘yBPY6N(/ `msZ+;-+~-+pqPmu:mnbj~Fk{b|m$AQktm}8_y~ Ze i^@*R|RZyNUAXAI!eE8p@0( 4"8ȈSMxwɣv.Hkų}`=%=YȪ^(SJhR&@B.A&׳Itp]//!ROOK}z?e{xxŎ%k8zNfkk׽Fz"zm#1>!M 4QԆ|f8ӗҽO!!']r|ew0@4 m3/!'ǧ(CїŪee/&AB^b}}@OQP}tR0j^(MaիnD.m-E>3lG. jN&j/z!-̀]=xn{BzhԕѨ##n~UKК4r}h-RH2@\*Z7{Ԁo3\~ת!䒐uR>Q$=&ςձ>gQt(yΪgz^00߳l# TKAbK`Hs1=zTlڍ2~7Giڸ)˻9n/5#>̒/Si}o|-@yDP{NbpD=l!Gv`=8Dr/Tf!:IEuTDA&R``ȦvzQM } WW TtW ʽdv/YCXY'CkBϩM/^@Wxh3nו,2l񒲵Tm{endstream endobj 56 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:41+02:00 2021-10-18T16:49:41+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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HSAUR3/inst/doc/Ch_quantile_regression.R0000644000175000017500000002462014133304562017717 0ustar nileshnilesh### R code from vignette source 'Ch_quantile_regression.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: QR-setup ################################################### library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) data("db", package = "gamlss.data") nboys <- with(db, sum(age > 2)) ################################################### ### code chunk number 4: QR-db ################################################### summary(db) db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) ################################################### ### code chunk number 5: QR-db-plot ################################################### db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", scales = list(x = list(relation = "free")), layout = c(2, 1), pch = 19, col = rgb(.1, .1, .1, .1)) ################################################### ### code chunk number 6: QR-db-lm2.9.23 ################################################### (lm2.9 <- lm(head ~ age, data = db, subset = age < 9)) (lm9.23 <- lm(head ~ age, data = db, subset = age > 9)) ################################################### ### code chunk number 7: QR-db-lm ################################################### (lm_mod <- lm(head ~ age:I(age < 9) + I(age < 9) - 1, data = db)) ################################################### ### code chunk number 8: QR-db-median ################################################### library("quantreg") (rq_med2.9 <- rq(head ~ age, data = db, tau = 0.5, subset = age < 9)) (rq_med9.23 <- rq(head ~ age, data = db, tau = 0.5, subset = age > 9)) ################################################### ### code chunk number 9: QR-db-lmrq2.9 ################################################### cbind(coef(lm2.9)[1], confint(lm2.9, parm = "(Intercept)")) cbind(coef(lm2.9)[2], confint(lm2.9, parm = "age")) summary(rq_med2.9, se = "rank") ################################################### ### code chunk number 10: QR-db-lmrq9.23 ################################################### cbind(coef(lm9.23)[1], confint(lm9.23, parm = "(Intercept)")) cbind(coef(lm9.23)[2], confint(lm9.23, parm = "age")) summary(rq_med9.23, se = "rank") ################################################### ### code chunk number 11: QR-db-tau ################################################### tau <- c(.01, .1, .25, .5, .75, .9, .99) ################################################### ### code chunk number 12: QR-db-age ################################################### gage <- c(2:9, 9:23) i <- 1:8 ################################################### ### code chunk number 13: QR-db-lm-fit_05 ################################################### idf <- data.frame(age = gage[i]) p <- predict(lm2.9, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p ################################################### ### code chunk number 14: QR-db-lm-fit ################################################### p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") p2.9 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] idf <- data.frame(age = gage[-i]) p <- predict(lm9.23, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") ################################################### ### code chunk number 15: QR-db-lm-fit2 ################################################### p9.23 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] round((q2.23 <- rbind(p2.9, p9.23)), 3) ################################################### ### code chunk number 16: QR-db-lm-plot ################################################### pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), q2.23[nrow(q2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), q2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) ################################################### ### code chunk number 17: QR-db-rq2.9 ################################################### (rq2.9 <- rq(head ~ age, data = db, tau = tau, subset = age < 9)) ################################################### ### code chunk number 18: QR-db-rq9.23 ################################################### (rq9.23 <- rq(head ~ age, data = db, tau = tau, subset = age > 9)) ################################################### ### code chunk number 19: QR-db-rq-fit ################################################### p2.23 <- rbind(predict(rq2.9, newdata = data.frame(age = gage[i])), predict(rq9.23, newdata = data.frame(age = gage[-i]))) ################################################### ### code chunk number 20: QR-db-rq-plot ################################################### pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), p2.23[nrow(p2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) ################################################### ### code chunk number 21: QR-db-rqss-fit ################################################### rqssmod <- vector(mode = "list", length = length(tau)) db$lage <- with(db, age^(1/3)) for (i in 1:length(tau)) rqssmod[[i]] <- rqss(head ~ qss(lage, lambda = 1), data = db, tau = tau[i]) ################################################### ### code chunk number 22: QR-db-rqss-pred ################################################### gage <- seq(from = min(db$age), to = max(db$age), length = 50) p <- sapply(1:length(tau), function(i) { predict(rqssmod[[i]], newdata = data.frame(lage = gage^(1/3))) }) ################################################### ### code chunk number 23: QR-db-rqss-plot ################################################### pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) apply(p, 2, function(x) panel.lines(gage, x)) panel.text(rep(max(db$age), length(tau)), p[nrow(p),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) HSAUR3/inst/doc/Ch_errata.Rnw0000644000175000017500000001672314133304452015463 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Errata} \setcounter{chapter}{21} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Errata]{Errata} %\bibliographystyle{LaTeXBibTeX/refstyle} %\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_multiple_linear_regression.R0000644000175000017500000002130614133304554021261 0ustar nileshnilesh### R code from vignette source 'Ch_multiple_linear_regression.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: MLR-setup ################################################### library("wordcloud") ################################################### ### code chunk number 4: MLR-hubble-tab ################################################### data("hubble", package = "gamair") names(hubble) <- c("galaxy", "velocity", "distance") toLatex(HSAURtable(hubble, package = "gamair"), pcol = 2, caption = paste("Distance and velocity for 24 galaxies."), label = "MLR-hubble-tab") ################################################### ### code chunk number 5: MLR-clouds-tab ################################################### data("clouds", package = "HSAUR3") names(clouds) <- c("seeding", "time", "sne", "cloudc", "prewet", "EM", "rain") toLatex(HSAURtable(clouds), pcol = 1, caption = paste("Cloud seeding experiments in Florida -- see text for", "explanations of the variables. Note that the \\Robject{clouds} data set has slightly different variable names."), label = "MLR-clouds-tab") ################################################### ### code chunk number 6: MLR-hubble-plot ################################################### plot(velocity ~ distance, data = hubble) ################################################### ### code chunk number 7: MLR-hubble-beta1 ################################################### sum(hubble$distance * hubble$velocity) / sum(hubble$distance^2) ################################################### ### code chunk number 8: MLR-hubble-lm ################################################### hmod <- lm(velocity ~ distance - 1, data = hubble) ################################################### ### code chunk number 9: MLR-hubble-lm ################################################### coef(hmod) ################################################### ### code chunk number 10: MLR-hubble-age ################################################### Mpc <- 3.09 * 10^19 ysec <- 60^2 * 24 * 365.25 Mpcyear <- Mpc / ysec 1 / (coef(hmod) / Mpcyear) ################################################### ### code chunk number 11: MLR-hubble-lmplot ################################################### layout(matrix(1:2, ncol = 2)) plot(velocity ~ distance, data = hubble) abline(hmod) plot(hmod, which = 1) ################################################### ### code chunk number 12: MLR-clouds-boxplots (eval = FALSE) ################################################### ## data("clouds", package = "HSAUR3") ## layout(matrix(1:2, nrow = 2)) ## bxpseeding <- boxplot(rain ~ seeding, data = clouds, ## ylab = "Rainfall", xlab = "Seeding") ## bxpecho <- boxplot(rain ~ EM, data = clouds, ## ylab = "Rainfall", xlab = "Echo Motion") ################################################### ### code chunk number 13: MLR-clouds-boxplots ################################################### layout(matrix(1:2, nrow = 2)) bxpseeding <- boxplot(rain ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rain ~ EM, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") ################################################### ### code chunk number 14: MLR-clouds-scatterplots ################################################### layout(matrix(1:4, nrow = 2)) plot(rain ~ time, data = clouds) plot(rain ~ cloudc, data = clouds) plot(rain ~ sne, data = clouds, xlab="S-Ne criterion") plot(rain ~ prewet, data = clouds) ################################################### ### code chunk number 15: MLR-clouds-outliers ################################################### rownames(clouds)[clouds$rain %in% c(bxpseeding$out, bxpecho$out)] ################################################### ### code chunk number 16: MLR-clouds-formula ################################################### clouds_formula <- rain ~ seeding + seeding:(sne + cloudc + prewet + EM) + time ################################################### ### code chunk number 17: MLR-clouds-modelmatrix ################################################### Xstar <- model.matrix(clouds_formula, data = clouds) ################################################### ### code chunk number 18: MLR-clouds-contrasts ################################################### attr(Xstar, "contrasts") ################################################### ### code chunk number 19: MLR-clouds-lm ################################################### clouds_lm <- lm(clouds_formula, data = clouds) class(clouds_lm) ################################################### ### code chunk number 20: MLR-clouds-summary ################################################### summary(clouds_lm) ################################################### ### code chunk number 21: MLR-clouds-coef ################################################### betastar <- coef(clouds_lm) betastar ################################################### ### code chunk number 22: MLR-clouds-vcov ################################################### Vbetastar <- vcov(clouds_lm) ################################################### ### code chunk number 23: MLR-clouds-sd ################################################### sqrt(diag(Vbetastar)) ################################################### ### code chunk number 24: MLR-clouds-lmplot ################################################### psymb <- as.numeric(clouds$seeding) plot(rain ~ sne, data = clouds, pch = psymb, xlab = "S-Ne criterion") abline(lm(rain ~ sne, data = clouds, subset = seeding == "no")) abline(lm(rain ~ sne, data = clouds, subset = seeding == "yes"), lty = 2) legend("topright", legend = c("No seeding", "Seeding"), pch = 1:2, lty = 1:2, bty = "n") ################################################### ### code chunk number 25: MLR-clouds-residfitted ################################################### clouds_resid <- residuals(clouds_lm) clouds_fitted <- fitted(clouds_lm) ################################################### ### code chunk number 26: MLR-clouds-residplot ################################################### plot(clouds_fitted, clouds_resid, xlab = "Fitted values", ylab = "Residuals", type = "n", ylim = max(abs(clouds_resid)) * c(-1, 1)) abline(h = 0, lty = 2) textplot(clouds_fitted, clouds_resid, words = rownames(clouds), new = FALSE) ################################################### ### code chunk number 27: MLR-clouds-qqplot ################################################### qqnorm(clouds_resid, ylab = "Residuals") qqline(clouds_resid) ################################################### ### code chunk number 28: MLR-clouds-cook (eval = FALSE) ################################################### ## plot(clouds_lm) ################################################### ### code chunk number 29: MLR-clouds-cook ################################################### plot(clouds_lm, which = 4, sub.caption = NULL) HSAUR3/inst/doc/Ch_principal_components_analysis.R0000644000175000017500000001555314133304555021775 0ustar nileshnilesh### R code from vignette source 'Ch_principal_components_analysis.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: PCA-heptathlon-recode ################################################### data("heptathlon", package = "HSAUR3") heptathlon$hurdles <- max(heptathlon$hurdles) - heptathlon$hurdles heptathlon$run200m <- max(heptathlon$run200m) - heptathlon$run200m heptathlon$run800m <- max(heptathlon$run800m) - heptathlon$run800m ################################################### ### code chunk number 4: PCA-heptathlon-scatter ################################################### score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) ################################################### ### code chunk number 5: PCA-options65 ################################################### w <- options("width") options(width = 65) ################################################### ### code chunk number 6: PCA-heptathlon-cor ################################################### round(cor(heptathlon[,-score]), 2) ################################################### ### code chunk number 7: PCA-optionsw ################################################### options(width = w$width) ################################################### ### code chunk number 8: PCA-heptathlon-PNG ################################################### heptathlon <- heptathlon[-grep("PNG", rownames(heptathlon)),] ################################################### ### code chunk number 9: PCA-heptathlon-scatter2 ################################################### score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) ################################################### ### code chunk number 10: PCA-options65 ################################################### w <- options("width") options(width = 65) ################################################### ### code chunk number 11: PCA-heptathlon-cor2 ################################################### round(cor(heptathlon[,-score]), 2) ################################################### ### code chunk number 12: PCA-optionsw ################################################### options(width = w$width) ################################################### ### code chunk number 13: PCA-options65 ################################################### w <- options("digits") options(digits = 4) ################################################### ### code chunk number 14: PCA-heptathlon-pca ################################################### heptathlon_pca <- prcomp(heptathlon[, -score], scale = TRUE) print(heptathlon_pca) ################################################### ### code chunk number 15: PCA-heptathlon-summary ################################################### summary(heptathlon_pca) ################################################### ### code chunk number 16: PCA-optionsw ################################################### options(digits = w$digits) ################################################### ### code chunk number 17: PCA-heptathlon-a1 ################################################### a1 <- heptathlon_pca$rotation[,1] a1 ################################################### ### code chunk number 18: PCA-heptathlon-scaling ################################################### center <- heptathlon_pca$center scale <- heptathlon_pca$scale ################################################### ### code chunk number 19: PCA-heptathlon-s1 ################################################### hm <- as.matrix(heptathlon[,-score]) drop(scale(hm, center = center, scale = scale) %*% heptathlon_pca$rotation[,1]) ################################################### ### code chunk number 20: PCA-heptathlon-s1 ################################################### predict(heptathlon_pca)[,1] ################################################### ### code chunk number 21: PCA-heptathlon-pca-plot ################################################### plot(heptathlon_pca) ################################################### ### code chunk number 22: PCA-heptathlon-sdev ################################################### sdev <- heptathlon_pca$sdev prop12 <- round(sum(sdev[1:2]^2)/sum(sdev^2)*100, 0) ################################################### ### code chunk number 23: PCA-heptathlon-biplot (eval = FALSE) ################################################### ## biplot(heptathlon_pca, col = c("gray", "black")) ################################################### ### code chunk number 24: PCA-heptathlon-biplot ################################################### tmp <- heptathlon[, -score] rownames(tmp) <- abbreviate(gsub(" \\(.*", "", rownames(tmp))) biplot(prcomp(tmp, scale = TRUE), col = c("black", "lightgray"), xlim = c(-0.5, 0.7)) ################################################### ### code chunk number 25: PCA-scorecor ################################################### cor(heptathlon$score, heptathlon_pca$x[,1]) ################################################### ### code chunk number 26: PCA-heptathlonscore ################################################### plot(heptathlon$score, heptathlon_pca$x[,1]) HSAUR3/inst/doc/Ch_simple_inference.pdf0000644000175000017500000030546514133304613017522 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3095 /Filter /FlateDecode /N 54 /First 424 >> stream xZYs8~_I* .rk*U>cg$'qZmNdCR~R%xl 4f}aDm$Bi VA|s$0 =A8'\zpx3I8< ǵ&\O\(EHaPB!a GD` RsI"J(aDbD3Ĉ!Z2M.bG"`3A)ZN0hO3؄ o'1I  |⠄MHI/aF&0IX3Xo! h|A`| {C7 s"Ŀ~Уga"#cBOu,=/*}t}l2wFP=a]av? ~[-T5X@G,C!-"j\nb独~{Zz+k#Z{|)Nw`䦃ڶ!6ZLjxZʻ\6[o_?롕޹\{JGB%H!@bH|EK0[E8tH yC{;_~gs95(mc *;kUA-1HD,>0r4n꼒.S{Vݛ1 idp`Lvú_Zto⴦KCtp=&r.̵MD C򏼭|=`}m|VGAQtP jUm="X֋zp#`9;ECµh8|Ƕl_'uiN!Z'&OEߓv,>EpFN @#NvPu13n~2V;+{)% [AkP@]^4Vʘ6z &T0@M.a\_V92Wwx]=*Fo AHx ˶r&tO&d2:8S1,JAWXaJyt^]ۯ{_lcOAm2ϓ ;L|hT2Wz]rHr=r BDU0[CQYQ$wCCYiHGFoy;,?Wcr>=\v~Es^&ki2uy WdM@ձ"Όew;evMendstream endobj 56 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:47+02:00 2021-10-18T16:49:47+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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VD2/Ku Rt>4 $ygM }"9Hn0 \ "jy'Ng8D H] Ux" endstream endobj startxref 115618 %%EOF HSAUR3/inst/doc/Ch_gam.Rnw0000644000175000017500000006234514133304452014752 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Generalized Additive Models} %%\VignetteDepends{mgcv,rpart,wordcloud,mboost} \setcounter{chapter}{9} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("mgcv") library("mboost") library("rpart") library("wordcloud") @ \chapter[Scatterplot Smoothers and Additive Models]{Scatterplot Smoothers and Generalized Additive Models: The Men's Olympic 1500m, Air Pollution in the US, Risk Factors for Kyphosis, and Women's Role in %' Society \label{GAM}} \section{Introduction} \section{Scatterplot Smoothers and Generalized Additive Models} \section{Analysis Using \R{}} \subsection{Olympic 1500m Times} To begin we will construct a scatterplot of winning time against the year the games were held. The \R{} code and the resulting plot are shown in Figure~\ref{GAM-men1500m-plot}. There is a very clear downward trend in the times over the years, and, in addition there is a very clear outlier namely the winning time for 1896. We shall remove this time from the data set and now concentrate on the remaining times. First we will fit a simple linear regression to the data and plot the fit onto the scatterplot. The code and the resulting plot are shown in Figure~\ref{GAM-men1500m-lm}. Clearly the linear regression model captures in general terms the downward trend in the times. Now we can add the fits given by the lowess smoother and by a cubic spline smoother; the resulting graph and the extra \R{} code needed are shown in Figure~\ref{GAM-men1500m-smooth}. Both non-parametric fits suggest some distinct departure from linearity, and clearly point to a quadratic model being more sensible than a linear model here. And fitting a parametric model that includes both a linear and a quadratic effect for the year gives a prediction curve very similar to the non-parametric curves; see Figure~\ref{GAM-men1500m-quad}. Here use of the non-parametric smoothers has effectively diagnosed our linear model and pointed the way to using a more suitable parametric model; this is often how such non-parametric models can be used most effectively. For these data, of course, it is clear that the simple linear model cannot be suitable if the investigator is interested in predicting future times since even the most basic knowledge of human physiology will tell us that times cannot continue to go down. There must be some lower limit to the time man can run 1500m. But in other situations use of the non-parametric smoothers may point to a parametric model that could not have been identified \emph{a priori}. \begin{figure} \begin{center} <>= plot(time ~ year, data = men1500m, xlab = "Year", ylab = "Winning time (sec)") @ \caption{Scatterplot of year and winning time. \label{GAM-men1500m-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= men1500m1900 <- subset(men1500m, year >= 1900) men1500m_lm <- lm(time ~ year, data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") abline(men1500m_lm) @ \caption{Scatterplot of year and winning time with fitted values from a simple linear model. \label{GAM-men1500m-lm}} \end{center} \end{figure} \begin{figure} \begin{center} <>= x <- men1500m1900$year y <- men1500m1900$time men1500m_lowess <- lowess(x, y) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m_lowess, lty = 2) men1500m_cubic <- gam(y ~ s(x, bs = "cr")) lines(x, predict(men1500m_cubic), lty = 3) @ \caption{Scatterplot of year and winning time with fitted values from a smooth non-parametric model. \label{GAM-men1500m-smooth}} \end{center} \end{figure} \begin{figure} \begin{center} <>= men1500m_lm2 <- lm(time ~ year + I(year^2), data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m1900$year, predict(men1500m_lm2)) @ \caption{Scatterplot of year and winning time with fitted values from a quadratic model. \label{GAM-men1500m-quad}} \end{center} \end{figure} It is of some interest to look at the predictions of winning times in future Olympics from both the linear and quadratic models. For example, for 2008 and 2012 the predicted times and their $95\%$ confidence intervals can be found using the following code \newpage <>= predict(men1500m_lm, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") predict(men1500m_lm2, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") @ \newpage For predictions far into the future both the quadratic and the linear model fail; we leave readers to get some more predictions to see what happens. We can compare the first prediction with the time actually recorded by the winner of the men's 1500m in Beijing 2008, Rashid Ramzi from Brunei, who won the event in $212.94$ seconds. The confidence interval obtained from the simple linear model does not include this value but the confidence interval for the prediction derived from the quadratic model does. \subsection{Air Pollution in US Cities} Unfortunately, we cannot fit an additive model for describing the $\text{SO}_2$ concentration based on all six covariates because this leads to more parameters than cities, i.e., more parameters than observations when using the default parameterization of \Rpackage{mgcv}. Thus, before we can apply the \Rcmd{gam} function from package \Rpackage{mgcv}, we have to decide which covariates should enter the model and which subset of these covariates should be allowed to deviate from a linear regression relationship. As briefly discussed in Section~\ref{GAM:VS}, we can fit an additive model using the iterative boosting algorithm as described by \cite{HSAUR:BuehlmannHothorn2007}. The complexity of the model is determined by an AIC criterion, which can also be used to determine an appropriate number of boosting iterations to choose. The methodology is available from package \Rpackage{mboost} \citep{PKG:mboost}. We start with a small number of boosting iterations ($100$ by default) and compute the AIC of the corresponding $100$ models: <>= library("mboost") USair_boost <- gamboost(SO2 ~ ., data = USairpollution) USair_aic <- AIC(USair_boost) USair_aic @ The AIC suggests that the boosting algorithm should be stopped after $\Sexpr{mstop(USair_aic)}$ iterations. The partial contributions of each covariate to the predicted $\text{SO}_2$ concentration are given in Figure~\ref{GAM-USairpollution-boostplot}. The plot indicates that all six covariates enter the model and the selection of a subset of covariates for modeling isn't appropriate in this case. However, the number of manufacturing enterprises seems to add linearly to the $\text{SO}_2$ concentration, which simplifies the model. Moreover, the average annual precipitation contribution seems to deviate from zero only for some extreme observations and one might refrain from using the covariate at all. \begin{figure} \begin{center} <>= USair_gam <- USair_boost[mstop(USair_aic)] layout(matrix(1:6, ncol = 3)) plot(USair_gam, ask = FALSE) @ \caption{Partial contributions of six exploratory covariates to the predicted $\text{SO}_2$ concentration. \label{GAM-USairpollution-boostplot}} \end{center} \end{figure} As always, an inspection of the model fit via a residual plot is worth the effort. Here, we plot the fitted values against the residuals and label the points with the name of the corresponding city using the \Rcmd{textplot} function from package \Rpackage{wordcloud}. Figure~\ref{GAM-USairpollution-residplot} shows at least two extreme observations. Chicago has a very large observed and fitted $\text{SO}_2$ concentration, which is due to the huge number of inhabitants and manufacturing plants (see Figure~\ref{GAM-USairpollution-boostplot} also). One smaller city, Providence, is associated with a rather large positive residual indicating that the actual $\text{SO}_2$ concentration is underestimated by the model. In fact, this small town has a rather high $\text{SO}_2$ concentration which is hardly explained by our model. Overall, the model doesn't fit the data very well, so we should avoid overinterpreting the model structure too much. In addition, since each of the six covariates contributes to the model, we aren't able to select a smaller subset of the covariates for modeling and thus fitting a model using \Rcmd{gam} is still complicated (and will not add much knowledge anyway). \begin{figure} \begin{center} <>= SO2hat <- predict(USair_gam) SO2 <- USairpollution$SO2 plot(SO2hat, SO2 - SO2hat, type = "n", xlim = c(-20, max(SO2hat) * 1.1), ylim = range(SO2 - SO2hat) * c(2, 1)) textplot(SO2hat, SO2 - SO2hat, rownames(USairpollution), show.lines = FALSE, new = FALSE) abline(h = 0, lty = 2, col = "grey") @ \caption{Residual plot of $\text{SO}_2$ concentration. \label{GAM-USairpollution-residplot}} \end{center} \end{figure} \subsection{Risk Factors for Kyphosis} \index{Spinogram} Before modeling the relationship between kyphosis and the three exploratory variables age, starting vertebral level of the surgery, and number of vertebrae involved, we investigate the partial associations by so-called \stress{spinograms}, as introduced in \Sexpr{ch("DAGD")}. The numeric exploratory covariates are discretized and their empirical relative frequencies are plotted against the conditional frequency of kyphosis in the corresponding group. Figure~\ref{GAM-kyphosis-plot} shows that kyphosis is absent in very young or very old children, children with a small starting vertebral level, and high number of vertebrae involved. \begin{figure} \begin{center} <>= layout(matrix(1:3, nrow = 1)) spineplot(Kyphosis ~ Age, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Number, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Start, data = kyphosis, ylevels = c("present", "absent")) @ \caption{Spinograms of the three exploratory variables and response variable \Robject{kyphosis}. \label{GAM-kyphosis-plot}} \end{center} \end{figure} The logistic additive model needed to describe the conditional probability of kyphosis given the exploratory variables can be fitted using function \Rcmd{gam}. Here, the dimension of the basis ($k$) has to be modified for \Robject{Number} and \Robject{Start} since these variables are heavily tied. As for generalized linear models, the \Robject{family} argument determines the type of model to be fitted, a logistic model in our case: <>= (kyphosis_gam <- gam(Kyphosis ~ s(Age, bs = "cr") + s(Number, bs = "cr", k = 3) + s(Start, bs = "cr", k = 3), family = binomial, data = kyphosis)) @ The partial contributions of each covariate to the conditional probability of kyphosis with confidence bands are shown in Figure~\ref{GAM-kyphosis-gamplot}. In essence, the same conclusions as drawn from Figure~\ref{GAM-kyphosis-plot} can be stated here. The risk of kyphosis being present decreases with higher starting vertebral level and lower number of vertebrae involved. Children about $100$ months old are under higher risk compared to younger or older children. \begin{figure} \begin{center} <>= trans <- function(x) binomial()$linkinv(x) layout(matrix(1:3, nrow = 1)) plot(kyphosis_gam, select = 1, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 2, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 3, shade = TRUE, trans = trans) @ \caption{Partial contributions of three exploratory variables with confidence bands. \label{GAM-kyphosis-gamplot}} \end{center} \end{figure} \subsection{Women's Role in Society} %' In Chapter~\ref{GLM}, we saw that a logistic regression with an interaction between gender and level of education described the data better than a main-effects only model. Using an additive logistic regression model, we can fit separate, possibly nonlinear, functions of levels of education to both genders: <>= data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ s(education, by = gender) womensrole_gam <- gam(fm1, data = womensrole, family = binomial()) @ The resulting model is best inspected by a plot (Figure~\ref{GAM-womensrole-gamplot}). For males, the log-odds of agreement decreases linearly with each additional year of education. For females, the log-odds is more or less constant up to five years of education and only then begins to decrease. After 15 years, there seems to be no further impact on the log-odds. When we plot the resulting fitted probabilities in a way similar to Figure~\ref{GLM-role2plot}, we see that the interaction is even more pronounced in the additive compared to the linear model. The flat curve for women with less than five years of education can be explained by the rather large variability of the answers in this area but the plateau to the right is due to two groups of highly educated women with a rather large proportion of agreement. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(womensrole_gam, select = 1, shade = TRUE) plot(womensrole_gam, select = 1, shade = TRUE) @ \caption{Effects of level of education for males (right) and females (left) on the log-odds scale derived from an additive logistic regression model. The shaded area denotes confidence bands. \label{GAM-womensrole-gamplot}} \end{center} \end{figure} <>= myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } @ \begin{figure} \begin{center} <>= myplot(predict(womensrole_gam, type = "response")) @ \caption{Effects of level of education for males (right) and females (left) on the log-odds scale derived from an additive logistic regression model. The shaded area denotes confidence bands. \label{GAM-womensrole-probplot}} \end{center} \end{figure} \section{Summary of Findings} \begin{description} \item[Olympic 1500m times] Here the use of a generalized additive model suggested that a quadratic model might best describe the data. When such a model was fitted it made reasonable predictions of the winner's times in the Olympic Games of 2008 and 2012. \item[Air pollution data] Finding a suitable model for these data was problematic because of the outliers in the data and the high correlations between some pairs of explanatory variables. Except for wind, the fitted partial contributions are well approximated by a linear function for most of the observations and it might be questioned if the more complex additive model is really needed. \item[Kyphosis] The risk of kyphosis being present decreases with higher starting vertebral level and lower number of vertebrae involved. Children about 100 months old are under higher risk compared to younger or older children. \item[Women's role in society] For males, the log-odds of agreement decreases linearly with each additional year of education. For females, the log-odds is more or less constant up to five years of education and only then begins to decrease. After $15$ years, there seems to be no further impact on the log-odds. \end{description} \section{Final Comments} Additive models offer flexible modeling tools for regression problems. They stand between generalized linear models, where the regression relationship is assumed to be linear, and more complex models like random forests (see \Sexpr{ch("RP")}) where the regression relationship remains unspecified. Smooth functions describing the influence of covariates on the response can be easily interpreted. Variable selection is a technically difficult problem in this class of models; boosting methods are one possibility to deal with this problem. \section*{Exercises} \begin{description} \exercise Consider the body fat data introduced in \Sexpr{ch("RP")}, Table~\ref{RP-bodyfat-tab}. First fit a generalized additive model assuming normal errors using function \Rcmd{gam}. Are all potential covariates informative? Check the results against a generalized additive model that underwent AIC-based variable selection (fitted using function \Rcmd{gamboost}). \exercise Again fit an additive model to the body fat data, but this time for a log-transformed response. Compare the two models, which one is more appropriate? \exercise Try to fit a logistic additive model to the glaucoma data discussed in \Sexpr{ch("RP")}. Which covariates should enter the model and how is their influence on the probability of suffering from glaucoma? \exercise Investigate the use of different types of scatterplot smoothers on the Hubble data in Table~\ref{MLR-hubble-tab} in Chapter~\ref{MLR-hubble-tab}. \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_graphical_display.Rnw0000644000175000017500000010257514133304452017665 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Data Analysis using Graphical Displays} %%\VignetteDepends{lattice, maps, maptools, sp} \setcounter{chapter}{1} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} \chapter[Data Analysis Using Graphical Displays]{Data Analysis Using Graphical Displays: Malignant Melanoma in the US and Chinese Health and \\ Family Life \label{DAGD}} \section{Introduction} \section{Initial Data Analysis} \section{Analysis Using \R{}} \subsection{Malignant Melanoma} \index{Boxplot|(} \index{Histogram|(} \index{Scatterplot|(} We might begin to examine the malignant melanoma data in Table~\ref{DAGD-USmelanoma-tab} by constructing a histogram or boxplot for \stress{all} the mortality rates in Figure~\ref{DAGD-USmelanoma-histbox}. The \Rcmd{plot}, \Rcmd{hist} and \Rcmd{boxplot} functions have already been introduced in \Sexpr{ch("AItR")} and we want to produce a plot where both techniques are applied at once. The \Rcmd{layout} function organizes two independent plots on one plotting device, for example on top of each other. Using this relatively simple technique (more advanced methods will be introduced later) we have to make sure that the $x$-axis is the same in both graphs. This can be done by computing a plausible range of the data, later to be specified in a plot via the \Rcmd{xlim} argument: <>= xr <- range(USmelanoma$mortality) * c(0.9, 1.1) xr @ Now, plotting both the histogram and the boxplot requires setting up the plotting device with equal space for two independent plots on top of each other. Calling the \Rcmd{layout} function on a matrix with two cells in two rows, containing the numbers one and two, leads to such a partitioning. The \Rcmd{boxplot} function is called first on the mortality data and then the \Rcmd{hist} function, where the range of the $x$-axis in both plots is defined by $(\Sexpr{xr[1]}, \Sexpr{xr[2]})$. One tiny problem to solve is the size of the margins; their defaults are too large for such a plot. As with many other graphical parameters, one can adjust their value for a specific plot using function \Rcmd{par}. The \R{} code and the resulting display are given in Figure~\ref{DAGD-USmelanoma-histbox}. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 2)) par(mar = par("mar") * c(0.8, 1, 1, 1)) boxplot(USmelanoma$mortality, ylim = xr, horizontal = TRUE, xlab = "Mortality") hist(USmelanoma$mortality, xlim = xr, xlab = "", main = "", axes = FALSE, ylab = "") axis(1) @ \caption{Histogram (top) and boxplot (bottom) of malignant melanoma mortality rates. \label{DAGD-USmelanoma-histbox}} \end{center} \end{figure} Both the histogram and the boxplot in Figure~\ref{DAGD-USmelanoma-histbox} indicate a certain skewness of the mortality distribution. Looking at the characteristics of all the mortality rates is a useful beginning but for these data we might be more interested in comparing mortality rates for ocean and non-ocean states. So we might construct two histograms or two boxplots. Such a \stress{parallel boxplot}, visualizing the conditional distribution of a numeric variable in groups as given by a categorical variable, are easily computed using the \Rcmd{boxplot} function. The continuous response variable and the categorical independent variable are specified via a \Rclass{formula} as described in \Sexpr{ch("AItR")}. Figure~\ref{DAGD-USmelanoma-boxocean} shows such parallel boxplots, as by default produced the \Rcmd{plot} function for such data, for the mortality in ocean and non-ocean states and leads to the impression that the mortality is increased in east or west coast states compared to the rest of the country. \begin{figure} \begin{center} <>= plot(mortality ~ ocean, data = USmelanoma, xlab = "Contiguity to an ocean", ylab = "Mortality") @ \caption{Parallel boxplots of malignant melanoma mortality rates by contiguity to an ocean. \label{DAGD-USmelanoma-boxocean}} \end{center} \end{figure} Histograms are generally used for two purposes: counting and displaying the distribution of a variable; according to \cite{HSAUR:Wilkinson1992}, `they are effective for neither'. Histograms can often be misleading for displaying distributions because of their dependence on the number of classes chosen. An alternative is to formally estimate the density function of a variable and then plot the resulting estimate; details of density estimation are given in \Sexpr{ch("DE")} but for the ocean and non-ocean states the two density estimates can be produced and plotted as shown in Figure~\ref{DAGD-USmelanoma-dens} which supports the impression from Figure~\ref{DAGD-USmelanoma-boxocean}. For more details on such density estimates we refer to \Sexpr{ch("DE")}. \begin{figure} \begin{center} <>= dyes <- with(USmelanoma, density(mortality[ocean == "yes"])) dno <- with(USmelanoma, density(mortality[ocean == "no"])) plot(dyes, lty = 1, xlim = xr, main = "", ylim = c(0, 0.018), xlab = "Mortality") lines(dno, lty = 2) legend("topleft", lty = 1:2, legend = c("Coastal State", "Land State"), bty = "n") @ \caption{Estimated densities of malignant melanoma mortality rates by contiguity to an ocean. \label{DAGD-USmelanoma-dens}} \end{center} \end{figure} Now we might move on to look at how mortality rates are related to the geographic location of a state as represented by the latitude and longitude of the center of the state. Here the main graphic will be the scatterplot. The simple $xy$ scatterplot has been in use since at least the eighteenth century and has many virtues -- indeed according to \cite{HSAUR:Tufte1983}: \begin{quote} The relational graphic -- in its barest form the scatterplot and its variants -- is the greatest of all graphical designs. It links at least two variables, encouraging and even imploring the viewer to assess the possible causal relationship between the plotted variables. It confronts causal theories that $x$ causes $y$ with empirical evidence as to the actual relationship between $x$ and $y$. \end{quote} Let's begin with simple scatterplots of mortality rate against longitude %%' and mortality rate against latitude which can be produced by the code preceding Figure~\ref{DAGD-USmelanoma-xy}. Again, the \Rcmd{layout} function is used for partitioning the plotting device, now resulting in two side-by-side plots. The argument to \Rcmd{layout} is now a matrix with only one row but two columns containing the numbers one and two. In each cell, the \Rcmd{plot} function is called for producing a scatterplot of the variables given in the \Rclass{formula}. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) plot(mortality ~ longitude, data = USmelanoma, ylab = "Mortality", xlab = "Longitude") plot(mortality ~ latitude, data = USmelanoma, ylab = "Mortality", xlab = "Latitude") @ \caption{Scatterplot of malignant melanoma mortality rates by geographical location. \label{DAGD-USmelanoma-xy}} \end{center} \end{figure} Since mortality rate is clearly related only to latitude we can now produce scatterplots of mortality rate against latitude separately for ocean and non-ocean states. Instead of producing two displays, one can choose different plotting symbols for either states. This can be achieved by specifying a vector of integers or characters to the \Rcmd{pch}, where the $i$th element of this vector defines the plot symbol of the $i$th observation in the data to be plotted. For the sake of simplicity, we convert the \Robject{ocean} factor to an \Rclass{integer} vector containing the numbers one for land states and two for ocean states. As a consequence, land states can be identified by the dot symbol and ocean states by triangles. It is useful to add a legend to such a plot, most conveniently by using the \Rcmd{legend} function. This function takes three arguments: a string indicating the position of the legend in the plot, a character vector of labels to be printed and the corresponding plotting symbols (referred to by integers). In addition, the display of a bounding box is anticipated (\Rcmd{bty = "n"}). \begin{figure} \begin{center} <>= plot(mortality ~ latitude, data = USmelanoma, pch = (1:2)[ocean], ylab = "Mortality", xlab = "Latitude") legend("topright", legend = c("Land state", "Coast state"), pch = 1:2, bty = "n") @ \caption{Scatterplot of malignant melanoma mortality rates against latitude. \label{DAGD-USmelanoma-lat}} \end{center} \end{figure} The scatterplot in Figure~\ref{DAGD-USmelanoma-lat} highlights that the mortality is lowest in the northern land states. Coastal states show a higher mortality than land states at roughly the same latitude. The highest mortalities can be observed for the south coastal states with latitude less than $32^\circ$, say, that is <>= subset(USmelanoma, latitude < 32) @ Alternatively, we also may simply want to look at a color-coded map of the United States, where each state is plotted in a color that corresponds to its mortality rate. It is fairly simple to set-up such a plot using the \Rpackage{sp} family of packages \citep{PKG:sp}. We start with loading a map of the mainland states, basically a number of polygons: <>= library("sp") library("maps") library("maptools") states <- map("state", plot = FALSE, fill = TRUE) @ It is of course important to match the mortality rates to the corresponding state. We therefore create unique names of the states in lower-case letters for both the polygons and the mortality data <>= IDs <- sapply(strsplit(states$names, ":"), function(x) x[1]) rownames(USmelanoma) <- tolower(rownames(USmelanoma)) @ Now we are ready to merge these two objects into a so-called \Rclass{SpatialPolygonsDataFrame} object. We first create a \Rclass{SpatialPolygons} object from the map in the correct reference system (WGS84, in our case) and then merge the polygons with the data <>= us1 <- map2SpatialPolygons(states, IDs=IDs, proj4string = CRS("+proj=longlat +datum=WGS84")) us2 <- SpatialPolygonsDataFrame(us1, USmelanoma) @ The resulting object \Robject{us2} can now be plotted using the \Rcmd{spplot} function, see Figure~\ref{DAGD-USmelanoma-long-lat}. The colors correspond to the mortality rate, as shown in the color legend to the right of the map. We see that darker grey values corresponding to higher mortality rates appear in the southern costal states, both on the east and the west coast in good agreement with our earlier results. \begin{figure} \begin{center} <>= spplot(us2, "mortality", col.regions = rev(grey.colors(100))) @ \caption{Map of the United States of America showing malignant melanoma mortality rates. \label{DAGD-USmelanoma-long-lat}} \end{center} \end{figure} Up to now we have primarily focused on the visualization of continuous variables. We now extend our focus to the visualization of categorical variables. \index{Boxplot|)} \index{Histogram|)} \index{Scatterplot|)} \subsection{Chinese Health and Family Life} \index{Barchart|(} \index{Spineplot|(} \index{Spinogram|(} One part of the questionnaire the Chinese Health and Family Life Survey focuses on is the self-reported health status. Two questions are interesting for us. The first one is `Generally speaking, do you consider the condition of your health to be excellent, good, fair, not good, or poor?'. The second question is `Generally speaking, in the past twelve months, how happy were you?'. The distribution of such variables is commonly visualized using barcharts where for each category the total or relative number of observations is displayed. Such a barchart can conveniently be produced by applying the \Rcmd{barplot} function to a tabulation of the data. The empirical density of the variable \Robject{R\_happy} is computed by the \Rcmd{xtabs} function for producing (contingency) tables; the resulting barchart is given in Figure~\ref{DAGD-CHFLS-happy}. \begin{figure} <>= barplot(xtabs(~ R_happy, data = CHFLS)) @ \caption{Bar chart of happiness. \label{DAGD-CHFLS-happy}} \end{figure} The visualization of two categorical variables could be done by conditional barcharts, i.e., barcharts of the first variable within the categories of the second variable. An attractive alternative for displaying such two-way tables are \stress{spineplots} \citep{HSAUR:Friendly1994,HSAUR:HofmannTheus2005,HSAUR:Chenetal2008}; the meaning of the name will become clear when looking at such a plot in Figure~\ref{DAGD-CHFLS-health_happy}. Before constructing such a plot, we produce a two-way table of the health status and self-reported happiness using the \Rcmd{xtabs} function: <>= xtabs(~ R_happy + R_health, data = CHFLS) @ <>= hh <- xtabs(~ R_health + R_happy, data = CHFLS) @ A \stress{spineplot} is a group of rectangles, each representing one cell in the two-way contingency table. The area of the rectangle is proportional with the number of observations in the cell. Here, we produce a mosaic plot of health status and happiness in Figure~\ref{DAGD-CHFLS-health_happy}. \begin{figure} <>= plot(R_happy ~ R_health, data = CHFLS, ylab = "Happiness", xlab = "Health") @ \caption{Spineplot of health status and happiness. \label{DAGD-CHFLS-health_happy}} \end{figure} Consider the right upper cell in Figure~\ref{DAGD-CHFLS-health_happy}, i.e., the $\Sexpr{hh["Excellent", "Very happy"]}$ very happy women with excellent health status. The width of the right-most bar corresponds to the frequency of women with excellent health status. The length of the top-right rectangle corresponds to the conditional frequency of very happy women given their health status is excellent. Multiplying these two quantities gives the area of this cell which corresponds to the frequency of women who are both very happy and enjoy an excellent health status. The conditional frequency of very happy women increases with increasing health status, whereas the conditional frequency of very unhappy or not too happy women decreases. When the association of a categorical and a continuous variable is of interest, say the monthly income and self-reported happiness, one might use parallel boxplots to visualize the distribution of the income depending on happiness. If we were studying self-reported happiness as response and income as independent variable, however, this would give a representation of the conditional distribution of income given happiness, but we are interested in the conditional distribution of happiness given income. One possibility to produce a more appropriate plot is called \stress{spinogram}. Here, the continuous $x$-variable is categorized first. Within each of these categories, the conditional frequencies of the response variable are given by stacked barcharts, in a way similar to spineplots. For happiness depending on log-income (since income is naturally skewed we use a log-transformation of the income) it seems that the proportion of unhappy and not too happy women decreases with increasing income whereas the proportion of very happy women stays rather constant. In contrast to spinograms, where bins, as in a histogram, are given on the $x$-axis, a \stress{conditional density plot} uses the original $x$-axis for a display of the conditional density of the categorical response given the independent variable. \begin{figure} <>= layout(matrix(1:2, ncol = 2)) plot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") cdplot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") @ \caption{Spinogram (left) and conditional density plot (right) of happiness depending on log-income. \label{DAGD-CHFLS-happy_income}} \end{figure} \index{Barchart|)} \index{Spineplot|)} \index{Spinogram|)} \index{Trellis plot|(} For our last example we return to scatterplots for inspecting the association between a woman's monthly income and the income of her partner. Both income variables have been computed and partially imputed from other self-reported variables and are only rough assessments of the real income. Moreover, the data itself is numeric but heavily tied, making it difficult to produce `correct' scatterplots because points will overlap. A relatively easy trick is to jitter the observation by adding a small random noise to each point in order to avoid overlapping plotting symbols. In addition, we want to study the relationship between both monthly incomes conditional on the woman's education. Such conditioning plots are called \stress{trellis} plots and are implemented in the package \Rpackage{lattice} \citep{PKG:lattice, HSAUR:Sarkar2008}. We utilize the \Rcmd{xyplot} function from package \Rpackage{lattice} to produce a scatterplot. The formula reads as already explained with the exception that a third \stress{conditioning} variable, \Robject{R\_edu} in our case, is present. For each level of education, a separate scatterplot will be produced. The plots are directly comparable since the axes remain the same for all plots. \begin{figure} <>= library("lattice") xyplot(jitter(log(R_income + 0.5)) ~ jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, pch = 19, col = rgb(.1, .1, .1, .1), ylab = "log(Wife's income + .5)", xlab = "log(Husband's income + .5)") @ <>= library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) xyplot(jitter(log(R_income + 0.5)) ~ jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, pch = 19, col = rgb(.1, .1, .1, .1), ylab = "log(Wife's income + .5)", xlab = "log(Husband's income + .5)") @ \caption{Scatterplot of jittered log-income of wife and husband, conditional on the wife's education. \label{DAGD-CHFLS-RAincome3}} \end{figure} The plot shown in Figure~\ref{DAGD-CHFLS-RAincome3} reveals several interesting issues. Some observations are positioned on a straight line with slope one, most probably an artifact of missing value imputation by linear models (as described in the data dictionary, see the documentation \texttt{?CHFLS}). Four constellations can be identified: both partners have zero income, the partner has no income, the woman has no income or both partners have a positive income. For couples where the woman has a university degree, the income of both partners is relatively high (except for two couples where only the woman has income). A small number of former junior college students live in relationships where only the man has income, the income of both partners seems only slightly positively correlated for the remaining couples. For lower levels of education, all four constellations are present. The frequency of couples where only the man has some income seems larger than the other way around. Ignoring the observations on the straight line, there is almost no association between the income of both partners. \index{Trellis plot|)} \section{Summary of Findings} Using relatively straightforward graphical techniques only on the two sets of data considered in this chapter we have been able to uncover a number of important features of each data set; \begin{description} \item[Melanoma mortality] Mortality is related only to the latitude of a state not to its longitude, mortality is higher for costal states than for land states, and the highest mortality is observed in the south costal states with latitude less than 32 degrees. \item[Health and family life] We saw that happiness depends on health status. Women reported to be very happy more often when they also reported a good or excellent health status. The dependency of happiness on the income of the women seems to be less clear, but we conclude that, conditional on education, the income of wives and their husbands is highly correlated. \end{description} \section{Final Comments} Producing publication-quality graphics is one of the major strengths of the \R{} system and almost anything is possible since graphics are programmable in \R{}. Naturally, this chapter can be only a very brief introduction to some commonly used displays and the reader is referred to specialized books, most important \cite{HSAUR:Murrell2005}, \cite{HSAUR:Sarkar2008}, and \cite{HSAUR:Chenetal2008}. Interactive 3D-graphics are available from package \Rpackage{rgl} \citep{PKG:rgl}. \section*{Exercises} \begin{description} \exercise The data in Table~\ref{DAGD-household-tab} are part of a data set collected from a survey of household expenditure and give the expenditure of $20$ single men and $20$ single women on four commodity groups. The units of expenditure are Hong Kong dollars, and the four commodity groups are \begin{description} \item[\Robject{housing}] housing, including fuel and light, \item[\Robject{food}] foodstuffs, including alcohol and tobacco, \item[\Robject{goods}] other goods, including clothing, footwear, and durable goods, \item[\Robject{service}] services, including transport and vehicles. \end{description} The aim of the survey was to investigate how the division of household expenditure between the four commodity groups depends on total expenditure and to find out whether this relationship differs for men and women. Use appropriate graphical methods to answer these questions and state your conclusions. <>= data("household", package = "HSAUR3") toLatex(HSAURtable(household), caption = paste("Household expenditure for single men and women."), label = "DAGD-household-tab") @ \exercise The data set shown in Table~\ref{DAGD-USstates-tab} contains values of seven variables for ten states in the US. The seven variables are \begin{description} \item[\Robject{Population}] population size divided by $1000$, \item[\Robject{Income}] average per capita income, \item[\Robject{Illiteracy}] illiteracy rate (\% population), \item[\Robject{Life.Expectancy}] life expectancy (years), \item[\Robject{Homicide}] homicide rate (per $1000$), \item[\Robject{Graduates}] percentage of high school graduates, \item[\Robject{Freezing}] average number of days per below freezing. \end{description} With these data \begin{enumerate} \item Construct a scatterplot matrix of the data labeling the points by state name (using function \Rcmd{text}). \item Construct a plot of life expectancy and homicide rate conditional on average per capita income. \end{enumerate} \begin{sidewaystable} \vspace*{12.5cm} \begin{center} <>= data("USstates", package = "HSAUR3") toLatex(HSAURtable(USstates), caption = paste("Socio-demographic variables for ten US states."), label = "DAGD-USstates-tab") @ \end{center} \end{sidewaystable} \exercise Mortality rates per $100,000$ from male suicides for a number of age groups and a number of countries are given in Table~\ref{DAGD-suicides2-tab}. Construct side-by-side box plots for the data from different age groups, and comment on what the graphic tells us about the data. <>= data("suicides2", package = "HSAUR3") toLatex(HSAURtable(suicides2), caption = paste("Mortality rates per $100,000$ from male suicides."), label = "DAGD-suicides2-tab", rownames = TRUE) @ \exercise \cite{HSAUR:FluryRiedwyl1988} report data that give various length measurements on $200$ Swiss bank notes. The data are available from package \Rpackage{mclust} \citep{PKG:mclust}; a sample of ten bank notes is given in Table~\ref{DAGD-banknote-tab}. <>= data("banknote", package = "mclust") banknote$Status <- NULL banknote <- banknote[c(1:5, 101:200),] toLatex(HSAURtable(banknote, pkg = "mclust", nrow = 10), caption = paste("Swiss bank note data."), label = "DAGD-banknote-tab", rownames = FALSE) @ Use whatever graphical techniques you think are appropriate to investigate whether there is any `pattern' or structure in the data. Do you observe something suspicious? \exercise The data in Table~\ref{DAGD-birds-tab} were originally derived from a study reported in \cite{HSAUR:Vuilleumier1970} which investigated numbers of bird species in isolated `islands' of paramo vegetation in the northern Andes. The aim of the study was to investigate how the number of species (\Robject{N}) is related to four other variables, \Robject{AR} (area of `island' in thousands of square km), \Robject{EL} (elevation in thousands of m), \Robject{Dec} (distance from Ecuador in km) and \Robject{DNI} (distance to the nearest `island' in km). Begin by constructing a scatterplot matrix of the data differentiating the islands on each panel by a different plotting symbol and on each diagonal panel showing the histogram of the associated variable. What can you conclude from this plot about how N is related to the other four variables? <>= data("birds", package = "HSAUR3") toLatex(HSAURtable(birds), caption = paste("Birds in paramo vegetation."), label = "DAGD-birds-tab", rownames = TRUE) @ \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_multidimensional_scaling.pdf0000644000175000017500000015374114133304611021264 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3528 /Filter /FlateDecode /N 73 /First 588 >> stream x[YSܸ~BoT*-kRȄm$6t̯ߑjkts泐i$ fI5L["Yfd?X6bA?iY!&Dbרk&@aB8b(, ꂅ@I(0SFHk&¤aa*LI'h|0$ia;ưP2ZoL1.bX>ޖ}&}f4ɀ.D,.g, }$%xiX@Va]X ؇UH ֯]?0F}"*X-֡.D3i@C*І9I,PAڟdcD;Pd!} PZҀ=Y(@:/h2F(plGȼr:f|{΁X[f霽:I,36M<رǶnye<eI:e1{pDV7*I|n]b<>Gm:,+Tcd9opm_l1'1xyxWi$Fsva,lm6X9U8IBAriđ)WwVy.^ycS[I2%f4#aȽ 6HLAx;@*,}p8c|G"]ǘ޺˶ 11 ؂q2?|w@{WHW@$&rcېxANj-Hik9[NdT%((f$g ?A銮Ϭ")+i˶1ia9$_KOC%46cJ7_`cRzg.ۘ+Ph^[@?t~=œ,/rj"vOo6A 56to*ќL[#P] W@o;Yi\B>ۗd] Dw/$l%d@A5[GM{Sd@I0]E^,Q) j-{nB[M薨Do[ z'N..3rP_|;̿?c>NOxhq9؋_K|ʯ<%@/xƳy6K~yɒ[[V.ȴ:`oydŊGWq>' սdAr!ggxx:5$[Gx`Ȫap:̭[Mc/զs4h->ݯp'j᝘>t_7qn8a !DX zupzTHr*$侟kۄwm|s/jtnK^ˆGuU@-j DD\o"[Il0Ė| i0PIޡB뇏 -Eu|# st,G5GKc!z}|ulᬤ":] z/"7 LuC놛6?r.b@b(#A" -ᄀzknCDk -!.renrWǘ+gʃܜeMNoz:b<,Κ?]}~ܺmqzuLF n╽GyϠW'֟Y^;PK"J @-pGPj*{XmӔ^B0^|X?tnFxϹiQFr C1'''.;^@'HE顧;J:߳gxl^~\)Y^N6Zv2+؈$' fZl>NR=ΪfhNhw.(z4^,1Zz\ :Jxr65│\&|1NqPRDaQ0U0]%rmP[FGw54% XaagX;=y\-{lQ|<8&C=|ՙ1۲eǯJ=ޑU*iѭp>hye+^qnÉws&)%`jj4@ӋŇc`fFLur{އhn磰A쨡nI &F Cݣx{~8V=8n-j(]s8$obٴ@@9Fe ŭߪuqT3FCtO!+SGtR^k [xDjOZB%=wb]|7}/\:/:wtAD2e)_!"ui_> AUڪdՅUIeq]ՄO Ћ^P?'7B‹Gsm`-:=]Fwѝ}7+nn*y5;Tz9HCPOOqZ+w&QW3Dbu?Uk.7y*Ku#iḄ ]eEr^ykRqi!ч?pqWYv3緷l;o4KڱDssN)5e=ȑRKy Lۋ4 VL}L붘? ћy }C wouxl(-RB$Bendstream endobj 75 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:45+02:00 2021-10-18T16:49:45+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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GY4K!翎 /ߙ(P1*fv #:cZ֞W²-:{2yEP/ʫ $Ň!1,AEqپfE)0O._R!iӘ^bA ʏ/)ͬ(swp..Z)0.Y%oFA_!|Upc=[,Pߏl=XV[jߴ] e2 _f?ZxM oeT.^߳{G?v*ʃA/߭s0qj3X엿T Aa5h<6GS exib@"x}Im徭ݰ__g/1eDZGDFjg5jU]y+)(fHWu\}6ѣ?oٹ?G G $*e tC~ڦ ްMN?3B8-XʾKdAOh;b\yynۄ[T]\HoETjr/eyi= zB6ѳ¯b:XeF+4-~'঱?嚱rHֿJ`ɛP$%3OEOX֓Ue>d+HuZi|*MAfgʔE&uиvs!K K:t^CZJ'r&jOfZ>ӭЧ]Zw}j<7( - 7ezd U0T_ǜS{2.f<rP<${LWno4<反ntG3\%ߋ21ZEJa2=ݍ aeRьOU\iEE[&⾛â~AwQoΈjbhwdPppqPcQ^FVјժe+%r9YU*w9 t:#E%BTVgpk!Zn++`]uW@Xr*:wa, 6>#p/?sp^c8 R։Rzp19`6,'H,fZ'alP c0[ 0nŲ d-#jb: m9_#= t3/mm2@^f< 9?i K4qNsk$-ä)뎂!*;I *WՉ3<:g[f_!뱏LFj-~Ӣ4{<1S} Н4{l]DLW{b8ÑK4+;KTTdHR% wdPiZ4_cNYoICA{ƠPXO xG^ wYޕ`4 F4#9pmO na4>#:Qa<:wAz"{BG~Euh]ˣ϶PD;d~΢1mG6e: 8d& Ĵ`}z/}8D܉l%Mhp`NN~19  4X"~3 _>_w._g9yad+܆fEa+̈́(/U SuCpJc!Ŀf Na P槖2!"JxF[}!?/3&4d3@c` |Ht0pR{2DZE_v }}DUÎh㷳wbW-W]4oUޜ.H\bO9=y#5N-\n|S05׍:W4yp93]X4`VMD?v~/cfj߫Gӿ1rhT]e}i7r =AbCh4?} Kȗd0͔[#vpNa.0~8硹 ~FvGhSMG7ܫY盶3739# 6G#i2k4xĬO":,YL}չFL =֞Tj2H;Y†b<Y5>4w/AFhT> stream xcd`ab`dddw 641~H3a!O/VY~'Y;zxyyX~/=[{TfFʢdMCKKs#KԢ<Ē 'G!8?93RA&J_\/1X/(NSG<$C!(8,5E-?D/17UR=土[PZZZ`d{N|q00~Ksp跲ֿ^_n=E'l~];\| pBIOpb1y4^}endstream endobj 84 0 obj << /Filter /FlateDecode /Subtype /Type1C /Length 5066 >> stream xX XSWھ1psU%jeںTq]+Z "o!$a kr¾ kD,jqT jkp3VSkm;CsпA*!%%QuyNVԀ& gn Փ% $T:XZͦdF9j.֐W9n_%80H% eYyd $2 %':r\IfI՛;t|RFzCS K3#59Bñ~BVj;h,> av F 蕮7lpb%M$<]s1 ԆJSSUPʼnڝ8n6o@~- A)a*6yڒr^3=y%%lflP@5D8u. .ߺj־Z>l=y v) dOT%newBgF%来lU"|Ih:p89HAsк 9" ߂lzzaox)hif`;ț0(8ZЦ74,mp*!1 'Fy> Ud&%.fJ@-\Sz(t% TFWps2D+6SdXnd#l4z`mxeXJnĎyHX# @ īlBm Y.B#(ܳž9IEEd|sQ_Vuf aJS(#^յ~/ihgN/.5k.)l_o͘h̷8  Z#p\l?\nKpwk^ h]%hh䌷Xl*CǷJHc٨۔`XqZv\Kn^<΂nQ[`[±<ی/@#U[]c>m Oann<= ' 5FSL"8>*<<**<*J3 WaU߫&㝰֧|%>Z;އO;P+2 9밪|= uuacWPgK*|[ASwCr̨Y B-oV䉵 ҅O|`$zEuFhN2A dPRRJ9ا!OtHúLܚGC[(ng -D3዁7X8O{f"w%r j?VFẊ K7nam8Qϧ\)ˎ7o`3l~wv' 37؂e}o {c=\izRd b#3t/Zn&|iKiȣ*咨dy\ u]L @4V[[Z3xrԂ̼#3ZͩŕEy:r|dS$)5N y(DBٰcɧNM "E3aDP~ԽXmiڟp|: |JZ {*xJR 3릋QlpHښ& I3lrgYaGTMV$}7=bO]J0põ(2g$TP~r:Dꬷw, %9/ '#A:NB(sktwa7"coĝ a ^A#όctgWh);XcwVE[_C vl-UO`'wc h$x쯒*Ք>\OXta?@jje]y>?)AKiEN7 GjھtF0m(d ۸9KC3ԩS]:K;0r>dtanqf"2]T0Q%GP #_eCˢvbm*ώ{=#;sO<} + a-ͤK pO0Mޟ1 s}O(%O1׵#WƗgjK 4ԶY"4kxzp_ s@)CG#OiŜ[u `]6Pȭ· I$FG2#6 66FQ/Hendstream endobj 85 0 obj << /Filter /FlateDecode /Subtype /Type1C /Length 1794 >> stream xSkTgd*|g RV*jD,mmH I̅ hH"K#K҈nam`mum=]~헠ey/|$! !HJ L6ci_d.xkR" Rԣ0?DM=-Bd  es9яا#o0[ȓD ss.[N4E& * HBeF/嵦e` S1  e+6fY (xHT/:LNLNk\3%0y $=o(F #(2(&^ L: hU:@: :/ MFAЛfTT4xN]!TT6?LJAk&)Z05J̋!8(hٗ_451Pez?_[+zMeW_0yMᲩ#|e;k3?k#"m+V&>*) T"$"D "fXb6MCȈAC;2WBRBB-ie_ɵ~=E |0즿Ys]"L)Bb"zf 쉞vI\{}oO5g@zqv ~uאr<'ڛ&f{I1Sܧ>p7FbK֫_+ BȷGU)os kb\unG3tt$rK.'{oR}OT8* cP44;~a<'R^ҿ*ka.մmuwZ]+7!=>9Ǥf$mZ&{R=!$muYvY,HDhk͜@+bd"5ʲZ=.[Şk|mVfB+;avb\ʼoAzwmm#ܰ_GHKexC,By"݅}pCmtgGgn>y![)J -]zK$7P.e-934Fgĥ$$fZ69h> stream xcd`ab`dddw441~H3a!=,ݝ[zxyyXV-={3#c~is~AeQfzFFcnjQfrbobIFjnb ZRaQRR`_^^[_nPYZZTWqr-(-I-ROI-c``` ``0d`bddYX~? _n],7<}~JsQ[ZƔfn*}/u/_н v.4{{'L.cu}ۺ9^;PRn.[tif|];q*r\,y8La`ˡ$endstream endobj 87 0 obj << /Filter /FlateDecode /Subtype /Type1C /Length 373 >> stream xjCMR72,B@DݹO   eb_mqCopyright (c) 1997, 2009 American Mathematical Society (), with Reserved Font Name CMR7.CMR7Computer Modern2p͋JiuP~>}L讧Ǻɋ !74/XWϡ=:4MFkgo0wCna  7 ڛ ﺊ^endstream endobj 88 0 obj << /Filter /FlateDecode /Length 1237 >> stream xVMS7ϯhIp%c];sXXYO4;ҒMR.m{#j9 ?wOO!ZE&Ϻwd}`w5yВ!G64A[G^NmWHShmOѣHMOhFc۞j؉{m[j&d,x2c!!GM}lF]蹴]Y]t CSGjm\2I F;΂:g%Dc)1֘ ƥN}I~_~\to;y PvwymVqS) 1QOd$Z>v*-XZ 3%1(=zɪ̄Dh'7CQGAM:{O-dn k!-a{UR./ ,͚keo4Ƌ"߱-Ru"K> CJy-3iE;Rkqs / V[&^2A L$F`I7{9̘ƪ3YZ YG喾 ߭&ЅXhTؙwNB%]Y::tl 6cw-%MPUFammRK 5_D*+*b/w> h0Mb&pyL><(cbce7rEHjy^.@$6FīߪtiN=jdUBql<  u=C.ڣFѪ*Z1wh.3dVXa X$BEzHljuE.Cd>^9X\,0qGjUŭ*od;%\v?w_hz(j 'Ӗ D`0qu9)B^>sݼ||TBl!U#V3YaK!~5_^*Xt]͒_#ok< U囡?{&vWB ]'hXi쩱4f mޥ]&KOr.<}ϓu8Yu:3dO|ͻ>u'j4^X?R4?{\ArY=/&uH]yqзߕMendstream endobj 89 0 obj << /Filter /FlateDecode /Length 2823 >> stream xYYo~_100h'}@@qdA" `Ht(|=]C {z誙F|[Bu&6w Ѽ\8);+U㭓]pn)"x Q 2v&*aTeSig:@k8b輭Z \)Cg\dJ DJ5LQ'&O4 mU&v)ל_de#4^N*ۜYwƉbpjz =]DƷh-bJ˺@|TN;!tlߜ`ȥ4_/WZ.Ӟ>7L_Dx 훗IB0?8BM\I-v);6rem}U7?CYmj]V7iiQV(J.CY]վng+ge%%`Gpã_ϘTͼ-ڲTV86GJb[V}YUWof0 s3ح0_1ϟ-Pc9 U23 U%7Lq5 -k$,˯gҶ a揊@*@}Z(j6ԤH_qN=|lt3 >;\|7svpUd?snouYՋC!w $ċԌ`;ܸ[M\ߚvVEc1:?4RBSzh,ѓBJ'A۠Qvr]5+e;ch#. 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Z $DU{ H/qH =2lyk@ endstream endobj startxref 54880 %%EOF HSAUR3/inst/doc/Ch_introduction_to_R.Rnw0000644000175000017500000015624114133304452017711 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{An Introduction to R} %%\VignetteDepends{sandwich} \setcounter{chapter}{0} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter{An Introduction to \R{} \label{AItR}} \setcounter{page}{1} \section{What is \R{}?} The \R{} system for statistical computing is an environment for data analysis and graphics. %% #Z %% and an implementation of the \R{} programming language. The root of \R{} is the \S{} language, developed by John Chambers and colleagues \citep{HSAUR:Becker+Chambers+Wilks:1988,HSAUR:Chambers+Hastie:1992,HSAUR:Chambers:1998} at Bell Laboratories (formerly AT\&T, now owned by Lucent Technologies) starting in the 1960s. The \S{} language was designed and developed as a programming language for data analysis tasks but in fact it is a full-featured programming language in its current implementations. The development of the \R{} system for statistical computing is heavily influenced by the open source idea: The base distribution of \R{} \index{Base distribution} and a large number of user-contributed extensions are available under the terms of the Free Software Foundation's GNU General %%' Public License in source code form. \index{GNU General Public License} This licence has two major implications for the data analyst working with \R. The complete source code is available and thus the practitioner can investigate the details of the implementation of a special method, make changes, and distribute modifications to colleagues. As a side effect, the \R{} system for statistical computing is available to everyone. All scientists, including, in particular, those working in developing countries, now have access to state-of-the-art tools for statistical data analysis without additional costs. With the help of the \R{} system for statistical computing, research really becomes reproducible when both the data and the results of all data analysis steps reported in a paper are available to the readers through an \R{} transcript file. \R{} is most widely used for teaching undergraduate and graduate statistics classes at universities all over the world because students can freely use the statistical computing tools. The base distribution of \R{} is maintained by a small group of statisticians, the \R{} Development Core Team. A huge amount of additional functionality is implemented in add-on packages \index{Add-on package} authored and maintained by a large group of volunteers. The main source of information about the \R{} system is the World Wide Web with the official home page of the \R{} project being \curl{http://www.R-project.org} All resources are available from this page: the \R{} system itself, a collection of add-on packages, manuals, documentation, and more. The intention of this chapter is to give a rather informal introduction to basic concepts and data manipulation techniques for the \R{} novice. Instead of a rigid treatment of the technical background, the most common tasks are illustrated by practical examples and it is our hope that this will enable readers to get started without too many problems. \section{Installing \R{}} \index{Base system|(} The \R{} system for statistical computing consists of two major parts: the base system and a collection of user-contributed add-on packages. The \R{} language is implemented in the base system. Implementations of statistical and graphical procedures are separated from the base system and are organized in the form of \stress{packages}. A package is \index{Add-on package} a collection of functions, examples, and documentation. The functionality of a package is often focused on a special statistical methodology. Both the base system and packages are distributed via the Comprehensive \R{} Archive Network (CRAN) accessible under \curl{http://CRAN.R-project.org} \index{Comprehensive R Archive Network (CRAN)@Comprehensive \R{} Archive Network (CRAN)} \subsection{The Base System and the First Steps \label{AItR:Base}} The base system is available in source form and in precompiled form for various Unix systems, Windows platforms and Mac OS X. For the data analyst, it is sufficient to download the precompiled binary distribution and install it locally. Windows users follow the link \curl{http://CRAN.R-project.org/bin/windows/base/release.htm} download the corresponding file (currently named \file{\Sexpr{HSAUR3:::exename()}}), execute it locally, and follow the instructions given by the installer. \index{Base system|)} \begin{wrapfigure}{lH}[0cm]{2cm} \includegraphics[width=1.95cm]{graphics/Rlogo_bw} \end{wrapfigure} Depending on the operating system, \R{} can be started either by typing `\texttt{R}' on the shell (Unix systems) or by clicking on the %' \R{} symbol (as shown left) created by the installer (Windows). \R{} comes without any frills and on start up shows simply a short introductory message including the version number and a prompt `\texttt{>}': %' \index{Prompt} <>= HSAUR3:::Rwelcome() @ <>= options(prompt = "> ") @ One can change the appearance of the prompt by <>= options(prompt = "R> ") @ and we will use the prompt \Rarg{R>} for the display of the code examples throughout this book. A \texttt{+} sign at the very beginning of a line indicates a continuing command after a newline. Essentially, the \R{} system evaluates commands typed on the \R{} prompt and returns the results of the computations. The end of a command is indicated by the return key. Virtually all introductory texts on \R{} start with an example using \R{} as a pocket calculator, and so do we: <>= x <- sqrt(25) + 2 @ This simple statement asks the \R{} interpreter to calculate $\sqrt{25}$ and then to add $2$. The result of the operation is assigned to an \R{} object \index{Object} with variable name \Robject{x}. The assignment operator \Roperator{<-} binds the value of its right-hand side to a variable name on the left-hand side. The value of the object \Robject{x} can be inspected simply by typing <>= x @ which, implicitly, calls the \Rcmd{print} method: <>= print(x) @ \subsection{Packages} \index{Add-on package|(} The base distribution already comes with some high-priority add-on packages, namely \begin{center} <>= colwidth <- 4 ip <- installed.packages(priority = "high") pkgs <- unique(ip[,"Package"]) pkgs <- paste("\\Rpackage{", pkgs, "}", sep = "") nrows <- ceiling(length(pkgs) / colwidth) pkgs <- c(pkgs, rep("", colwidth * nrows - length(pkgs))) cat(paste(c("\\begin{tabular}{", paste(rep("l", colwidth), collapse=""), "}"), collapse = ""), "\n", file = "tables/rec.tex", append = FALSE) for (i in 1:nrows) { cat(paste(pkgs[(1:colwidth) + (i-1)*colwidth], collapse = " & "), file = "tables/rec.tex", append = TRUE) cat("\\\\ \n", file = "tables/rec.tex", append = TRUE) } cat("\\end{tabular}\n", file = "tables/rec.tex", append = TRUE) rm(ip, nrows) @ \input{tables/rec} \end{center} Some of the packages listed here %% #Z %% are maintained by members of the \R{} core development team and implement standard statistical functionality, for example linear models, classical tests, a huge collection of high-level plotting functions or tools for survival analysis; many of these will be described and used in later chapters. Others provide basic infrastructure, for example for graphic systems, code analysis tools, graphical-user interfaces or other utilities. <>= cp <- available.packages(contriburl = "http://CRAN.r-project.org/src/contrib") ncp <- sum(!rownames(cp) %in% pkgs) rm(cp, pkgs) @ Packages not included in the base distribution can be installed directly from the \R{} prompt. At the time of writing this chapter, $\Sexpr{ncp}$ user-contributed packages covering almost all fields of statistical methodology were available. Certain so-called `task views' for special topics, such as statistics in the social sciences, environmetrics, robust statistics, etc., describe important and helpful packages and are available from \curl{http://CRAN.R-project.org/web/views/} <>= rm(ncp, colwidth, i) @ Given that an Internet connection is available, a package is installed by supplying the name of the package to the function \Rcmd{install.packages}. If, for example, add-on functionality for robust estimation of covariance matrices via sandwich estimators \index{Sandwich estimator} is required (for example in \Sexpr{ch("ALDII")}), the \Rpackage{sandwich} package \citep{PKG:sandwich} can be downloaded and installed via <>= install.packages("sandwich") @ The package functionality is available after \stress{attaching} the package by <>= library("sandwich") @ A comprehensive list of available packages can be obtained from \curl{http://CRAN.R-project.org/web/packages/} Note that on Windows operating systems, precompiled versions of packages are downloaded and installed. %%Currently, the service of overnight compilation of all packages on %%CRAN for the Windows platform is kindly offered by Uwe Ligges from the %%University of Dortmund, Germany. In contrast, packages are compiled locally before they are installed on Unix systems. \index{Add-on package|)} \section{Help and Documentation \label{AItR:HDN}} \index{Help system|(} Roughly, three different forms of documentation for the \R{} system for statistical computing may be distinguished: online help that comes with the base distribution or packages, electronic manuals, and publications work in the form of books, etc. The help system is a collection of manual pages describing each user-visible function and data set that comes with \R{}. A manual page is shown in a pager or Web browser when the name of the function we would like to get help for is supplied to the \Rcmd{help} function <>= help("mean") @ or, for short, \begin{Verbatim} R> ?mean \end{Verbatim} Each manual page consists of a general description, the argument list of the documented function with a description of each single argument, information about the return value of the function and, optionally, references, cross-links and, in most cases, executable examples. The function \Rcmd{help.search} is helpful for searching within manual pages. An overview on documented topics in an add-on package is given, for example for the \Rpackage{sandwich} package, by <>= help(package = "sandwich") @ Often a package comes along with an additional document describing the package functionality and giving examples. Such a document is called a \Rclass{vignette} \citep{HSAUR:Leisch2003,HSAUR:Gentleman2005}. For example, the \Rpackage{sandwich} package vignette is opened using <>= vignette("sandwich", package = "sandwich") @ More extensive documentation is available electronically from the collection of manuals at \curl{http://CRAN.R-project.org/manuals.html} For the beginner, at least the first and the second document of the following four manuals \citep{HSAUR:AItR,HSAUR:RDIE,HSAUR:RIA,HSAUR:WRE} are mandatory: \begin{description} \item[An Introduction to R] A more formal introduction to data analysis with \R{} than this chapter. \item[R Data Import/Export] A very useful description of how to read and write various external data formats. \item[R Installation and Administration] Hints for installing \R{} on special platforms. \item[Writing \R{} Extensions] The authoritative source on how to write \R{} programs and packages. \end{description} Both printed and online publications are available, the most important ones are \booktitle{Modern Applied Statistics with \S{}} \citep{HSAUR:VenablesRipley2002}, \booktitle{Introductory Statistics with \R{}} \citep{HSAUR:Dalgaard2002}, \booktitle{\R{} Graphics} \citep{HSAUR:Murrell2005} and the \R{} Newsletter, freely available from \curl{http://CRAN.R-project.org/doc/Rnews/} In case the electronically available documentation and the answers to frequently asked questions (FAQ), available from \curl{http://CRAN.R-project.org/faqs.html} \index{Frequently asked questions (FAQ)} have been consulted but a problem or question remains unsolved, the \texttt{r-help} email list is the right place to get answers to well-thought-out questions. It is helpful to read the posting guide \curl{http://www.R-project.org/posting-guide.html} before starting to ask. \index{Help system|)} \section{Data Objects in \R{}} \index{Forbes 2000 ranking|(} The data handling and manipulation techniques explained in this chapter will be illustrated by means of a data set of $2000$ world leading companies, the Forbes 2000 list for the year 2004 collected by \booktitle{Forbes Magazine}. This list is originally available from \curl{http://www.forbes.com} and, as an \R{} data object, it is part of the \Rpackage{HSAUR3} package (\textit{Source}: From Forbes.com, New York, New York, 2004. With permission.). In a first step, we make the data available for computations within \R. The \Rcmd{data} function searches for data objects of the specified name (\Robject{"Forbes2000"}) in the package specified via the \Rarg{package} argument and, if the search was successful, attaches the data object to the global environment: \index{Forbes2000 data@\Robject{Forbes2000} data} <>= data("Forbes2000", package = "HSAUR3") ls() @ <>= x <- c("x", "Forbes2000") print(x) @ The output of the \Rcmd{ls} function lists the names of all objects currently stored in the global environment, and, as the result of the previous command, a variable named \Robject{Forbes2000} is available for further manipulation. The variable \Robject{x} arises from the pocket calculator example in Subsection~\ref{AItR:Base}. As one can imagine, printing a list of $2000$ companies via <>= print(Forbes2000) @ <>= print(Forbes2000[1:3,]) cat("...\n") @ will not be particularly helpful in gathering some initial information about the data; it is more useful to look at a description of their structure found by using the following command <>= str(Forbes2000) @ <>= str(Forbes2000, vec.len = 2, strict.width = "cut", width = 60) @ The output of the \Rcmd{str} function tells us that \Robject{Forbes2000} is an object of class \Rclass{data.frame}, the most important data structure for handling tabular statistical data in \R. As expected, information about $2000$ observations, i.e., companies, are stored in this object. For each observation, the following eight variables are available: \begin{description} \item[\Robject{rank}] the ranking of the company, \item[\Robject{name}] the name of the company, \item[\Robject{country}] the country the company is situated in, \item[\Robject{category}] a category describing the products the company produces, \item[\Robject{sales}] the amount of sales of the company in billion US dollars, \item[\Robject{profits}] the profit of the company in billion US dollars, \item[\Robject{assets}] the assets of the company in billion US dollars, \item[\Robject{marketvalue}] the market value of the company in billion US dollars. \end{description} A similar but more detailed description is available from the help page for the \Robject{Forbes2000} object: <>= help("Forbes2000") @ or \begin{Verbatim} R> ?Forbes2000 \end{Verbatim} All information provided by \Rcmd{str} can be obtained by specialized functions as well and we will now have a closer look at the most important of these. The \R{} language is an object-oriented programming language, \index{Object-oriented programming language} so every object is an instance of a class. The name of the class of an object can be determined by <>= class(Forbes2000) @ Objects of class \Rclass{data.frame} represent data the traditional table-oriented way. Each row is associated with one single observation and each column corresponds to one variable. The dimensions of such a table can be extracted using the \Rcmd{dim} function <>= dim(Forbes2000) @ Alternatively, the numbers of rows and columns can be found using <>= nrow(Forbes2000) ncol(Forbes2000) @ The results of both statements show that \Robject{Forbes2000} has $\Sexpr{nrow(Forbes2000)}$ rows, i.e., observations, the companies in our case, with eight variables describing the observations. The variable names are accessible from <>= names(Forbes2000) @ The values of single variables can be extracted from the \Robject{Forbes2000} object by their names, for example the ranking of the companies <>= class(Forbes2000[,"rank"]) @ is stored as an integer variable. Brackets \Robject{[]} always indicate a subset \index{Subset} of a larger object, in our case a single variable extracted from the whole table. Because \Rclass{data.frame}s have two dimensions, observations and variables, the comma is required in order to specify that we want a subset of the second dimension, i.e., the variables. The rankings for all $\Sexpr{nrow(Forbes2000)}$ companies are represented in a \Rclass{vector} structure the length of which is given by <>= length(Forbes2000[,"rank"]) @ A \Rclass{vector} is the elementary structure for data handling in \R{} and is a set of simple elements, all being objects of the same class. For example, a simple vector of the numbers one to three can be constructed by one of the following commands <>= 1:3 c(1,2,3) seq(from = 1, to = 3, by = 1) @ The unique names of all $\Sexpr{nrow(Forbes2000)}$ companies are stored in a character vector \index{character vector@\Rclass{character} vector} <>= class(Forbes2000[,"name"]) length(Forbes2000[,"name"]) @ and the first element of this vector is <>= Forbes2000[,"name"][1] @ Because the companies are ranked, Citigroup is the world's largest %' company according to the Forbes 2000 list. Further details on vectors and subsetting are given in Section~\ref{AItR:BDM}. Nominal measurements are represented by \Rclass{factor} variables in \R, such as the category of the company's business segment %%' <>= class(Forbes2000[,"category"]) @ Objects of class \Rclass{factor} and \Rclass{character} basically differ in the way their values are stored internally. Each element of a vector of class \Rclass{character} is stored as a \Rclass{character} variable whereas an integer variable indicating the level of a \Rclass{factor} is saved for \Rclass{factor} objects. In our case, there are <>= nlevels(Forbes2000[,"category"]) @ different levels, i.e., business categories, which can be extracted by <>= levels(Forbes2000[,"category"]) @ <>= levels(Forbes2000[,"category"])[1:3] cat("...\n") @ As a simple summary statistic, the frequencies of the levels of such a \Rclass{factor} variable can be found from <>= table(Forbes2000[,"category"]) @ <>= table(Forbes2000[,"category"])[1:3] cat("...\n") @ The sales, assets, profits, and market value variables are of type \Robject{numeric}, the natural data type for continuous or discrete measurements, for example <>= class(Forbes2000[,"sales"]) @ and simple summary statistics such as the mean, median, and range can be found from <>= median(Forbes2000[,"sales"]) mean(Forbes2000[,"sales"]) range(Forbes2000[,"sales"]) @ The \Rcmd{summary} method can be applied to a numeric vector to give a set of useful summary statistics, namely the minimum, maximum, mean, median, and the $25\%$ and $75\%$ quartiles; for example <>= summary(Forbes2000[,"sales"]) @ \section{Data Import and Export} \index{Data import and export|(} In the previous section, the data from the Forbes 2000 list of the world's largest %%' companies were loaded into \R{} from the \Rpackage{HSAUR3} package but we will now explore practically more relevant ways to import data into the \R{} system. The most frequent data formats the data analyst is confronted with are comma separated files, \index{Comma separated files} \EXCEL{} spreadsheets, \index{Excel spreadsheets@\EXCEL{} spreadsheets} files in \SPSS{} format \index{SPSS file format@\SPSS{} file format} and a variety of \SQL{} data base engines. \index{SQL data bases@\SQL{} data bases} Querying data bases is a nontrivial task and requires additional knowledge about querying languages, and we therefore refer to the \booktitle{\R{} Data Import/Export} manual -- see Section~\ref{AItR:HDN}. <>= pkgpath <- system.file(package = "HSAUR2") mywd <- getwd() filep <- file.path(pkgpath, "rawdata") setwd(filep) @ We assume that a comma-separated file containing the Forbes 2000 list is available as \file{Forbes2000.csv} (such a file is part of the \Rpackage{HSAUR3} source package in directory \file{HSAUR3/inst/rawdata}). When the fields are separated by commas and each row begins with a name (a text format typically created by \EXCEL{}), we can read in the data as follows using the \Rcmd{read.table} function <>= csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1) @ The argument \Rarg{header = TRUE} indicates that the entries in the first line of the text file \Robject{"Forbes2000.csv"} should be interpreted as variable names. Columns are separated by a comma (\Rcmd{sep = ","}), users of continental versions of \EXCEL{} should take care of the character symbol coding for decimal points (by default \Rcmd{dec = "."}). Finally, the first column should be interpreted as row names but not as a variable (\Rarg{row.names = 1}). Alternatively, the function \Rcmd{read.csv} can be used to read comma-separated files. The function \Rcmd{read.table} by default guesses the class of each variable from the specified file. In our case, character variables are stored as factors <>= class(csvForbes2000[,"name"]) @ which is only suboptimal since the names of the companies are unique. However, we can supply the types for each variable to the \Rarg{colClasses} argument <>= csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1, colClasses = c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric")) class(csvForbes2000[,"name"]) @ and check if this object is identical to our previous Forbes 2000 list object <>= all.equal(csvForbes2000, Forbes2000) @ The argument \Rarg{colClasses} expects a character vector of length equal to the number of columns in the file. Such a vector can be supplied by the \Rcmd{c} function that combines the objects given in the parameter list into a \Rclass{vector} <>= classes <- c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric") length(classes) class(classes) @ An \R{} interface to the open data base connectivity (ODBC) standard \index{Open data base connectivity standard (ODBC)} is available in package \Rpackage{RODBC} and its functionality can be used to access \EXCEL{} and \ACCESS{} files directly: <>= library("RODBC") cnct <- odbcConnectExcel("Forbes2000.xls") sqlQuery(cnct, "select * from \"Forbes2000\\$\"") @ The function \Rcmd{odbcConnectExcel} opens a connection to the specified \EXCEL{} or \ACCESS{} file which can be used to send \SQL{} queries to the data base engine and retrieve the results of the query. <>= setwd(mywd) @ Files in \SPSS{} format are read in a way similar to reading comma-separated files, using the function \Rcmd{read.spss} from package \Rpackage{foreign} (which comes with the base distribution). Exporting data from \R{} is now rather straightforward. A comma-separated file readable by \EXCEL{} can be constructed from a \Rclass{data.frame} object via <>= write.table(Forbes2000, file = "Forbes2000.csv", sep = ",", col.names = NA) @ The function \Rcmd{write.csv} is one alternative and the functionality implemented in the \Rpackage{RODBC} package can be used to write data directly into \EXCEL{} spreadsheets as well. \index{Saving R objects@Saving \R{} objects} Alternatively, when data should be saved for later processing in \R{} only, \R{} objects of arbitrary kind can be stored into an external binary file via <>= save(Forbes2000, file = "Forbes2000.rda") @ where the extension \file{.rda} is standard. We can get the file names of all files with extension \file{.rda} from the working directory <>= list.files(pattern = "\\.rda") @ and we can load the contents of the file into \R{} by <>= load("Forbes2000.rda") @ \index{Data import and export|)} \section{Basic Data Manipulation \label{AItR:BDM}} \index{Data manipulation|(} The examples shown in the previous section have illustrated the importance of \Rclass{data.frame}s for storing and handling tabular data in \R. Internally, a \Rclass{data.frame} is a \Rclass{list} of vectors of a common length $n$, the number of rows of the table. Each of those vectors represents the measurements of one variable and we have seen that we can access such a variable by its name, for example the names of the companies <>= companies <- Forbes2000[,"name"] @ Of course, the \Robject{companies} vector is of class \Rclass{character} and of length $\Sexpr{length(companies)}$. A subset \index{Subset} of the elements of the vector \Robject{companies} can be extracted using the \Rcmd{[]} subset operator. For example, the largest of the $2000$ companies listed in the Forbes 2000 list is <>= companies[1] @ and the top three companies can be extracted utilizing an integer vector of the numbers one to three: <>= 1:3 companies[1:3] @ In contrast to indexing with positive integers, negative indexing returns \index{negative indexing} all elements that are \stress{not} part of the index vector given in brackets. For example, all companies except those with numbers four to two thousand, i.e., the top three companies, are again <>= companies[-(4:2000)] @ The complete information about the top three companies can be printed in a similar way. Because \Rclass{data.frame}s have a concept of rows and columns, we need to separate the subsets corresponding to rows and columns by a comma. The statement <>= Forbes2000[1:3, c("name", "sales", "profits", "assets")] @ extracts the variables \Robject{name}, \Robject{sales}, \Robject{profits} and \Robject{assets} for the three largest companies. Alternatively, a single variable can be extracted from a \Rclass{data.frame} by <>= companies <- Forbes2000$name @ which is equivalent to the previously shown statement <>= companies <- Forbes2000[,"name"] @ We might be interested in extracting the largest companies with respect to an alternative ordering. The three top-selling companies can be computed along the following lines. First, we need to compute the ordering of the companies' sales %%' <>= order_sales <- order(Forbes2000$sales) @ which returns the indices of the ordered elements of the numeric vector \Robject{sales}. Consequently the three companies with the lowest sales are <>= companies[order_sales[1:3]] @ The indices of the three top sellers are the elements $1998, 1999$ and $2000$ of the integer vector \Robject{order\_sales} <>= Forbes2000[order_sales[c(2000, 1999, 1998)], c("name", "sales", "profits", "assets")] @ Another way of selecting vector elements is the use of a logical vector being \Robject{TRUE} when the corresponding element is to be selected and \Robject{FALSE} otherwise. The companies with assets of more than $1000$ billion US dollars are <>= Forbes2000[Forbes2000$assets > 1000, c("name", "sales", "profits", "assets")] @ where the expression \Robject{Forbes2000\$assets > 1000} indicates a logical vector of length $2000$ with <>= table(Forbes2000$assets > 1000) @ elements being either \Robject{FALSE} or \Robject{TRUE}. In fact, for some of the companies the measurement of the \Robject{profits} variable are missing. In \R, missing values are treated by a special symbol, \Robject{NA}, indicating \index{NA symbol@\Robject{NA} symbol} that this measurement is not available. \index{Missing values} The observations with profit information missing can be obtained via <>= na_profits <- is.na(Forbes2000$profits) table(na_profits) Forbes2000[na_profits, c("name", "sales", "profits", "assets")] @ where the function \Rcmd{is.na} returns a logical vector being \Robject{TRUE} when the corresponding element of the supplied vector is \Robject{NA}. A more comfortable approach is available when we want to remove all observations with at least one missing value from a \Rclass{data.frame} object. The function \Rcmd{complete.cases} takes a \Rclass{data.frame} and returns a logical vector being \Robject{TRUE} when the corresponding observation does not contain any missing value: <>= table(complete.cases(Forbes2000)) @ Subsetting \Rclass{data.frame}s driven by logical expressions may induce a lot of typing which can be avoided. The \Rcmd{subset} function takes a \Rclass{data.frame} as first argument and a logical expression as second argument. For example, we can select a subset of the Forbes 2000 list consisting of all companies situated in the United Kingdom by <>= UKcomp <- subset(Forbes2000, country == "United Kingdom") dim(UKcomp) @ i.e., $\Sexpr{nrow(UKcomp)}$ of the $2000$ companies are from the UK. Note that it is not necessary to extract the variable \Robject{country} from the \Rclass{data.frame} \Robject{Forbes2000} when formulating the logical expression with \Rcmd{subset}. \index{Data manipulation|)} \section{Computing with Data} \subsection{Simple Summary Statistics} Two functions are helpful for getting an overview about \R{} objects: \Rcmd{str} and \Rcmd{summary}, where \Rcmd{str} is more detailed about data types and \Rcmd{summary} gives a collection of sensible summary statistics. For example, applying the \Rcmd{summary} method to the \Robject{Forbes2000} data set, <>= summary(Forbes2000) @ results in the following output <>= summary(Forbes2000) @ From this output we can immediately see that most of the companies are situated in the US and that most of the companies are working in the banking sector as well as that negative profits, or losses, up to $\Sexpr{abs(round(min(Forbes2000$profits, na.rm = TRUE)))}$ billion US dollars occur. Internally, \Rcmd{summary} is a so-called \stress{generic function} \index{Generic function} with methods for a multitude of classes, i.e., \Rcmd{summary} can be applied to objects of different classes and will report sensible results. Here, we supply a \Rclass{data.frame} object to \Rcmd{summary} where it is natural to apply \Rcmd{summary} to each of the variables in this \Rclass{data.frame}. Because a \Rclass{data.frame} is a \Rclass{list} with each variable being an element of that \Rclass{list}, the same effect can be achieved by <>= lapply(Forbes2000, summary) @ \index{apply family@\Rcmd{apply} family} The members of the \Rcmd{apply} family help to solve recurring tasks for each element of a \Rclass{data.frame}, \Rclass{matrix}, \Rclass{list} or for each level of a \Rclass{factor}. It might be interesting to compare the profits in each of the $\Sexpr{nlevels(Forbes2000$category)}$ categories. To do so, we first compute the median profit for each category from <>= mprofits <- tapply(Forbes2000$profits, Forbes2000$category, median, na.rm = TRUE) @ a command that should be read as follows. For each level of the factor \Robject{category}, determine the corresponding elements of the numeric vector \Robject{profits} and supply them to the \Rcmd{median} function with additional argument \Rarg{na.rm = TRUE}. The latter one is necessary because \Robject{profits} contains missing values which would lead to a non-sensible result of the \Rcmd{median} function <>= median(Forbes2000$profits) @ The three categories with highest median profit are computed from the vector of sorted median profits <>= rev(sort(mprofits))[1:3] @ where \Rcmd{rev} rearranges the vector of median profits \Rcmd{sort}ed from smallest to largest. Of course, we can replace the \Rcmd{median} function with \Rcmd{mean} or whatever is appropriate in the call to \Rcmd{tapply}. In our situation, \Rcmd{mean} is not a good choice, because the distributions of profits or sales are naturally skewed. Simple graphical tools for the inspection of the empirical distributions are introduced later on and in \Sexpr{ch("DAGD")}. \subsection{Customizing Analyses} \index{Functions|(} In the preceding sections we have done quite complex analyses on our data using functions available from \R{}. However, the real power of the system comes to light when writing our own functions for our own analysis tasks. Although \R{} is a full-featured programming language, writing small helper functions for our daily work is not too complicated. We'll study two example cases. At first, we want to add a robust measure of variability to the location measures computed in the previous subsection. In addition to the median profit, computed via <>= median(Forbes2000$profits, na.rm = TRUE) @ we want to compute the inter-quartile range, i.e., the difference between the 3rd and 1st quartile. Although a quick search in the manual pages (via \texttt{help("interquartile")}) brings function \Rcmd{IQR} to our attention, we will approach this task without making use of this tool, but using function \Rcmd{quantile} for computing sample quantiles only. A function in \R{} is nothing but an object, and all objects are created equal. Thus, we `just' have to assign a \Rclass{function} object to a variable. A \Rclass{function} object consists of an argument list, defining arguments and possibly default values, and a body defining the computations. The body starts and ends with braces. Of course, the body is assumed to be valid \R{} code. In most cases we expect a function to return an object, therefore, the body will contain one or more \Rcmd{return} statements the arguments of which define the return values. Returning to our example, we'll name our function \Rcmd{iqr}. The \Rcmd{iqr} function should operate on numeric vectors, therefore it should have an argument \Robject{x}. This numeric vector will be passed on to the \Rcmd{quantile} function for computing the sample quartiles. The required difference between the $3^\text{rd}$ and $1^\text{st}$ quartile can then be computed using \Rcmd{diff}. The definition of our function reads as follows <>= iqr <- function(x) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE) return(diff(q)) } @ A simple test on simulated data from a standard normal distribution shows that our first function actually works, a comparison with the \Rcmd{IQR} function shows that the result is correct: <>= xdata <- rnorm(100) iqr(xdata) IQR(xdata) @ However, when the numeric vector contains missing values, our function fails as the following example shows: <>= xdata[1] <- NA iqr(xdata) @ <>= xdata[1] <- NA cat(try(iqr(xdata))) @ In order to make our little function more flexible it would be helpful to add all arguments of \Rcmd{quantile} to the argument list of \Rcmd{iqr}. The copy-and-paste approach that first comes to mind is likely to lead to inconsistencies and errors, for example when the argument list of \Rcmd{quantile} changes. Instead, the dot argument, a wildcard for any argument, is more appropriate and we redefine our function accordingly: <>= iqr <- function(x, ...) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE, ...) return(diff(q)) } iqr(xdata, na.rm = TRUE) IQR(xdata, na.rm = TRUE) @ Now, we can assess the variability of the profits using our new \Rcmd{iqr} tool: <>= iqr(Forbes2000$profits, na.rm = TRUE) @ Since there is no difference between functions that have been written by one of the \R{} developers and user-created functions, we can compute the inter-quartile range of profits for each of the business categories by using our \Rcmd{iqr} function inside a \Rcmd{tapply} statement; <>= iqr_profits <- tapply(Forbes2000$profits, Forbes2000$category, iqr, na.rm = TRUE) @ and extract the categories with the smallest and greatest variability <>= levels(Forbes2000$category)[which.min(iqr_profits)] levels(Forbes2000$category)[which.max(iqr_profits)] @ We observe less variable profits in tourism enterprises compared with profits in the pharmaceutical industry. As other members of the \Rcmd{apply} family, \Rcmd{tapply} is very helpful when the same task is to be done more than one time. Moreover, its use is more convenient compared to the usage of \Rcmd{for} loops. For the sake of completeness, we will compute the category-wise inter-quartile range of the profits using a \Rcmd{for} loop. \index{Functions|)} \index{Loops|(} Like a \Rclass{function}, a \Rcmd{for} loop consists of a body, i.e., a chain of \R{} commands to be executed. In addition, we need a set of values and a variable that iterates over this set. Here, the set we are interested in is the business categories: <>= bcat <- Forbes2000$category iqr_profits2 <- numeric(nlevels(bcat)) names(iqr_profits2) <- levels(bcat) for (cat in levels(bcat)) { catprofit <- subset(Forbes2000, category == cat)$profit this_iqr <- iqr(catprofit, na.rm = TRUE) iqr_profits2[levels(bcat) == cat] <- this_iqr } @ Compared to the usage of \Rcmd{tapply}, the above code is rather complicated. At first, we have to set up a vector for storing the results and assign the appropriate names to it. Next, inside the body of the \Rcmd{for} loop, the \Rcmd{iqr} function has to be called on the appropriate subset of all companies of the current business category \Robject{cat}. The corresponding inter-quartile range must then be assigned to the correct vector element in the result vector. Luckily, such complicated constructs will be used in only one of the remaining chapters of the book and are almost always avoidable in practical data analyses. \index{Loops|)} \subsection{Simple Graphics} The degree of skewness of a distribution can be investigated by constructing histograms using the \Rcmd{hist} function. (More sophisticated alternatives such as smooth density estimates will be considered in \Sexpr{ch("DE")}.) \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 2)) hist(Forbes2000$marketvalue) hist(log(Forbes2000$marketvalue)) @ \caption{Histograms of the market value and the logarithm of the market value for the companies contained in the Forbes 2000 list. \label{AItR:densplot}} \end{center} \end{figure} For example, the code for producing Figure~\ref{AItR:densplot} first divides the plot region into two equally spaced rows (the \Rcmd{layout} function) and then plots the histograms of the raw market values in the upper part using the \Rcmd{hist} function. The lower part of the figure depicts the histogram for the log-transformed market values which appear to be more symmetric. Bivariate relationships of two continuous variables are usually depicted as scatterplots. In \R, regression relationships are specified by so-called \stress{model formulae} which, in a simple bivariate case, may look like <>= fm <- marketvalue ~ sales class(fm) @ with the dependent variable on the left-hand side and the independent variable on the right-hand side. The tilde separates left- and right-hand sides. Such a model formula can be passed to a model function (for example to the linear model function as explained in \Sexpr{ch("MLR")}). The \Rcmd{plot} generic function implements a \Rclass{formula} method as well. Because the distributions of both market value and sales are skewed we choose to depict their logarithms. A raw scatterplot of $2000$ data points (Figure~\ref{AItR:scatter-raw}) is rather uninformative due to areas with very high density. This problem can be avoided by choosing a transparent color for the dots as shown in Figure~\ref{AItR:scatter}. \begin{figure} \begin{center} <>= plot(log(marketvalue) ~ log(sales), data = Forbes2000, pch = ".") @ \caption{Raw scatterplot of the logarithms of market value and sales. \label{AItR:scatter-raw}} \end{center} \end{figure} \begin{figure} \begin{center} <>= plot(log(marketvalue) ~ log(sales), data = Forbes2000, col = rgb(0,0,0,0.1), pch = 16) @ \caption{Scatterplot with transparent shading of points of the logarithms of market value and sales. \label{AItR:scatter}} \end{center} \end{figure} If the independent variable is a factor, a boxplot representation is a natural choice. For four selected countries, the distributions of the logarithms of the market value may be visually compared in Figure~\ref{AItR:box}. Prior to calling the \Rcmd{plot} function on our data, we have to remove empty levels from the \Robject{country} variable, because otherwise the $x$-axis would show all and not only the selected countries. This task is most easily performed by subsetting the corresponding factor with additional argument \Rcmd{drop = TRUE}. \index{Boxplot} \begin{figure} \begin{center} <>= tmp <- subset(Forbes2000, country %in% c("United Kingdom", "Germany", "India", "Turkey")) tmp$country <- tmp$country[,drop = TRUE] plot(log(marketvalue) ~ country, data = tmp, ylab = "log(marketvalue)", varwidth = TRUE) @ \caption{Boxplots of the logarithms of the market value for four selected countries, the width of the boxes is proportional to the square roots of the number of companies. \label{AItR:box}} \end{center} \end{figure} Here, the width of the boxes are proportional to the square root of the number of companies for each country and extremely large or small market values are depicted by single points. More elaborate graphical methods will be discussed in \Sexpr{ch("DAGD")}. \index{Forbes 2000 ranking|)} \section{Organizing an Analysis} <>= file.create("analysis.R") @ Although it is possible to perform an analysis typing all commands directly on the \R{} prompt it is much more comfortable to maintain a separate text file collecting all steps necessary to perform a certain data analysis task. Such an \R{} transcript file, for example called \file{analysis.R} created with your favorite text editor, can be sourced into \R{} using the \Rcmd{source} command <>= source("analysis.R", echo = TRUE) @ When all steps of a data analysis, i.e., data preprocessing, transformations, simple summary statistics and plots, model building and inference as well as reporting, are collected in such an \R{} transcript file, the analysis can be reproduced at any time, maybe with corrected or updated data as it frequently happens in our consulting practice. <>= file.remove("analysis.R") @ \section{Summary of Findings} Data manipulation precedes every statistical analysis and is often more complex than the final model fitting and display. The \R{} language in itself is very powerful and allows efficient data manipulation. For really large data sets that do not fit into the random access memory of the computer, we have to store the data elsewhere, for example in database systems or flat files. Packages for accessing the data from these sources are described in the `Large memory and out-of-memory data' section of the `High-performance and parallel computing' task view. \section{Final Comments} Reading data into \R{} is possible in many different ways, including direct connections to data base engines. Tabular data are handled by \Rclass{data.frame}s in \R{}, and the usual data manipulation techniques such as sorting, ordering or subsetting can be performed by simple \R{} statements. An overview on data stored in a \Rclass{data.frame} is given mainly by two functions: \Rcmd{summary} and \Rcmd{str}. Simple graphics such as histograms and scatterplots can be constructed by applying the appropriate \R{} functions (\Rcmd{hist} and \Rcmd{plot}) and we shall give many more examples of these functions and those that produce more interesting graphics in later chapters. \section*{Exercises} \begin{description} \exercise Calculate the median profit for the companies in the US and the median profit for the companies in the UK, France, and Germany. \exercise Find all German companies with negative profit. \exercise To which business category do most of the Bermuda island companies belong? \exercise For the $50$ companies in the Forbes data set with the highest profits, plot sales against assets (or some suitable transformation of each variable), labeling each point with the appropriate country name which may need to be abbreviated (using \Rcmd{abbreviate}) to avoid making the plot look too `messy'. %%' \exercise Find the average value of sales for the companies in each country in the Forbes data set, and find the number of companies in each country with profits above $5$ billion US dollars. \exercise List all the products made by companies in the UK. \exercise Plot sales against market value for companies in the UK and in Germany using different plotting symbols for the two countries. \exercise For the ten companies in the UK with the greatest profits construct a bar chart of profits labeled with the companies' name. \exercise How many of the $20$ companies with the greatest market value are from the US and how many are from the UK? \exercise Construct a histogram of profits for all companies in Germany with assets above three billion dollars; how many such companies are there? And which product does the company with the greatest profit make? \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_bayesian_inference.pdf0000644000175000017500000024737214133304606020030 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3146 /Filter /FlateDecode /N 76 /First 609 >> stream xZYs8~_Ij*q[SĉxmܙEmNd1CQ9׀Hmƣڒi$@7dS:2c,(;fbKN2!;&PT* m41aa2KT4vTaRZ&-ˈIgP08LH1h2Ӥb4LY<)g:Nce: LEH 3(L 80 $:)10"Y*DPDNZn$iŜ2T3g-!41)\+ǐ F0cK?H&`m\F1C1qX$$V`@ZӡTHi` V%23$٘u,; % $ :PVbG_;Pa-4O,e/0~3CN,g<]@|d|S~_Ǐ=eyy^,tΞT|vl%b ,-A? o%H>~ܜlGV AX`r#~ ګ޽[FNaHF/g3!$sR RE^ћ4Dc$fEƵ9^5Ii*Z8ϊϹRr$`yڜMj {ӐBȩT7YCmmJE ;q@Ek򮘌B, ђz\|'$O!Ew6Ez7 Z:l^~}M rMK1dט4urL+eZ^Vu/R? ?|u{ǻP=~0$YaVd|?G;%=0T RhoiyEv^:yTX:(Tb1jਤ*YߛJh"&58jIWDE5#/ň !ai+Au%ݍ | 2xM3,,<0NҤw.  ~_~k>OY>SrO_K/tgk>9)dt`yU%¿oC/?G2"7_Rt$I6Kr|vZ6ٙ_|g 2v^U|Y^AHbCn%; {?w0C;E~Vw;:NmiCl]vֲ沟6"7v[{e2aR z=p ;wN?x\Z!Z7&V+ENk>/'w@EypJ%np.깦 M: +5C֋)gh"l6 7B<`ڬ;Eڇ{"s7ËxzmH&goZ>T;~߻??ro['U L3$&HXAeÁ+~U: :< tҋ2 Ofr@oK)Ez ./l}b?i얩^f=Qx`*lۭ Mjnp!'O..UB Dߦ,Wͽknջ}nl5G?0&6c;_*M@fp7`J}cM[rdYͦ)O>Ūm> _cZ4Kp_,\(ihs9b]ʤ)e᭡^xwQAQoi)kyV;૿ݶ%SڑK;":zpRfd )\BQ6T|n?}AF+hRL?hPcR0D! _1fs)mהof$)ۭLeB*;:jZ[* IͨTGk)=6j˿fiw -L,iJ d V'PglD< "rС f4bHbuڰޯ&HBGu#:4›  ӽ4gfONN] .t9^" Yj_-9Y9.aZ+'DϭrD__Uy]f&1klPC+G_: }?G2\GY64p}\w nYFW,$6)BS9,Sk%yMSL64]~iZvX-%P~.YWu=Ҧ bwzOfZkzZ @ywA#7шZ[ zQuOw$G^LG+8[*UWeYUէrUO߿|a%4c:><6pr&6lX$j! =M{ӖF9pFjT#Sg6FsPɸM?Ur4|`)muM'ݰ[/~Asq;.Vo\)H_ˬ?K߇"s!A: чrtG{s6rLp*\nayendstream endobj 78 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:41+02:00 2021-10-18T16:49:41+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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fitted(object) } ################################################### ### code chunk number 4: ALDI-plot-BtheB ################################################### data("BtheB", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) ylim <- range(BtheB[,grep("bdi", names(BtheB))], na.rm = TRUE) tau <- subset(BtheB, treatment == "TAU")[, grep("bdi", names(BtheB))] boxplot(tau, main = "Treated as Usual", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) btheb <- subset(BtheB, treatment == "BtheB")[, grep("bdi", names(BtheB))] boxplot(btheb, main = "Beat the Blues", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) ################################################### ### code chunk number 5: ALDI-long-BtheB ################################################### data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) ################################################### ### code chunk number 6: ALDI-showlong-BtheB ################################################### subset(BtheB_long, subject %in% c("1", "2", "3")) ################################################### ### code chunk number 7: ALDI-fit-BtheB ################################################### library("lme4") BtheB_lmer1 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (1 | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) BtheB_lmer2 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (time | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) anova(BtheB_lmer1, BtheB_lmer2) ################################################### ### code chunk number 8: ALDI-summary-BtheB ################################################### summary(BtheB_lmer1) ################################################### ### code chunk number 9: ALDI-summary-BtheB-p ################################################### cftest(BtheB_lmer1) ################################################### ### code chunk number 10: ALDI-qqnorm-BtheB ################################################### layout(matrix(1:2, ncol = 2)) qint <- ranef(BtheB_lmer1)$subject[["(Intercept)"]] qres <- residuals(BtheB_lmer1) qqnorm(qint, ylab = "Estimated random intercepts", xlim = c(-3, 3), ylim = c(-20, 20), main = "Random intercepts") qqline(qint) qqnorm(qres, xlim = c(-3, 3), ylim = c(-20, 20), ylab = "Estimated residuals", main = "Residuals") qqline(qres) ################################################### ### code chunk number 11: ALDI-dropout ################################################### bdi <- BtheB[, grep("bdi", names(BtheB))] plot(1:4, rep(-0.5, 4), type = "n", axes = FALSE, ylim = c(0, 50), xlab = "Months", ylab = "BDI") axis(1, at = 1:4, labels = c(0, 2, 3, 5)) axis(2) for (i in 1:4) { dropout <- is.na(bdi[,i + 1]) points(rep(i, nrow(bdi)) + ifelse(dropout, 0.05, -0.05), jitter(bdi[,i]), pch = ifelse(dropout, 20, 1)) } HSAUR3/inst/doc/Ch_gam.pdf0000644000175000017500000043363314133304607014761 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3405 /Filter /FlateDecode /N 58 /First 463 >> stream xZr۸}_I*$*Y/#9=3y%D2_O$MxM4ncL2|rvB! X,d~:?U0W0 PB+.}5!A2 I{I]2(Ax),<͔PL)Lɘ hR bbm=I,> Eo> GF 3>q3T` ̉BΘ o1~4xcƏW"^FޫLPr6b|{Lʯ=9M,UB%.l;K6/QSNi'i'zPgRyNO35ί5O_t'&Mw&,|/O޲Ig4Y8R:LVG=NO3nWXr&9hx6]t=se HlozdNZ$ BM) !57B¢f'uwYm/cK-rDg{vqmn9t'YygZb&Icf~o9|񢾅1E dv*7=WF],vvi2a8rFbA{S^mN?(UlPB^&iG"&.DiftakN%bhģ<&_]BCƏΏOç,OWQ{Z9dEfAvr>>lp-gɜD<7|ݹd? x'F!v>.;ihnVݒڇx_!0lrKM]d Ț:P8x<XDzOKcJ F,(0`9 ŷ%_~ȏ  ?>|g"Yfɣ5~]Dk fK޼;lbYCu ˭eJQ"R"3H4B[NHr"r2ݩLe@Œn1k3Ç|>VclVm[>V=Ơ jlvydVPUNyV]{GC.lm؎WVX@ʿNz/ t&|h+.hϬӒ іB &W:S Sglܾ|TzM>~|lwB{^wݎ 7)\%B< @p!P#}Lʁ4R/0,ƘTZWo+;Us+e po#S߀ AEAT} A5@@n&P8j@ paGi7,K@17 kPx o@,2%#`vh?hŒ(+vPĖ U9Ǧa{.-4m5Wƭ1;9~xs2O_7_{mAj ǯiPhQ02}Wճ1dKcV5NkuK<_4Z NH!*JeJQW:Sm)~/"/f21!n|joKnuKܔP{Vr<΢Mi[(S:Yh](^AT;G'/ ú \B*2P?A_aYyujt#E}I5E9+LYS#*K}g J.evRz,ګEVA(4bސpnp` R'"j'V74BgÄ{Ǜ7ώ⛋Uv,>GWE0HP`; t,mn*5fᄍfU{u7OV– ޕς{`^p93nCkq?:c8Xoĸ vwH3U$jμM5ް3Xd&)8= ! a+ [ ى 0 ?НOT6D~`I?e^/N$ [hs{ Y úfk[gڊ/NiP;H 2mB#ʻ:Q:#eڪ܌S=2HU fR#4#Aއ5YP.h؅m9#4m@Fr$ͬV}ߔ+x a yP;`mP '|S-#ߍ_W/tFuxh4~~&(I}g H,jtPu.-r#Ǽ!UN 5RKOBSZ#J %4}ޱ5CvVПZǴĶ ),^H~LH TÿCLJʱ t`~o> *(<>4Uendstream endobj 60 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:43+02:00 2021-10-18T16:49:43+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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\documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analyzing Longitudinal Data II} %%\VignetteDepends{gee,lme4} \setcounter{chapter}{13} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= options(digits = 3) if (!interactive()) { print.summary.gee <- function (x, digits = NULL, quote = FALSE, prefix = "", ...) { if (is.null(digits)) digits <- options()$digits else options(digits = digits) cat("...") cat("\nModel:\n") cat(" Link: ", x$model$link, "\n") cat(" Variance to Mean Relation:", x$model$varfun, "\n") if (!is.null(x$model$M)) cat(" Correlation Structure: ", x$model$corstr, ", M =", x$model$M, "\n") else cat(" Correlation Structure: ", x$model$corstr, "\n") cat("\n...") nas <- x$nas if (!is.null(nas) && any(nas)) cat("\n\nCoefficients: (", sum(nas), " not defined because of singularities)\n", sep = "") else cat("\n\nCoefficients:\n") print(x$coefficients, digits = digits) cat("\nEstimated Scale Parameter: ", format(round(x$scale, digits))) cat("\n...\n") invisible(x) } } @ \chapter[Analyzing Longitudinal Data II]{ Analyzing Longitudinal Data II -- Generalized Estimation Equations and Linear Mixed Effect Models: Treating Respiratory Illness and Epileptic Seizures \label{ALDII}} \section{Introduction} \section{Methods for Non-normal Distributions} \section{Analysis Using \R{}: GEE} \subsection{Beat the Blues Revisited} To use the \Rcmd{gee} function, package \Rpackage{gee} \citep{PKG:gee} has to be installed and attached: <>= library("gee") @ The \Rcmd{gee} function is used in a similar way to the \Rcmd{lme} function met in \Sexpr{ch("ALDI")} with the addition of the features of the \Rcmd{glm} function that specify the appropriate error distribution for the response and the implied link function, and an argument to specify the structure of the working correlation matrix. Here we will fit an independence structure and then an exchangeable structure. The \R{} code for fitting generalized estimation equations to the \Robject{BtheB\_long} data (as constructed in \Sexpr{ch("ALDI")}) with identity working correlation matrix is as follows (note that the \Rcmd{gee} function assumes the rows of the \Rclass{data.frame} \Robject{BtheB\_long} to be ordered with respect to subjects): <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt" @ <>= osub <- order(as.integer(BtheB_long$subject)) BtheB_long <- BtheB_long[osub,] btb_gee <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "independence") @ and with exchangeable correlation matrix: <>= btb_gee1 <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "exchangeable") @ The \Rcmd{summary} method can be used to inspect the fitted models; the results are shown in Figures~\ref{ALDII-gee-summary} and \ref{ALDII-gee1-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{btb\_gee} model (slightly abbreviated). \label{ALDII-gee-summary}} \SchunkLabel <>= summary(btb_gee) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{btb\_gee1} model (slightly abbreviated). \label{ALDII-gee1-summary}} \SchunkLabel <>= summary(btb_gee1) @ \SchunkRaw \subsection{Respiratory Illness \label{ALDII:resp}} The baseline status, i.e., the status for \Robject{month == 0}, will enter the models as an explanatory variable and thus we have to rearrange the \Rclass{data.frame} \Robject{respiratory} in order to create a new variable \Robject{baseline}: <>= data("respiratory", package = "HSAUR3") resp <- subset(respiratory, month > "0") resp$baseline <- rep(subset(respiratory, month == "0")$status, rep(4, 111)) resp$nstat <- as.numeric(resp$status == "good") resp$month <- resp$month[, drop = TRUE] @ <>= names(resp)[names(resp) == "treatment"] <- "trt" levels(resp$trt)[2] <- "trt" @ The new variable \Robject{nstat} is simply a dummy coding for a poor respiratory status. Now we can use the data \Robject{resp} to fit a logistic regression model and GEE models with an independent and an exchangeable correlation structure as follows. <>= resp_glm <- glm(status ~ centre + trt + gender + baseline + age, data = resp, family = "binomial") resp_gee1 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) resp_gee2 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) @ \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_glm} model. \label{ALDII-resp-glm-summary}} \SchunkLabel <>= summary(resp_glm) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_gee1} model (slightly abbreviated). \label{ALDII-resp-gee1-summary}} \SchunkLabel <>= summary(resp_gee1) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_gee2} model (slightly abbreviated). \label{ALDII-resp-gee2-summary}} \SchunkLabel <>= summary(resp_gee2) @ \SchunkRaw The estimated treatment effect taken from the exchangeable structure GEE model is \Sexpr{round(coef(resp_gee2)["trttrt"], 3)} which, using the robust standard errors, has an associated $95\%$ confidence interval <>= se <- summary(resp_gee2)$coefficients["trttrt", "Robust S.E."] coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975) @ These values reflect effects on the log-odds scale. Interpretation becomes simpler if we exponentiate the values to get the effects in terms of odds. This gives a treatment effect of \Sexpr{round(exp(coef(resp_gee2)["trttrt"]), 3)} and a $95\%$ confidence interval of <>= exp(coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975)) @ The odds of achieving a `good' respiratory status with the active treatment is between %' about twice and seven times the corresponding odds for the placebo. \subsection{Epilepsy} Moving on to the count data in \Robject{epilepsy} from Table~\ref{ALDII-epilepsy-tab}, we begin by calculating the means and variances of the number of seizures for all interactions between treatment and period: <>= data("epilepsy", package = "HSAUR3") itp <- interaction(epilepsy$treatment, epilepsy$period) tapply(epilepsy$seizure.rate, itp, mean) tapply(epilepsy$seizure.rate, itp, var) @ Some of the variances are considerably larger than the corresponding means, which for a Poisson variable may suggest that overdispersion may be a problem, see \Sexpr{ch("GLM")}. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) ylim <- range(epilepsy$seizure.rate) placebo <- subset(epilepsy, treatment == "placebo") progabide <- subset(epilepsy, treatment == "Progabide") boxplot(seizure.rate ~ period, data = placebo, ylab = "Number of seizures", xlab = "Period", ylim = ylim, main = "Placebo") boxplot(seizure.rate ~ period, data = progabide, main = "Progabide", ylab = "Number of seizures", xlab = "Period", ylim = ylim) @ \caption{Boxplots of numbers of seizures in each two-week period post randomization for placebo and active treatments. \label{ALDII-plot1}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) ylim <- range(log(epilepsy$seizure.rate + 1)) boxplot(log(seizure.rate + 1) ~ period, data = placebo, main = "Placebo", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) boxplot(log(seizure.rate + 1) ~ period, data = progabide, main = "Progabide", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) @ \caption{Boxplots of log of numbers of seizures in each two-week period post randomization for placebo and active treatments. \label{ALDII-plot2}} \end{center} \end{figure} We can now fit a Poisson regression model to the data assuming independence using the \Rcmd{glm} function. We also use the GEE approach to fit an independence structure, followed by an exchangeable structure using the following \R{} code: <>= per <- rep(log(2),nrow(epilepsy)) epilepsy$period <- as.numeric(epilepsy$period) names(epilepsy)[names(epilepsy) == "treatment"] <- "trt" fm <- seizure.rate ~ base + age + trt + offset(per) epilepsy_glm <- glm(fm, data = epilepsy, family = "poisson") epilepsy_gee1 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) epilepsy_gee2 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) epilepsy_gee3 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = FALSE, scale.value = 1) @ As usual we inspect the fitted models using the \Rcmd{summary} method, the results are given in Figures~\ref{ALDII-epilepsy-glm-summary}, \ref{ALDII-epilepsy-gee1-summary}, \ref{ALDII-epilepsy-gee2-summary}, and \ref{ALDII-epilepsy-gee3-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_glm} model. \label{ALDII-epilepsy-glm-summary}} \SchunkLabel <>= summary(epilepsy_glm) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee1} model (slightly abbreviated). \label{ALDII-epilepsy-gee1-summary}} \SchunkLabel <>= summary(epilepsy_gee1) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee2} model (slightly abbreviated). \label{ALDII-epilepsy-gee2-summary}} \SchunkLabel <>= summary(epilepsy_gee2) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{epilepsy\_gee3} model (slightly abbreviated). \label{ALDII-epilepsy-gee3-summary}} \SchunkLabel <>= summary(epilepsy_gee3) @ \SchunkRaw \section{Analysis Using \R{}: Random Effects} As an example of using generalized mixed models for the analysis of longitudinal data with a non-normal response, the following logistic model will be fitted to the respiratory illness data \begin{eqnarray*} \text{logit}(\P(\text{status} = \text{good})) & = & \beta_0 + \beta_1 \text{treatment} + \beta_2 \text{time} + \beta_3 \text{gender} \\% & & + \beta_4 \text{age} + \beta_5 \text{centre} + \beta_6 \text{baseline} + u \end{eqnarray*} where $u$ is a subject-specific random effect. The necessary \R{} code for fitting the model using the \Rcmd{glmer} function from package \Rpackage{lme4} \citep{PKG:lme4,HSAUR:Bates2005} is: <>= library("lme4") resp_lmer <- glmer(status ~ baseline + month + trt + gender + age + centre + (1 | subject), family = binomial(), data = resp) exp(fixef(resp_lmer)) @ The significance of the effects as estimated by this random effects model and by the GEE model described in Section~\ref{ALDII:resp} is generally similar. But as expected from our previous discussion the estimated coefficients are substantially larger. While the estimated effect of treatment on a randomly sampled individual, given the set of observed covariates, is estimated by the marginal model using GEE to increase the log-odds of being disease free by $\Sexpr{round(coef(resp_gee2)["trttrt"], 3)}$, the corresponding estimate from the random effects model is $\Sexpr{round(fixef(resp_lmer)["trttrt"], 3)}$. These are not inconsistent results but reflect the fact that the models are estimating different parameters. The random effects estimate is conditional upon the patient's random effect, a quantity that is rarely known in practice. Were we to examine the log-odds of the average predicted probabilities with and without treatment (averaged over the random effects) this would give an estimate comparable to that estimated within the marginal model. <>= su <- summary(resp_lmer) if (!interactive()) { summary <- function(x) { cat("\n...\n") cat("Fixed effects:\n") lme4V <- packageDescription("lme4")$Version if (compareVersion("0.999999-2", lme4V) >= 0) { printCoefmat(su@coefs) } else { printCoefmat(su$coefficients) } cat("\n...\n") } } @ \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for the \Robject{resp\_lmer} model (abbreviated). \label{ALDII-resp-lmer-summary}} \SchunkLabel <>= summary(resp_lmer) @ \SchunkRaw \clearpage \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_multiple_linear_regression.Rnw0000644000175000017500000005606514133304452021635 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Multiple Linear Regression} %%\VignetteDepends{wordcloud} \setcounter{chapter}{5} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("wordcloud") @ \chapter[Simple and Multiple Linear Regression]{Simple and Multiple Linear Regression: \\ How Old is the Universe and Cloud Seeding \label{MLR}} \section{Introduction} \index{Age of the Universe} \cite{HSAUR:Freedmanetal2001} give the relative velocity and the distance of $24$ galaxies, according to measurements made using the Hubble Space Telescope -- the data are contained in the \Rpackage{gamair} package accompanying \cite{HSAUR:Wood2006}, see Table~\ref{MLR-hubble-tab}. Velocities are assessed by measuring the Doppler red shift in the spectrum of light observed from the galaxies concerned, although some correction for `local' velocity components is required. Distances are measured using the known relationship between the period of Cepheid variable stars and their luminosity. How can these data be used to estimate the age of the universe? Here we shall show how this can be done using simple linear regression. <>= data("hubble", package = "gamair") names(hubble) <- c("galaxy", "velocity", "distance") toLatex(HSAURtable(hubble, package = "gamair"), pcol = 2, caption = paste("Distance and velocity for 24 galaxies."), label = "MLR-hubble-tab") @ \vspace*{-1cm} \textit{Source}: From Freedman W. L., et al., \textit{The Astrophysical Journal}, 553, 47--72, 2001. With permission. \vspace*{1cm} \index{Cloud seeding} {\tabcolsep3.5pt <>= data("clouds", package = "HSAUR3") names(clouds) <- c("seeding", "time", "sne", "cloudc", "prewet", "EM", "rain") toLatex(HSAURtable(clouds), pcol = 1, caption = paste("Cloud seeding experiments in Florida -- see text for", "explanations of the variables. Note that the \\Robject{clouds} data set has slightly different variable names."), label = "MLR-clouds-tab") @ } Weather modification, or cloud seeding, is the treatment of individual clouds or storm systems with various inorganic and organic materials in the hope of achieving an increase in rainfall. Introduction of such material into a cloud that contains supercooled water, that is, liquid water colder than zero degrees Celsius, has the aim of inducing freezing, with the consequent ice particles growing at the expense of liquid droplets and becoming heavy enough to fall as rain from clouds that otherwise would produce none. The data shown in Table~\ref{MLR-clouds-tab} were collected in the summer of 1975 from an experiment to investigate the use of massive amounts of silver iodide ($100$ to $1000$ grams per cloud) in cloud seeding to increase rainfall \citep{HSAUR:Woodleyetal1977}. In the experiment, which was conducted in an area of Florida, 24 days were judged suitable for seeding on the basis that a measured suitability criterion, denoted \stress{S-Ne}, was not less than $1.5$. Here \stress{S} is the `seedability', %' the difference between the maximum height of a cloud if seeded and the same cloud if not seeded predicted by a suitable cloud model, and \stress{Ne} is the number of hours between $1300$ and $1600$ G.M.T. with $10$ centimeter echoes in the target; this quantity biases the decision for experimentation against naturally rainy days. Consequently, optimal days for seeding are those on which seedability is large and the natural rainfall early in the day is small. On suitable days, a decision was taken at random as to whether to seed or not. For each day the following variables were measured: \begin{description} \item[\Robject{seeding}] a factor indicating whether seeding action occurred (yes or no), \item[\Robject{time}] number of days after the first day of the experiment, \item[\Robject{cloudc}] the percentage cloud cover in the experimental area, measured using radar, \item[\Robject{prewet}] the total rainfall in the target area one hour before seeding (in cubic meters $\times 10^{7}$), \item[\Robject{EM}] a factor showing whether the radar echo was moving or stationary, \item[\Robject{rain}] the amount of rain in cubic meters $\times 10^{7}$, \item[\Robject{sne}] suitability criterion, see above. \end{description} The objective in analyzing these data is to see how rainfall is related to the explanatory variables and, in particular, to determine the effectiveness of seeding. The method to be used is \stress{multiple linear regression}. \section{Simple Linear Regression} \section{Multiple Linear Regression \label{MLR-MLR}} \subsection{Regression Diagnostics} \section{Analysis Using \R{}} \subsection{Estimating the Age of the Universe} Prior to applying a simple regression to the data it will be useful to look at a plot to assess their major features. The \R{} code given in Figure~\ref{MLR-hubble-plot} produces a scatterplot of velocity and distance. \begin{figure} \begin{center} <>= plot(velocity ~ distance, data = hubble) @ \caption{Scatterplot of velocity and distance. \label{MLR-hubble-plot}} \end{center} \end{figure} The diagram shows a clear, strong relationship between velocity and distance. The next step is to fit a simple linear regression model to the data, but in this case the nature of the data requires a model without intercept because if distance is zero so is relative speed. So the model to be fitted to these data is \begin{eqnarray*} \text{velocity} = \beta_1 \text{distance} + \varepsilon. \end{eqnarray*} This is essentially what astronomers call Hubble's Law and $\beta_1$ is known as Hubble's constant; $\beta_1^{-1}$ gives an approximate age of the universe. To fit this model we are estimating $\beta_1$ using formula (\ref{MLR:beta1}). Although this operation is rather easy <>= sum(hubble$distance * hubble$velocity) / sum(hubble$distance^2) @ it is more convenient to apply \R's linear modeling function <>= hmod <- lm(velocity ~ distance - 1, data = hubble) @ Note that the model formula specifies a model without intercept. We can now extract the estimated model coefficients via <>= coef(hmod) @ and add this estimated regression line to the scatterplot; the result is shown in Figure~\ref{MLR-hubble-lmplot}. In addition, we produce a scatterplot of the residuals $y_i - \hat{y}_i$ against fitted values $\hat{y}_i$ to assess the quality of the model fit. It seems that for higher distance values the variance of velocity increases; however, we are interested in only the estimated parameter $\hat{\beta}_1$ which remains valid under variance heterogeneity (in contrast to $t$-tests and associated $p$-values). Now we can use the estimated value of $\beta_1$ to find an approximate value for the age of the universe. The Hubble constant itself has units of $\text{km} \times \text{sec}^{-1} \times \text{Mpc}^{-1}$. A mega-parsec (Mpc) is $3.09 \times 10^{19}$km, so we need to divide the estimated value of $\beta_1$ by this amount in order to obtain Hubble's constant with units of $\text{sec}^{-1}$. The approximate age of the universe in seconds will then be the inverse of this calculation. Carrying out the necessary computations <>= Mpc <- 3.09 * 10^19 ysec <- 60^2 * 24 * 365.25 Mpcyear <- Mpc / ysec 1 / (coef(hmod) / Mpcyear) @ gives an estimated age of roughly $12.8$ billion years. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) plot(velocity ~ distance, data = hubble) abline(hmod) plot(hmod, which = 1) @ \caption{Scatterplot of velocity and distance with estimated regression line (left) and plot of residuals against fitted values (right). \label{MLR-hubble-lmplot}} \end{center} \end{figure} \subsection{Cloud Seeding} Again, a graphical display highlighting the most important aspects of the data will be helpful. Here we will construct boxplots of the rainfall in each category of the dichotomous explanatory variables and scatterplots of rainfall against each of the continuous explanatory variables. \begin{figure} \begin{center} <>= data("clouds", package = "HSAUR3") layout(matrix(1:2, nrow = 2)) bxpseeding <- boxplot(rain ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rain ~ EM, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") @ <>= layout(matrix(1:2, nrow = 2)) bxpseeding <- boxplot(rain ~ seeding, data = clouds, ylab = "Rainfall", xlab = "Seeding") bxpecho <- boxplot(rain ~ EM, data = clouds, ylab = "Rainfall", xlab = "Echo Motion") @ \caption{Boxplots of \Robject{rain}. \label{MLR-rainfall-boxplot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:4, nrow = 2)) plot(rain ~ time, data = clouds) plot(rain ~ cloudc, data = clouds) plot(rain ~ sne, data = clouds, xlab="S-Ne criterion") plot(rain ~ prewet, data = clouds) @ \caption{Scatterplots of \Robject{rain} against the continuous covariates. \label{MLR-rainfall-scplot}} \end{center} \end{figure} Both the boxplots (Figure~\ref{MLR-rainfall-boxplot}) and the scatterplots (Figure~\ref{MLR-rainfall-scplot}) show some evidence of outliers. The row names of the extreme observations in the \Robject{clouds} \Rclass{data.frame} can be identified via <>= rownames(clouds)[clouds$rain %in% c(bxpseeding$out, bxpecho$out)] @ where \Robject{bxpseeding} and \Robject{bxpecho} are variables created by \Rcmd{boxplot} in Figure~\ref{MLR-rainfall-boxplot}. Now we shall not remove these observations but bear in mind during the modeling process that they may cause problems. In this example it is sensible to assume that the effect of some of the other explanatory variables is modified by seeding and therefore consider a model that includes seeding as covariate and, furthermore, allows interaction terms \index{Interaction} for \Robject{seeding} with each of the covariates except \Robject{time}. This model can be described by the \Rclass{formula} <>= clouds_formula <- rain ~ seeding + seeding:(sne + cloudc + prewet + EM) + time @ and the design matrix $\X^\star$ can be computed via <>= Xstar <- model.matrix(clouds_formula, data = clouds) @ By default, treatment contrasts have been applied to the dummy codings of the factors \Robject{seeding} and \Robject{EM} as can be seen from the inspection of the \Robject{contrasts} attribute of the model matrix <>= attr(Xstar, "contrasts") @ The default contrasts can be changed via the \Rarg{contrasts.arg} argument to \Rcmd{model.matrix} or the \Robject{contrasts} argument to the fitting function, for example \Rcmd{lm} or \Rcmd{aov} as shown in \Sexpr{ch("ANOVA")}. However, such internals are hidden and performed by high-level model-fitting functions such as \Rcmd{lm} which will be used to fit the linear model defined by the \Rclass{formula} \Robject{clouds\_formula}: <>= clouds_lm <- lm(clouds_formula, data = clouds) class(clouds_lm) @ The result of the model fitting is an object of class \Rclass{lm} for which a \Rcmd{summary} method showing the conventional regression analysis output is available. The output in Figure~\ref{MLR-clouds-summary} shows the estimates $\hat{\beta}^\star$ with corresponding standard errors and $t$-statistics as well as the $F$-statistic with associated $p$-value. \renewcommand{\nextcaption}{\R{} output of the linear model fit for the \Robject{clouds} data. \label{MLR-clouds-summary}} \SchunkLabel <>= summary(clouds_lm) @ \SchunkRaw Many methods are available for extracting components of the fitted model. The estimates $\hat{\beta}^\star$ can be assessed via \newpage <>= betastar <- coef(clouds_lm) betastar @ and the corresponding covariance matrix $\Cov(\hat{\beta}^\star)$ is available from the \Rcmd{vcov} method <>= Vbetastar <- vcov(clouds_lm) @ where the square roots of the diagonal elements are the standard errors as shown in Figure~\ref{MLR-clouds-summary} <>= sqrt(diag(Vbetastar)) @ \begin{figure} \begin{center} <>= psymb <- as.numeric(clouds$seeding) plot(rain ~ sne, data = clouds, pch = psymb, xlab = "S-Ne criterion") abline(lm(rain ~ sne, data = clouds, subset = seeding == "no")) abline(lm(rain ~ sne, data = clouds, subset = seeding == "yes"), lty = 2) legend("topright", legend = c("No seeding", "Seeding"), pch = 1:2, lty = 1:2, bty = "n") @ \caption{Regression relationship between S-Ne criterion and rainfall with and without seeding. \label{MLR-clouds-lmplot}} \end{center} \end{figure} In order to investigate the quality of the model fit, we need access to the residuals and the fitted values. The residuals can be found by the \Rcmd{residuals} method and the fitted values of the response from the \Rcmd{fitted} (or \Rcmd{predict}) method <>= clouds_resid <- residuals(clouds_lm) clouds_fitted <- fitted(clouds_lm) @ Now the residuals and the fitted values can be used to construct diagnostic plots; for example the residual plot in Figure~\ref{MLR-resid} where each observation is labelled by its number (using \Rcmd{textplot} from package \Rpackage{wordclouds}). Observations $1$ and $15$ give rather large residual values and the data should perhaps be reanalysed after these two observations are removed. The normal probability plot of the residuals shown in Figure~\ref{MLR-qqplot} shows a reasonable agreement between theoretical and sample quantiles, however, observations $1$ and $15$ are extreme again. \begin{figure} \begin{center} <>= plot(clouds_fitted, clouds_resid, xlab = "Fitted values", ylab = "Residuals", type = "n", ylim = max(abs(clouds_resid)) * c(-1, 1)) abline(h = 0, lty = 2) textplot(clouds_fitted, clouds_resid, words = rownames(clouds), new = FALSE) @ \caption{Plot of residuals against fitted values for \Robject{clouds} seeding data. \label{MLR-resid}} \end{center} \end{figure} \begin{figure} \begin{center} <>= qqnorm(clouds_resid, ylab = "Residuals") qqline(clouds_resid) @ \caption{Normal probability plot of residuals from cloud seeding model \Robject{clouds\_lm}. \label{MLR-qqplot}} \end{center} \end{figure} An index plot of the Cook's distances for each observation %' (and many other plots including those constructed above from using the basic functions) can be found from applying the \Rcmd{plot} method to the object that results from the application of the \Rcmd{lm} function. \begin{figure} \begin{center} <>= plot(clouds_lm) @ <>= plot(clouds_lm, which = 4, sub.caption = NULL) @ \caption{Index plot of Cook's distances for cloud seeding data. %' \label{MLR-cook}} \end{center} \end{figure} Figure~\ref{MLR-cook} suggests that observations 2 and 18 have undue influence on the estimated regression coefficients, but the two outliers identified previously do not. Again it may be useful to look at the results after these two observations have been removed (see Exercise 6.2). %% \ref{MLR-ex2}) \index{Regression diagnostics|)} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_simple_inference.R0000644000175000017500000002256014133304572017146 0ustar nileshnilesh### R code from vignette source 'Ch_simple_inference.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: SI-setup ################################################### library("vcd") if (!interactive()) { print.htest <- function (x, digits = 4, quote = TRUE, prefix = "", ...) { cat("\n") cat(strwrap(x$method, prefix = "\t"), sep = "\n") cat("\n") cat("data: ", x$data.name, "\n") out <- character() if (!is.null(x$statistic)) out <- c(out, paste(names(x$statistic), "=", format(round(x$statistic, 4)))) if (!is.null(x$parameter)) out <- c(out, paste(names(x$parameter), "=", format(round(x$parameter, 3)))) if (!is.null(x$p.value)) { fp <- format.pval(x$p.value, digits = digits) out <- c(out, paste("p-value", if (substr(fp, 1, 1) == "<") fp else paste("=", fp))) } cat(strwrap(paste(out, collapse = ", ")), sep = "\n") if (!is.null(x$conf.int)) { cat(format(100 * attr(x$conf.int, "conf.level")), "percent confidence interval:\n", format(c(x$conf.int[1], x$conf.int[2])), "\n") } if (!is.null(x$estimate)) { cat("sample estimates:\n") print(x$estimate, ...) } cat("\n") invisible(x) } } ################################################### ### code chunk number 4: SI-roomwidth-data ################################################### data("roomwidth", package = "HSAUR3") ################################################### ### code chunk number 5: SI-roomwidth-convert ################################################### convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) ################################################### ### code chunk number 6: SI-roomwidth-summary ################################################### tapply(roomwidth$width * convert, roomwidth$unit, summary) tapply(roomwidth$width * convert, roomwidth$unit, sd) ################################################### ### code chunk number 7: SI-roomwidth-boxplot ################################################### layout(matrix(c(1,2,1,3), nrow = 2, ncol = 2, byrow = FALSE)) boxplot(I(width * convert) ~ unit, data = roomwidth, ylab = "Estimated width (feet)", varwidth = TRUE, names = c("Estimates in feet", "Estimates in meters (converted to feet)")) feet <- roomwidth$unit == "feet" qqnorm(roomwidth$width[feet], ylab = "Estimated width (feet)") qqline(roomwidth$width[feet]) qqnorm(roomwidth$width[!feet], ylab = "Estimated width (meters)") qqline(roomwidth$width[!feet]) ################################################### ### code chunk number 8: SI-roomwidth-formula ################################################### I(width * convert) ~ unit ################################################### ### code chunk number 9: SI-roomwidth-tt-T-hide ################################################### tt <- t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) ################################################### ### code chunk number 10: SI-roomwidth-tt-T ################################################### t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) ################################################### ### code chunk number 11: SI-roomwidth-tt-F ################################################### t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = FALSE) ################################################### ### code chunk number 12: SI-roomwidth-wt ################################################### wilcox.test(I(width * convert) ~ unit, data = roomwidth, conf.int = TRUE) ################################################### ### code chunk number 13: SI-roomwidth-wt-hide ################################################### pwt <- round(wilcox.test(I(width * convert) ~ unit, data = roomwidth)$p.value, 3) ################################################### ### code chunk number 14: SI-waves-data ################################################### data("waves", package = "HSAUR3") ################################################### ### code chunk number 15: SI-wavese-boxplot ################################################### mooringdiff <- waves$method1 - waves$method2 layout(matrix(1:2, ncol = 2)) boxplot(mooringdiff, ylab = "Differences (Newton meters)", main = "Boxplot") abline(h = 0, lty = 2) qqnorm(mooringdiff, ylab = "Differences (Newton meters)") qqline(mooringdiff) ################################################### ### code chunk number 16: SI-waves-tt ################################################### t.test(mooringdiff) ################################################### ### code chunk number 17: SI-waves-wt ################################################### pwt <- round(wilcox.test(mooringdiff)$p.value, 3) ################################################### ### code chunk number 18: SI-waves-wt ################################################### wilcox.test(mooringdiff) ################################################### ### code chunk number 19: SI-water-data ################################################### data("water", package = "HSAUR3") ################################################### ### code chunk number 20: SI-water-plot ################################################### nf <- layout(matrix(c(2, 0, 1, 3), 2, 2, byrow = TRUE), c(2, 1), c(1, 2), TRUE) psymb <- as.numeric(water$location) plot(mortality ~ hardness, data = water, pch = psymb) abline(lm(mortality ~ hardness, data = water)) legend("topright", legend = levels(water$location), pch = c(1,2), bty = "n") hist(water$hardness) boxplot(water$mortality) ################################################### ### code chunk number 21: SI-water-cor ################################################### cor.test(~ mortality + hardness, data = water) ################################################### ### code chunk number 22: SI-water-cor ################################################### cr <- round(cor.test(~ mortality + hardness, data = water)$estimate, 3) ################################################### ### code chunk number 23: SI-pistonrings-chisq-hide ################################################### chisqt <- chisq.test(pistonrings) ################################################### ### code chunk number 24: SI-pistonrings-chisq ################################################### data("pistonrings", package = "HSAUR3") chisq.test(pistonrings) ################################################### ### code chunk number 25: SI-pistonrings-resid ################################################### chisq.test(pistonrings)$residuals ################################################### ### code chunk number 26: SI-assoc-plot ################################################### library("vcd") assoc(pistonrings) ################################################### ### code chunk number 27: SI-rearrests-data ################################################### data("rearrests", package = "HSAUR3") rearrests ################################################### ### code chunk number 28: SI-rearrests-mcnemar ################################################### mcs <- round(mcnemar.test(rearrests, correct = FALSE)$statistic, 2) ################################################### ### code chunk number 29: SI-arrests-mcnemar ################################################### mcnemar.test(rearrests, correct = FALSE) ################################################### ### code chunk number 30: SI-arrests-binom ################################################### binom.test(rearrests[2], n = sum(rearrests[c(2,3)])) HSAUR3/inst/doc/Ch_graphical_display.pdf0000644000175000017500000061767614133304610017701 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 5135 /Filter /FlateDecode /N 84 /First 698 >> stream xh kK-*ej$ϣxy߰z~)16lP(jlX1֌j䗍F\4+AlDZ ,#X{4) $qnu6=¶H!ޡ?i YcگTix߿7xˡZ|CFlXJ0Pa6/Dƚ0 AT]td ʌpj%/s&Ayسc cڔA=aZ dM_TJ]֨K\* ⩋Hыz,.eq)]|MK _v#z:r!,ʋiewBdLHU1w#44މ+A*U9*h۸/G6h }7u-Vs{mbn:Ӄ~ ON LlRkr)ZAHY4eZ,qP:@;B2 bWSN{n>uj8y0f.5c0CsHLZg7ؕ+ N"W ;d7H}?\[}z^;n HcQu)6YU@0bmF\lYTaڤ pn E1+>Ŀ 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ŨnwBP RyPnlLԎ V3JqN PBx5nz `dXJP-htX'BCQ' d&<]ݾz<=\/2B7uh3O^ž'+gC5] ߿|_?g'kR]ŏӿ3>𷫒S^V*q}ǣ|l H Y.?2blѠn>wZsƣUrp,'ĐhEq[_v4Tv@RLvHAUk`l\I[i?=\ qNa6|S+>lZ\׳)Yѕ mb:؃"ڍ$IY9DJ u5Ms'׌~rf! 帰('~^[}h',UtΔkR[9s14)BcE٥q{$m42_qfendstream endobj 108 0 obj << /Type /XRef /Length 127 /Filter /FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 109 /ID [<807e07c6c47e180ab3240a33fc2bb4f5>] >> stream xcb&F~0 $8JC?߫@6~P, ȃH}`xDrH)tDJI/M 63"Y.uyr,D-v"Hλ`L`P'e endstream endobj startxref 186288 %%EOF HSAUR3/inst/doc/Ch_graphical_display.R0000644000175000017500000002226214133304533017312 0ustar nileshnilesh### R code from vignette source 'Ch_graphical_display.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: DAGD-USmelanoma-histbox ################################################### xr <- range(USmelanoma$mortality) * c(0.9, 1.1) xr ################################################### ### code chunk number 4: DAGD-USmelanoma-histbox ################################################### layout(matrix(1:2, nrow = 2)) par(mar = par("mar") * c(0.8, 1, 1, 1)) boxplot(USmelanoma$mortality, ylim = xr, horizontal = TRUE, xlab = "Mortality") hist(USmelanoma$mortality, xlim = xr, xlab = "", main = "", axes = FALSE, ylab = "") axis(1) ################################################### ### code chunk number 5: DAGD-USmelanoma-boxocean ################################################### plot(mortality ~ ocean, data = USmelanoma, xlab = "Contiguity to an ocean", ylab = "Mortality") ################################################### ### code chunk number 6: DAGD-USmelanoma-dens ################################################### dyes <- with(USmelanoma, density(mortality[ocean == "yes"])) dno <- with(USmelanoma, density(mortality[ocean == "no"])) plot(dyes, lty = 1, xlim = xr, main = "", ylim = c(0, 0.018), xlab = "Mortality") lines(dno, lty = 2) legend("topleft", lty = 1:2, legend = c("Coastal State", "Land State"), bty = "n") ################################################### ### code chunk number 7: DAGD-USmelanoma-xy ################################################### layout(matrix(1:2, ncol = 2)) plot(mortality ~ longitude, data = USmelanoma, ylab = "Mortality", xlab = "Longitude") plot(mortality ~ latitude, data = USmelanoma, ylab = "Mortality", xlab = "Latitude") ################################################### ### code chunk number 8: DAGD-USmelanoma-lat ################################################### plot(mortality ~ latitude, data = USmelanoma, pch = (1:2)[ocean], ylab = "Mortality", xlab = "Latitude") legend("topright", legend = c("Land state", "Coast state"), pch = 1:2, bty = "n") ################################################### ### code chunk number 9: DAGD-USmelanoma-south ################################################### subset(USmelanoma, latitude < 32) ################################################### ### code chunk number 10: DAGD-USmelanoma-long-lat-data ################################################### library("sp") library("maps") library("maptools") states <- map("state", plot = FALSE, fill = TRUE) ################################################### ### code chunk number 11: DAGD-USmelanoma-long-lat-names ################################################### IDs <- sapply(strsplit(states$names, ":"), function(x) x[1]) rownames(USmelanoma) <- tolower(rownames(USmelanoma)) ################################################### ### code chunk number 12: DAGD-USmelanoma-long-lat-sp ################################################### us1 <- map2SpatialPolygons(states, IDs=IDs, proj4string = CRS("+proj=longlat +datum=WGS84")) us2 <- SpatialPolygonsDataFrame(us1, USmelanoma) ################################################### ### code chunk number 13: DAGD-USmelanoma-long-lat ################################################### spplot(us2, "mortality", col.regions = rev(grey.colors(100))) ################################################### ### code chunk number 14: DAGD-CHFLS-happy ################################################### barplot(xtabs(~ R_happy, data = CHFLS)) ################################################### ### code chunk number 15: DAGD-CHFLS-health_happy_xtabs ################################################### xtabs(~ R_happy + R_health, data = CHFLS) ################################################### ### code chunk number 16: DAGD-CHFLS-health_happy_xtabs2 ################################################### hh <- xtabs(~ R_health + R_happy, data = CHFLS) ################################################### ### code chunk number 17: DAGD-CHFLS-health_happy ################################################### plot(R_happy ~ R_health, data = CHFLS, ylab = "Happiness", xlab = "Health") ################################################### ### code chunk number 18: DAGD-CHFLS-happy_income ################################################### layout(matrix(1:2, ncol = 2)) plot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") cdplot(R_happy ~ log(R_income + 1), data = CHFLS, ylab = "Happiness", xlab = "log(Income + 1)") ################################################### ### code chunk number 19: DAGD-CHFLS-RAincome3 (eval = FALSE) ################################################### ## library("lattice") ## xyplot(jitter(log(R_income + 0.5)) ~ ## jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, ## pch = 19, col = rgb(.1, .1, .1, .1), ## ylab = "log(Wife's income + .5)", ## xlab = "log(Husband's income + .5)") ################################################### ### code chunk number 20: DAGD-CHFLS-RAincome3 ################################################### library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) xyplot(jitter(log(R_income + 0.5)) ~ jitter(log(A_income + 0.5)) | R_edu, data = CHFLS, pch = 19, col = rgb(.1, .1, .1, .1), ylab = "log(Wife's income + .5)", xlab = "log(Husband's income + .5)") ################################################### ### code chunk number 21: DAGD-household-tab ################################################### data("household", package = "HSAUR3") toLatex(HSAURtable(household), caption = paste("Household expenditure for single men and women."), label = "DAGD-household-tab") ################################################### ### code chunk number 22: DAGD-USstates-tab ################################################### data("USstates", package = "HSAUR3") toLatex(HSAURtable(USstates), caption = paste("Socio-demographic variables for ten US states."), label = "DAGD-USstates-tab") ################################################### ### code chunk number 23: DAGD-suicides2-tab ################################################### data("suicides2", package = "HSAUR3") toLatex(HSAURtable(suicides2), caption = paste("Mortality rates per $100,000$ from male suicides."), label = "DAGD-suicides2-tab", rownames = TRUE) ################################################### ### code chunk number 24: DAGD-banknote-tab ################################################### data("banknote", package = "mclust") banknote$Status <- NULL banknote <- banknote[c(1:5, 101:200),] toLatex(HSAURtable(banknote, pkg = "mclust", nrow = 10), caption = paste("Swiss bank note data."), label = "DAGD-banknote-tab", rownames = FALSE) ################################################### ### code chunk number 25: DAGD-birds-tab ################################################### data("birds", package = "HSAUR3") toLatex(HSAURtable(birds), caption = paste("Birds in paramo vegetation."), label = "DAGD-birds-tab", rownames = TRUE) HSAUR3/inst/doc/Ch_simultaneous_inference.pdf0000644000175000017500000031775614133304613020767 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3651 /Filter /FlateDecode /N 63 /First 507 >> stream xZYs۶~oMXItz3%['4nnHFr(RvTw&b988ˇH3l4S2t2l*Y)Y$eXI_LD3T&LȥTȤHQ0i- #)gPT1d7K91URLkrt7':;aƢLI%uƬ1+ǔ`ɉЊ)eR4KeX*eʲԂhQthcm̴``p-si7Xs8NSD7#RkbAsi ԀB xkbL= ,гĠg)1eLHHRpY, 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Vup lt[7EAa:k hS9]*UXxsʬ)&:Jwc]w;=XwʴdDV'I$ԤS Q Hg0ha _mdb\ E+=RھS/p.ъ餻bV,kY1Y1%$L;9H}oT"fBiF4FZSJ'5L#")t4NoP8lP$QDtFO`nT IE@,'V8o6I誾լ0910 |*&ml{xh_m-׋Vߍ^;Pಪ`:=^tM5*@OO0]e)')][ [.k)۩Ȧ;!]Y1܊vt9<ni4G !u(& 9R˗ ,7B\>$k> stream GPL Ghostscript 9.50 2021-10-18T16:49:47+02:00 2021-10-18T16:49:47+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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&(B)OmlϴDžh" Mkh֖}2.> v@tm5mKFxl|/屒VcE}I 4w}Lz#t5yU}-y6 -> -Ϛ]8Cr*J#`, =荸U}fR, W+Mt}{;(؏:މȌETNja-O9yg66NB-Ց!sYYTzLX8ʷ'*ժf:dL ޾"+pzgȟ2FZj(4^ ؟gK*lNo|zSvopi;GN6 ضpB/O7CY+HyrT.:tuQ'e;/T4ӴNKAرV Lp256r(ianp1QvU0ӛFh:S4?Wwf I;&v^Ӵ /b`w?Gɨِ9:Gtup̕چ  cEa!}5M4fd b@T@15v@/~+qwOV̭ӗ.^k{Շ#]9%ܴa[Xυmm7uz,16W`/ ltی5Ow7yQ cI0O~A!5U]Gy驯[}g_[hq-a?hl'I|| "]Tl.%Xo=u$9/oeYd?)| Bb]:! dĸ<ߖdMRŶ$HJz#Rn*U3蝂zxηr5l6{4ɘR@{?%5yhٿ"> stream xMolu֮Q.ha%5H jd 8ԅڹIwGS {mtwm7[XYāɠLhh|'1jo o$al!H4z\R}Em7ZۉM/oYfUmQߌMGIGS@0y8ctv2|l;3=nܜ>0}A/E >p.o+׹ {9;ʆNC?},FٵV]_8ņAzV)A$ZuaD2-Uh2щzpDhL0D))"u?/O*`(tp{>TReo J}>A$+<4pnsO@|r>QҔX-IH)<)Pj ˥$d"e_A?6%hE;L= EORw $sϝf#/-/S8}>Ѐ[UjxIRE1eF6S!=i1:;9 , P1awe]}ï{?,sޑ endstream endobj 159 0 obj << /Filter /FlateDecode /Subtype /Type1C /Length 1005 >> stream xRkLSgN/J4U sT(aQИj)1@q278[@q̩~52$tq.A8 @le8 t|]lyy_IDa<⪩(O;PI'3BHX/FB/~x/ H0یI Kt))GTU2^7tgMҠbuY.Sp/*;?hP4,U5E+l7vxxi~L0Սڽ=!EkШeRxRGZä0&Z}Jle@Id'&RXmWVV90<3B)pArlr~k.W[;깎WN};J=͸N^knȯt|qD3=tH" ÷>NNb_g w{sWݚy Lole2䄠[|Fxa'}fd:Mr,Ty<훔$\TڸS]Օ #;e{/30 bHOpZJnd͆X j:^܊'?;yj)s0Fz*=$Hȥ>hئ2{{ܸ#uwx_+k!jgTOFu@ZUH%S2m.)/}E8UN@XPez$vmz>C{Q2yԳtoLesK˃w9%;1\o*b‡^ $).PPlIH +EyH> QviF"U In~.3Ufl.\> stream xUOHQ߸&̻n,n5+O&:84;"D*Q"[4Z0/K ,bt71K{^ Nwvw8LG j2U㵁 A}..Deh%Vb* }TW`M .X_mA^}&AN)D^s)gh- jo&|W#| Kl> stream x\o$7r~_0COi8pNCFU,id ۯ&=lI^;rbUzVb+gG)jFWGQ{1QPnt13aV0Gg(mؠ1Z6f-c*wpq:(w4c2Oe%6X]}w$BWէ'T5):<"e˕4z LIeW'G?|?c4~ϯ0m4֨_X'!WztR >"bJ?//Dp&aLô_1hpñ2wah'#89Gʩ DVGQ ȶAU*A7VJY#Hbp#}2(9<:4çH+ĨH-c{m6a^q@_wVBe?!D$!aUҢp1^arMM!ǰa[ Tx۵ S6Paȧ=ܧJ`䑫 A @H'n62[-@^Ǚ]R?'9,]2kHp&%D'@(AIREx/ \V.@"-m6ܖ!f⻛ h48ְ{KĚyxQeCF :(n`Bf?EI5/&Q!2OB2Bw<5I']xw'[-˛pVp[~b Śin&W00Σ=l}#xm+t 0F 36f%M]BX*(l9xxΘ1N.)pd,8i%)Jd|EayN'~_PܚeWHȂN84|U\x vU0'ޱaز]72Af+Cmu{wwM|IxsZp+U{bQe`3U?bgr(H:XCf亸cJ !9|¾{ݗenP ?8~p8L;6$_7Lw}H`(N|bGg?lzÕlU>u;6{.'A>U6z,HM!8߅S΢LR`F8}SzZl+b%uSrQT*ݖڕyҹW3:Lmi]Ciyim;/׾+F0,ڀrӖm$ϕp:˯]N|R3kBנC==E.f&#7vD(}}FC%MNoϰμ%2OY(뻋~=Ӌ7nm Mh[fLe&ԓW9GY]$U| DJWe\ZAi"VO/!8 [R8DGe( /nPӟjdt1 B;A1@Fu8 l?vXR_My^^3 ~X6]Ŕv!쒥<ٽmBW2giHǞgI>ҜO|0Å2xO5,gknZ]wJ+Aĺro=F|JJtfx2&Y]/ [qdDp+QxOï4qW]U 3OQjOoDς,R3S A+9kţQ)KN>7HՌW&2yXN}A\drcPf8ʃMO]:tn(]gPW+3*)5-\tSU#zY;ݿ 賦.}a*惙Ӎ(nCٱK- 7}Ӱ.g8w3W,|&j?&\ώ"<3k7ǟq{pŻD?-q߿+'^]=Jnb1UbX>gI#' g5w&/hx>܂=#F0cPrY |yz㬈ѿHendstream endobj 162 0 obj << /Filter /FlateDecode /Subtype /Type1C /Length 282 >> stream x=K@XAcZNZ[)}[jD|+cz4˙P';(&\Ϗ=)Ez6v&s'sʧǵ}=2W7 eqYA2^0gsLmu]7pXC5Yq`[as،(Z|:=l4!r $ 4$8=#% m-w໳kF( B| ce7{Ծ+"L@߉8aF*> stream x\YY mv-cSwm˲,ch=cLSs@ćA*Lj8IOo{ˇ#58;9)'+୓Sp푏b N: ^N>;#&Tg ʪ'kTPڙFO8bmTgNa2.2S#A3T!n7яG2t(/!Vp/ !iTv8=z=ZWl4B? 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Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Multidimensional Scaling} %%\VignetteDepends{ape,wordcloud,MASS} \setcounter{chapter}{19} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= x <- library("ape") library("wordcloud") @ \chapter[Multidimensional Scaling]{Multidimensional Scaling: British Water Voles and Voting in US Congress \label{MDS}} \section{Introduction} \section{Multidimensional Scaling} \section{Analysis Using \R{}} We can apply classical scaling to the distance matrix for populations of water voles using the \R{} function \Rcmd{cmdscale}. The following code finds the classical scaling solution and computes the two criteria for assessing the required number of dimensions as described above. <>= data("watervoles", package = "HSAUR3") voles_mds <- cmdscale(watervoles, k = 13, eig = TRUE) voles_mds$eig @ Note that some of the eigenvalues are negative. The criterion $P_2$ can be computed by <>= sum(abs(voles_mds$eig[1:2]))/sum(abs(voles_mds$eig)) @ and the criterion suggested by \cite{HSAUR:Mardiaetal1979} is <>= sum((voles_mds$eig[1:2])^2)/sum((voles_mds$eig)^2) @ The two criteria for judging number of dimensions differ considerably, but both values are reasonably large, suggesting that the original distances between the water vole populations can be represented adequately in two dimensions. The two-dimensional solution can be plotted by extracting the coordinates from the \Robject{points} element of the \Robject{voles\_mds} object; the plot is shown in Figure~\ref{MDS-watervoles-plot}. The \Rcmd{textplot} function from package \Rpackage{wordcloud} can be used to annotate the plot with non-overlapping text. \begin{figure} \begin{center} <>= x <- voles_mds$points[,1] y <- voles_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") textplot(x, y, words = colnames(watervoles), new = FALSE) @ \caption{Two-dimensional solution from classical multidimensional scaling of distance matrix for water vole populations. \label{MDS-watervoles-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= library("ape") st <- mst(watervoles) plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") for (i in 1:nrow(watervoles)) { w1 <- which(st[i, ] == 1) segments(x[i], y[i], x[w1], y[w1]) } textplot(x, y, words = colnames(watervoles), new = FALSE) @ \caption{Minimum spanning tree for the \Robject{watervoles} data. \label{MDS-watervoles-mst}} \end{center} \end{figure} We shall now apply non-metric scaling to the voting behavior shown in Table~\ref{MDS-voting-tab}. Non-metric scaling is available with function \Rcmd{isoMDS} from package \Rpackage{MASS} \citep{HSAUR:VenablesRipley2002}: <>= library("MASS") data("voting", package = "HSAUR3") voting_mds <- isoMDS(voting) @ and we again depict the two-dimensional solution (Figure~\ref{MDS-voting-plot}). The Figure suggests that voting behavior is essentially along party lines, although there is more variation among Republicans. The voting behavior of one of the Republicans (Rinaldo) seems to be closer to his democratic colleagues rather than to the voting behavior of other Republicans. \begin{figure} \begin{center} <>= x <- voting_mds$points[,1] y <- voting_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(voting_mds$points[,1])*1.2, type = "n") textplot(x, y, words = colnames(voting), new = FALSE) voting_sh <- Shepard(voting[lower.tri(voting)], voting_mds$points) @ \caption{Two-dimensional solution from non-metric multidimensional scaling of distance matrix for voting matrix. \label{MDS-voting-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= plot(voting_sh, pch = ".", xlab = "Dissimilarity", ylab = "Distance", xlim = range(voting_sh$x), ylim = range(voting_sh$x)) lines(voting_sh$x, voting_sh$yf, type = "S") @ \caption{The Shepard diagram for the \Robject{voting} data shows some discrepancies between the original dissimilarities and the multidimensional scaling solution. \label{MDS-voting-shepard}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_analysis_of_variance.pdf0000644000175000017500000026050514133304605020366 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3059 /Filter /FlateDecode /N 54 /First 424 >> stream xZ[Sܸ~?BoT*|dJwLB23caL?_K7!x,[RKj7eyLi3O*&(L3@ #q 9~T?>s=i#gXcn00!w|WWbr,A|!"@A1>*G&!+AAVx6-%8!A~QG(6J1Vd󙷜YBA[j@OtE_@ 袅X\B[ڍpע%WIvߪ,3ywNYm1#C S|$/DrqS$j;=bD̔<}JYӓ8e~s|>o@"0R~UFvbOP+ |0|@`IʠFSR[m64h?F$y dj,t#X9bmHw#b!˗leO&;_l6bHY쬈[Wђ#o`dBV5m(WQnFr vd_\M+`?Q$P(+(o 罰lJQ# !% )GxLt2UzR i{;$uODњ0hf6% [z'W0-IoMw|9i:O|w~01.e[JU)NZ+c<5BIªte>SW: rao+ Up- ׄ6@[at8- YB;pN-` FLqAaǘR鼌!bZg95w uvvlWWCj 0ڡG$ZKڻ^L669Kcy^i0Z2YivBE3i~CPk-575&2VBDe+Îk۰´]XfhxI4; no}fC~;ڟ~G׀zp<@u/96>545 \ܖh/cHxv>7 ubŷSo;˴dez/l-0jbm u[[M?=Sx]mڕƱEi];-{vQUnwnmܖu [A>pF(Q6Mg19}Nϗ46p1%*~1ʶY:G.kaԓp{M5eS-:mއ:hZomiX q֊sїeTzQhl7Nߟl؏11XZ+.DG83AHՍhAwVj@]is(FR&1JejCqQN5cs!R}x/hYɾԧnF'4+l$<_' x2mT$XZ{|JB&iٷ굁ڕl*15ϧPEm#E\urP;]BraO7[hzQO1Oi>+b}}9/ES2^R 4)#j߃ bN^qk*kLW'q E6oB|sfboguտ~{L}ˡbo4>j(m@Ǫ3Là< TwFME[d%5C B[a+MdۅR'd3MN0蠙.m}ih/`@w't~֣6}(h{.Of|wy4+(x^leWò֦>&E8޵C5; 2z C-S'Փ @5jm hA71} 2,C8Pl ]/öLNNYW4e>d+G}' jKJwx~EFtTxehY b;}7T%U[ f6 a;up;F^6W>ci9#+B6k.oU;O e#d?>+Aw%YQE hQ/yUC`kk")肬'"GET @2ck59`al1kphDHӲ0,Wx7^t{lH:endstream endobj 56 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:41+02:00 2021-10-18T16:49:41+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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d[4<@ɷL`R7}DrAC)V]"@$i`kA${1dV/ 6-̮`s0yL~<@Q@>DiP;ލ_ endstream endobj startxref 90004 %%EOF HSAUR3/inst/doc/Ch_meta_analysis.R0000644000175000017500000001255014133304545016466 0ustar nileshnilesh### R code from vignette source 'Ch_meta_analysis.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: MA-smoking-OR-hand ################################################### data("smoking", package = "HSAUR3") odds <- function(x) (x[1] * (x[4] - x[3])) / ((x[2] - x[1]) * x[3]) weight <- function(x) ((x[2] - x[1]) * x[3]) / sum(x) W <- apply(smoking, 1, weight) Y <- apply(smoking, 1, odds) sum(W * Y) / sum(W) ################################################### ### code chunk number 4: MA-smoking-OR ################################################### library("rmeta") smokingOR <- meta.MH(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking)) ################################################### ### code chunk number 5: MA-smoking-OR-summary ################################################### summary(smokingOR) ################################################### ### code chunk number 6: MA-smoking-OR-plot ################################################### plot(smokingOR, ylab = "") ################################################### ### code chunk number 7: MA-smoking-random ################################################### (smokingDSL <- meta.DSL(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking))) ################################################### ### code chunk number 8: MA-BCG-odds ################################################### data("BCG", package = "HSAUR3") BCG_OR <- meta.MH(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) BCG_DSL <- meta.DSL(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) ################################################### ### code chunk number 9: MA-BCGOR-summary ################################################### summary(BCG_OR) ################################################### ### code chunk number 10: MA-BCGDSL-summary ################################################### summary(BCG_DSL) ################################################### ### code chunk number 11: BCG-studyweights ################################################### studyweights <- 1 / (BCG_DSL$tau2 + BCG_DSL$selogs^2) y <- BCG_DSL$logs BCG_mod <- lm(y ~ Latitude + Year, data = BCG, weights = studyweights) ################################################### ### code chunk number 12: MA-mod-summary ################################################### summary(BCG_mod) ################################################### ### code chunk number 13: BCG-Latitude-plot ################################################### plot(y ~ Latitude, data = BCG, ylab = "Estimated log-OR") abline(lm(y ~ Latitude, data = BCG, weights = studyweights)) ################################################### ### code chunk number 14: MA-funnel-ex ################################################### set.seed(290875) sigma <- seq(from = 1/10, to = 1, length.out = 35) y <- rnorm(35) * sigma gr <- (y > -0.5) layout(matrix(1:2, ncol = 1)) plot(y, 1/sigma, xlab = "Effect size", ylab = "1 / standard error") plot(y[gr], 1/(sigma[gr]), xlim = range(y), xlab = "Effect size", ylab = "1 / standard error") ################################################### ### code chunk number 15: MA-smoking-funnel ################################################### funnelplot(smokingDSL$logs, smokingDSL$selogs, summ = smokingDSL$logDSL, xlim = c(-1.7, 1.7)) abline(v = 0, lty = 2) HSAUR3/inst/doc/Ch_errata.R0000644000175000017500000000350014133304525015104 0ustar nileshnilesh### R code from vignette source 'Ch_errata.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE HSAUR3/inst/doc/Ch_missing_values.Rnw0000644000175000017500000006351314133304452017234 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Missing Values} %%\VignetteDepends{mice} \setcounter{chapter}{15} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Missing Values]{Missing Values: Lowering Blood Pressure During Surgery \label{MV}} \section{Introduction} \index{Blood pressure} It is sometimes necessary to lower a patient's blood pressure during surgery, using a hypotensive drug. Such drugs are administered continuously during the relevant phase of the operation; because the duration of this phase varies so does the total amount of drug administered. Patients also vary in the extent to which the drugs succeed in lowering blood pressure. The sooner the blood pressure rises again to normal after the drug is discontinued, the better. The data in Table~\ref{MV-bp-tab} \citep[a missing-value version of the data presented by][]{HSAUR:RobertsonArmitage1959} relate to a particular hypotensive drug and give the time in minutes before the patient's systolic blood pressure returned to 100mm of mercury (the recovery time), the logarithm (base 10) of the dose of drug in milligrams, and the average systolic blood pressure achieved while the drug was being administered. The question of interest is how is the recovery time related to the other two variables? For some patients the recovery time was not recorded and the missing values are indicated as NA in Table~\ref{MV-bp-tab}. <>= data("bp", package = "HSAUR3") toLatex(HSAURtable(bp), pcol = 2, caption = paste("Blood pressure data."), label = "MV-bp-tab") @ \section{Analyzing Multiply Imputed Data} \label{MI:ana} From the analysis of each data set we need to look at the estimates of the quantity of interest, say $Q$, and the variance of the estimates. We let $\hat{Q}_i$ be the estimate from the $i$th data set and $S_i$ its corresponding variance. The combined estimate of the quantity of interest is \begin{eqnarray*} \bar{Q} = \frac{1}{m}\sum_{i = 1}^m \hat{Q}_i. \end{eqnarray*} To find the combined variance involves first calculating the within-imputation variance, \begin{eqnarray*} \bar{S} = \frac{1}{m}\sum_{i = 1}^m S_i \end{eqnarray*} followed by the between-imputation variance, \begin{eqnarray*} B = \frac{1}{m - 1} \sum_{i = 1}^m (\hat{Q}_i - \bar{Q})^2 \end{eqnarray*} then the required total variance can now be found from \begin{eqnarray*} T = \bar{S} + (1 + m^{-1}) B \end{eqnarray*} This total variance is made up of two components; the first which preserves the natural variability, $\bar{S}$, is simply the average of the variance estimates for each imputed data set and is analogous to the variance that would be suitable if we did not need to account for missing data; the second component, $B$, estimates uncertainty caused by missing data by measuring how the point estimates vary from data set to data set. More explanation of how the formula for $T$ arises is given in \cite{HSAUR:vanBuuren2012}. The overall standard error is simply the square root of $T$. A significance test for $Q$ and a confidence interval is found from the usual test statistic, ($Q-$ hypothesized value of $Q$)/$\sqrt{T}$, the value of which is referred to a Student's $t$-distribution. The question arises however as to what is the appropriate value for the degrees of freedom of the test, say $v_0$? \cite{HSAUR:Rubin1987} suggests that the answer to this question is given by; \begin{eqnarray*} v_0 = (m - 1) (1 + 1/r^2) \end{eqnarray*} where \begin{eqnarray*} r = \frac{B + B / m}{\bar{S}} \end{eqnarray*} But \cite{HSAUR:BarnardRubin1999} noted that using this value of $v_0$ can produce values that are larger than the degrees of freedom in the complete data, a result which they considered `clearly inappropriate'. Consequently they developed an adapted version that does not lead to the same problem. Barnard and Rubin's revised value for the degrees of freedom of the $t$-test in which we are interested is $v_1$ given by; \begin{eqnarray*} v_1 = \frac{v_0 v_2}{v_0 + v_2} \end{eqnarray*} where \begin{eqnarray*} v_2 = \frac{n(n-1)(1 - \lambda)}{n + 2} \end{eqnarray*} and \begin{eqnarray*} \lambda = \frac{r}{\sqrt{r^2 + 1}}. \end{eqnarray*} The quantity $v_1$ is always less than or equal to the degrees of freedom of the test applied to the hypothetically complete data. \citep[For more details see][]{HSAUR:vanBuuren2012}. \index{Imputation|)} \section{Analysis Using \R{}} To begin we shall analyze the blood pressure data in Table~\ref{MV-bp-tab} using the complete-case approach, i.e., by simply removing the data for patients where the recovery time is missing. To begin we might simply count the number of missing values using the sapply function as follows: <>= sapply(bp, function(x) sum(is.na(x))) @ So there are ten missing values of recovery time but no missing values amongst the other two variables. Now we use the \Rcmd{summary} function to look at some basic statistics of the complete data for recovery time: <>= summary(bp$recovtime, na.rm = TRUE) @ And next we can calculate the complete data estimate of the standard deviation of recover time <>= sd(bp$recovtime, na.rm = TRUE) @ The final numerical results we might be interested in are the correlations of recovery time with blood pressure and of recovery time with logdose. These can be found as follows: <>= with(bp, cor(bloodp, recovtime, use = "complete.obs")) with(bp, cor(logdose, recovtime, use = "complete.obs")) @ And a useful graphic of the data is a scatterplot matrix which we can construct using \Rcmd{pairs}. The scatterplot matrix is given in Figure~\ref{MV-bp-pairs-cc}. \begin{figure} \begin{center} <>= layout(matrix(1:3, nrow = 1)) plot(bloodp ~ logdose, data = bp) plot(recovtime ~ bloodp, data = bp) plot(recovtime ~ logdose, data = bp) @ \caption{Scatterplots of the complete cases of the \Robject{bp} data. \label{MV-bp-pairs-cc}} \end{center} \end{figure} To investigate how recovery time is related to blood pressure and logdose we might begin by fitting a multiple linear regression model (see Chapter~\ref{MLR}). The relevant command and the summary of the results is shown in Figure~\ref{MV-bp-lm-cc}. Note that this summary output reports that ten observations with missing values were removed prior to the analysis; this is default for many models in \R. \renewcommand{\nextcaption}{\R{} output of the complete-case linear model for the \Robject{bp} data. \label{MV-bp-lm-cc}} \SchunkLabel <>= summary(lm(recovtime ~ bloodp + logdose, data = bp)) @ \SchunkRaw Now let us see what happens when we impute the missing values of the recovery time variable simply by the mean of the complete case; for this we will use the \Rpackage{mice} \citep{PKG:mice} package; <>= library("mice") @ We begin by creating a new data set, \Robject{imp}, which will contain the three variables log-dose, blood pressure, and recovery time with the missing values in the latter replaced by the mean recovery time of the complete cases; <>= imp <- mice(bp, method = "mean", m = 1, maxit = 1) @ So now we can find the summary statistics of recovery time to compare with those given previously <>= with(imp, summary(recovtime)) @ Making the comparison we see that only the values of the first and third quantile and the median have changed. The minimum and maximum values are the same and so, of course, is the mean. But of more interest is what happens to the sample standard deviation; its value for the imputed data can be found using: <>= with(imp, sd(recovtime)) @ The value for the imputed data, $\Sexpr{round(with(imp, sd(recovtime))[["analyses"]][[1]], 2)}$ is, as we would expect, lower than that for the complete data, $\Sexpr{round(with(bp, sd(recovtime, na.rm = TRUE)), 2)}$. What about the correlations? <>= with(imp, cor(bloodp, recovtime)) with(imp, cor(logdose, recovtime)) @ The correlations of blood pression and recovery time are very similar before ($\Sexpr{round(with(bp, cor(bloodp, recovtime, use = "complete.obs")), 2)}$) after ($\Sexpr{round(with(imp, cor(bloodp, recovtime))[["analyses"]][[1]], 2)}$) imputation. For log-dose, imputation changes the correlation from $\Sexpr{round(with(bp, cor(logdose, recovtime, use = "complete.obs")), 2)}$ to $\Sexpr{round(with(imp, cor(logdose, recovtime))[["analyses"]][[1]], 2)}$. The scatterplot of the imputed data is found as given by the code displayed with Figure~\ref{MV-bp-pairs-imp}. For mean imputation, the imputed value of the recovery time is constant for all observations and so they appear as a series of points along the value of the mean value of the observed recovery times namely, $\Sexpr{round(with(bp, mean(recovtime, na.rm = TRUE)), 2)}$. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) @ \caption{Scatterplots of the imputed \Robject{bp} data. Imputed observations are depicted as triangles. \label{MV-bp-pairs-imp}} \end{center} \end{figure} \renewcommand{\nextcaption}{\R{} output of the mean imputation linear model for the \Robject{bp} data. \label{MV-bp-lm-imp}} \SchunkLabel <>= with(imp, summary(lm(recovtime ~ bloodp + logdose))) @ \SchunkRaw Comparison of the multiple linear regression results in Figure~\ref{MV-bp-lm-imp} with those in Figure~\ref{MV-bp-lm-cc} show some interesting differences, for example, the standard errors of the regression coefficients are somewhat lower for the mean imputed data but the conclusions drawn from the results in each table would be broadly similar. \index{Predictive mean matching} The single imputation of a sample mean is not to be recommended and so we will move on to using a more sophisticated multiple imputation procedure know as \stress{predictive mean matching}. The method is described in detail in \cite{HSAUR:vanBuuren2012} who considers it both easy-to-use and versatile. And imputations outside the observed data range will not occur so that problems with meaningless imputations, for example, a negative recovery time, will not occur. The method is labeled \Robject{pmm} in the \Rpackage{mice} package and here we will apply it to the blood pressure data with $m = 10$ (we need to fix the seed in order to make the result reproducible): <>= imp_ppm <- mice(bp, m = 10, method = "pmm", print = FALSE, seed = 1) @ The scatterplot of the imputed data is found as given by the code displayed with Figure~\ref{MV-bp-pairs-imp-mice}. We only show the imputed recovery times from the first iteration ($m = 1$).The imputed recovery times now take different values. \begin{figure} \begin{center} <>= layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) @ \caption{Scatterplots of the multiple imputed \Robject{bp} data (first iteration). Imputed observations are depicted as triangles. \label{MV-bp-pairs-imp-mice}} \end{center} \end{figure} From the resulting object we can compute the mean and standard deviations of recovery time for each of the $m = 10$ iterations. We first extract these numbers from the \Robject{analyses} element of the returned object, convert this list to a vector, and use the \Rcmd{summary} function to compute the usual summary statistics: <>= summary(unlist(with(imp_ppm, mean(recovtime))$analyses)) summary(unlist(with(imp_ppm, sd(recovtime))$analyses)) @ We do the same with the correlations as follows <>= summary(unlist(with(imp_ppm, cor(bloodp, recovtime))$analyses)) summary(unlist(with(imp_ppm, cor(logdose, recovtime))$analyses)) @ The estimate of the mean of the blood pressure data from the multiply imputed results is $\Sexpr{round(mean(unlist(with(imp_ppm, mean(recovtime))$analyses)) , 2)}$, very similar to the values found previously. Similarly the estimate of the standard deviation of the data is $\Sexpr{round(mean(unlist(with(imp_ppm, sd(recovtime))$analyses)) , 2)}$ which lies between the complete data estimate and the \emph{mean-imputed} value. The two correlation estimates are also very close to the previous values. The variation in the estimates of mean, standard deviation, and correlations across the ten imputation is relatively small apart from that for the correlation between log-dose and recovery time -- here there is considerable variation in the values for the ten imputations. Finally, we will fit a linear model to each of the imputed samples and then find the summary statistics for the ten sets of regression coefficients: the results are given in Figure~\ref{MV-bp-lm-cc-mice}: <>= fit <- with(imp_ppm, lm(recovtime ~ bloodp + logdose)) @ \renewcommand{\nextcaption}{\R{} output of the multiple imputed linear model for the \Robject{bp} data. \label{MV-bp-lm-cc-mice}} \SchunkLabel <>= summary(pool(fit)) @ \SchunkRaw The result for blood pressure is similar to the previous complete data and mean-imputed results with the regression coefficient for this variable being highly significant $(p = \Sexpr{round(summary(pool(fit))["bloodp", 5], 3)})$. But the result for log dose differs from those found previously; for the multiply imputed data the regression coefficient for log dose is not significant at the $5\%$ level $(p = \Sexpr{round(summary(pool(fit))["logdose", 5], 3)})$ whereas in both of the previous two analyses it was significant. This finding reflects the greater variation of the value of the correlation between log dose and recovery time in the ten imputations noted above. (Remember that the standard errors in Figure~\ref{MV-bp-lm-cc-mice} computed by \Rcmd{pool} arise from the formulae given in Section~\ref{MI:ana}.) Now suppose we wish to test the hypothesis that in the population from which the sample data in Table~\ref{MV-bp-tab} arises a mean recovery time of $27$ minutes. We will test this hypothesis in the usual way using Student's t-test applied to the complete-data, the singly imputed data, and the multiply imputed data: <>= with(bp, t.test(recovtime, mu = 27)) with(imp, t.test(recovtime, mu = 27))$analyses[[1]] @ For the multiply imputed data we need to use the \Rcmd{lm} function to get the equivalent of the $t$-test by modeling recovery time minus $27$ with an intercept only and testing for zero intercept. So the code needed is: <>= fit <- with(imp_ppm, lm(I(recovtime - 27) ~ 1)) summary(pool(fit)) @ Looking at the results of the three analyses we see that the complete-case analysis fails to reject the hypothesis at the $5\%$ level whereas the other two analyses lead to results that are statistically significant at the level. This simple (and perhaps rather artificial) example demonstrates that different conclusions can be reached by the different approaches. \section{Summary of Findings} The estimated standard deviation of the blood pressure is lower when computed from the mean-imputed data than from the complete data. The corresponding value from the multiply imputed data lies between these two values. The estimate of the mean from the multiply imputed data is very similar to the value obtained in the complete data analysis. (The value from the singly imputed data is, of course, the same as from the complete data.) The estimates of the correlations between blood pressure and recovery time and log dose and recovery time are very similar in all three analyses but the variation in the latter across the ten multiple imputations is considerable and this results in the regression coefficient for log dose being less significant than in the other two analyses. Testing the hypothesis that the population mean of recovery time is $27$ minutes using complete-case analysis leads to a different conclusion than is arrived at by the two multiple imputations approaches. \section{Final Comments} Missing values are an ever-present possibility in all types of studies although everything possible should be done to avoid them. But when data contain missing values multiple imputation can be used to provide valid inferences for parameter estimates from the incomplete data. If carefully handled, multiple imputation can cope with missing data in all types of variables. In this chapter we have given only a brief account of dealing with missing values; a detailed account is available in the issue of \stress{Statistical Methods in Medical Research entitled Multiple Imputation: Current Perspectives} (Volume 16, Number 3, 2007) and in \cite{HSAUR:vanBuuren2012}. \section*{Exercises} \begin{description} \exercise The data in Table~\ref{MI-UStemp-tab} give the lowest temperatures (in Fahrenheit) recorded in various months for cities in the US; missing values are indicated by NA. Calculate the correlation matrix of the data using \begin{enumerate} \item the complete-case approach, \item the available-data approach, and \item a multiple-imputation approach. \end{enumerate} Find the principal components of the data using each of three correlation matrices and plot the cities in the space of the first two components of each solution. <>= data("UStemp", package = "HSAUR3") toLatex(HSAURtable(UStemp), caption = "Lowest temperatures in Fahrenheit recorded in various months for cities in the US.", label = "MI-UStemp-tab", rownames = TRUE) @ \exercise Find $95\%$ confidence intervals for the population means of the lowest temperature in each month using \begin{enumerate} \item the complete-case approach, \item the mean value imputation, and \item a multiple-imputation approach. \end{enumerate} \exercise Find the correlation matrix for the four months in Table~\ref{MI-UStemp-tab} using complete-case analysis, listwise deletion, and multiple imputation. \end{description} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_logistic_regression_glm.R0000644000175000017500000003274614133304543020560 0ustar nileshnilesh### R code from vignette source 'Ch_logistic_regression_glm.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: GLM-plasma-plot ################################################### data("plasma", package = "HSAUR3") layout(matrix(1:2, ncol = 2)) cdplot(ESR ~ fibrinogen, data = plasma) cdplot(ESR ~ globulin, data = plasma) ################################################### ### code chunk number 4: GLM-plasma-fit1 ################################################### plasma_glm_1 <- glm(ESR ~ fibrinogen, data = plasma, family = binomial()) ################################################### ### code chunk number 5: GLM-plasma-summary-1 ################################################### summary(plasma_glm_1) ################################################### ### code chunk number 6: GLM-plasma-confint ################################################### ci <- confint(plasma_glm_1)["fibrinogen",] ################################################### ### code chunk number 7: GLM-plasma-confint ################################################### confint(plasma_glm_1, parm = "fibrinogen") ################################################### ### code chunk number 8: GLM-plasma-confint ################################################### print(ci) ################################################### ### code chunk number 9: GLM-plasma-exp ################################################### exp(coef(plasma_glm_1)["fibrinogen"]) ################################################### ### code chunk number 10: GLM-plasma-exp-ci ################################################### ci <- exp(confint(plasma_glm_1, parm = "fibrinogen")) ################################################### ### code chunk number 11: GLM-plasma-exp-ci ################################################### exp(confint(plasma_glm_1, parm = "fibrinogen")) ################################################### ### code chunk number 12: GLM-plasma-exp-ci ################################################### print(ci) ################################################### ### code chunk number 13: GLM-plasma-fit2 ################################################### plasma_glm_2 <- glm(ESR ~ fibrinogen + globulin, data = plasma, family = binomial()) ################################################### ### code chunk number 14: GLM-plasma-summary-2 ################################################### summary(plasma_glm_2) ################################################### ### code chunk number 15: GLM-plasma-anova-hide ################################################### plasma_anova <- anova(plasma_glm_1, plasma_glm_2, test = "Chisq") ################################################### ### code chunk number 16: GLM-plasma-anova ################################################### anova(plasma_glm_1, plasma_glm_2, test = "Chisq") ################################################### ### code chunk number 17: GLM-plasma-predict ################################################### prob <- predict(plasma_glm_2, type = "response") ################################################### ### code chunk number 18: GLM-plasma-bubble ################################################### plot(globulin ~ fibrinogen, data = plasma, xlim = c(2, 6), ylim = c(25, 55), pch = ".") symbols(plasma$fibrinogen, plasma$globulin, circles = prob, add = TRUE) ################################################### ### code chunk number 19: GLM-womensrole-fit1 ################################################### data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ gender + education womensrole_glm_1 <- glm(fm1, data = womensrole, family = binomial()) ################################################### ### code chunk number 20: GLM-womensrole-summary-1 ################################################### summary(womensrole_glm_1) ################################################### ### code chunk number 21: GLM-womensrole-probfit ################################################### role.fitted1 <- predict(womensrole_glm_1, type = "response") ################################################### ### code chunk number 22: GLM-plot-setup ################################################### myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } ################################################### ### code chunk number 23: GLM-role-fitted1 ################################################### myplot(role.fitted1) ################################################### ### code chunk number 24: GLM-womensrole-fit2 ################################################### fm2 <- cbind(agree,disagree) ~ gender * education womensrole_glm_2 <- glm(fm2, data = womensrole, family = binomial()) ################################################### ### code chunk number 25: GLM-womensrole-summary-2 ################################################### summary(womensrole_glm_2) ################################################### ### code chunk number 26: GLM-role-fitted2 ################################################### role.fitted2 <- predict(womensrole_glm_2, type = "response") myplot(role.fitted2) ################################################### ### code chunk number 27: GLM-role-plot2 ################################################### res <- residuals(womensrole_glm_2, type = "deviance") plot(predict(womensrole_glm_2), res, xlab="Fitted values", ylab = "Residuals", ylim = max(abs(res)) * c(-1,1)) abline(h = 0, lty = 2) ################################################### ### code chunk number 28: GLM-polyps-fit1 ################################################### data("polyps", package = "HSAUR3") polyps_glm_1 <- glm(number ~ treat + age, data = polyps, family = poisson()) ################################################### ### code chunk number 29: GLM-polyps-summary-1 ################################################### summary(polyps_glm_1) ################################################### ### code chunk number 30: GLM-polyp-quasi ################################################### polyps_glm_2 <- glm(number ~ treat + age, data = polyps, family = quasipoisson()) summary(polyps_glm_2) ################################################### ### code chunk number 31: GLM-backpain-clogit ################################################### library("survival") backpain_glm <- clogit(I(status == "case") ~ driver + suburban + strata(ID), data = backpain) ################################################### ### code chunk number 32: GLM-backpain-print ################################################### print(backpain_glm) ################################################### ### code chunk number 33: GLM-CHFLS-polr ################################################### library("MASS") opts <- options(contrasts = c("contr.treatment", "contr.helmert")) CHFLS_polr <- polr(R_happy ~ ., data = CHFLS, Hess = TRUE) options(opts) ################################################### ### code chunk number 34: GLM-CHFLS-polr ################################################### summary(CHFLS_polr) ################################################### ### code chunk number 35: GLM-CHFLS-polr-helmert ################################################### H <- with(CHFLS, contr.helmert(table(R_health))) rownames(H) <- levels(CHFLS$R_health) colnames(H) <- paste(levels(CHFLS$R_health)[-1], "- avg") H ################################################### ### code chunk number 36: GLM-CHFLS-polr-cftest ################################################### library("multcomp") op <- options(digits = 2) cf <- cftest(CHFLS_polr) cftest <- function(x, digits = max(3, getOption("digits") - 3)) { x <- cf cat("\n\t", "Simultaneous Tests for General Linear Hypotheses\n\n") if (!is.null(x$type)) cat("Multiple Comparisons of Means:", x$type, "Contrasts\n\n\n") call <- if (isS4(x$model)) x$model@call else x$model$call if (!is.null(call)) { cat("Fit: ") print(call) cat("\n") } pq <- x$test mtests <- cbind(pq$coefficients, pq$sigma, pq$tstat, pq$pvalues) error <- attr(pq$pvalues, "error") pname <- switch(x$alternativ, less = paste("Pr(<", ifelse(x$df == 0, "z", "t"), ")", sep = ""), greater = paste("Pr(>", ifelse(x$df == 0, "z", "t"), ")", sep = ""), two.sided = paste("Pr(>|", ifelse(x$df == 0, "z", "t"), "|)", sep = "")) colnames(mtests) <- c("Estimate", "Std. Error", ifelse(x$df == 0, "z value", "t value"), pname) type <- pq$type if (!is.null(error) && error > .Machine$double.eps) { sig <- which.min(abs(1/error - (10^(1:10)))) sig <- 1/(10^sig) } else { sig <- .Machine$double.eps } cat("Linear Hypotheses:\n") alt <- switch(x$alternative, two.sided = "==", less = ">=", greater = "<=") rownames(mtests) <- rownames(mtests) printCoefmat(mtests, digits = digits, has.Pvalue = TRUE, P.values = TRUE, eps.Pvalue = sig) switch(type, univariate = cat("(Univariate p values reported)"), `single-step` = cat("(Adjusted p values reported -- single-step method)"), Shaffer = cat("(Adjusted p values reported -- Shaffer method)"), Westfall = cat("(Adjusted p values reported -- Westfall method)"), cat("(Adjusted p values reported --", type, "method)")) cat("\n\n") invisible(x) } ################################################### ### code chunk number 37: GLM-CHFLS-polr-cftest ################################################### library("multcomp") cftest(CHFLS_polr) ################################################### ### code chunk number 38: GLM-CHFLS-polr-cftest ################################################### options(op) ################################################### ### code chunk number 39: GLM-CHFLS-pred-1 ################################################### CHFLS[1,] ################################################### ### code chunk number 40: GLM-CHFLS-pred-2 ################################################### nd <- CHFLS[rep(1, nlevels(CHFLS$R_health)),] nd$R_health <- ordered(levels(nd$R_health), labels = levels(nd$R_health)) ################################################### ### code chunk number 41: GLM-CHFLS-pred-3 ################################################### (dens <- predict(CHFLS_polr, newdata = nd, type = "probs")) ################################################### ### code chunk number 42: GLM-CHFLS-pred-plot ################################################### library("lattice") D <- expand.grid(R_health = nd$R_health, R_happy = ordered(LETTERS[1:4])) D$dens <- as.vector(dens) barchart(dens ~ R_happy | R_health, data = D, ylab = "Density", xlab = "Happiness",) ################################################### ### code chunk number 43: GLM-findings ################################################### ci <- round(exp(confint(plasma_glm_1, parm = "fibrinogen")), 2) ci <- paste("(", paste(ci, collapse = ","), ")", sep = "") HSAUR3/inst/doc/Ch_multidimensional_scaling.R0000644000175000017500000001066714133304552020717 0ustar nileshnilesh### R code from vignette source 'Ch_multidimensional_scaling.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: MDS-setup ################################################### x <- library("ape") library("wordcloud") ################################################### ### code chunk number 4: MDS-voles-cmdscale ################################################### data("watervoles", package = "HSAUR3") voles_mds <- cmdscale(watervoles, k = 13, eig = TRUE) voles_mds$eig ################################################### ### code chunk number 5: MDS-voles-criterion1 ################################################### sum(abs(voles_mds$eig[1:2]))/sum(abs(voles_mds$eig)) ################################################### ### code chunk number 6: MDS-voles-criterion2 ################################################### sum((voles_mds$eig[1:2])^2)/sum((voles_mds$eig)^2) ################################################### ### code chunk number 7: MDS-watervoles-plot ################################################### x <- voles_mds$points[,1] y <- voles_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") textplot(x, y, words = colnames(watervoles), new = FALSE) ################################################### ### code chunk number 8: MDS-watervoles-mst ################################################### library("ape") st <- mst(watervoles) plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(x)*1.2, type = "n") for (i in 1:nrow(watervoles)) { w1 <- which(st[i, ] == 1) segments(x[i], y[i], x[w1], y[w1]) } textplot(x, y, words = colnames(watervoles), new = FALSE) ################################################### ### code chunk number 9: MDS-voting ################################################### library("MASS") data("voting", package = "HSAUR3") voting_mds <- isoMDS(voting) ################################################### ### code chunk number 10: MDS-voting-plot ################################################### x <- voting_mds$points[,1] y <- voting_mds$points[,2] plot(x, y, xlab = "Coordinate 1", ylab = "Coordinate 2", xlim = range(voting_mds$points[,1])*1.2, type = "n") textplot(x, y, words = colnames(voting), new = FALSE) voting_sh <- Shepard(voting[lower.tri(voting)], voting_mds$points) ################################################### ### code chunk number 11: MDS-voting-Shepard ################################################### plot(voting_sh, pch = ".", xlab = "Dissimilarity", ylab = "Distance", xlim = range(voting_sh$x), ylim = range(voting_sh$x)) lines(voting_sh$x, voting_sh$yf, type = "S") HSAUR3/inst/doc/Ch_introduction_to_R.pdf0000644000175000017500000061211514133304610017705 0ustar nileshnilesh%PDF-1.5 % 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GǼ_qIFx<.x%+z{>퇒q^U'7Y.l&#a9b5Xh6nBhZigZvGX|LǠ+Ǡû`{r50W[8!a^-nj\DV߬SDfQ":fM f1͚HiUdgEZ?>Tt0O:y˷G/6 yM ۀoGnflըgİW lhVx,2W4l1ٞ`t&)AH4khF{JMwZ_!]LX=z7O.vWv-{ U+k_ub+ʷ1ɶq[sUu_YuTN䗳㢛&hlui2vdq۽{mkۮȭt~9G:ԢcQ+2fc< r dI(cheqNEMMoYe!<k´.9IJpj 7Hޞc*.=p~pw<̛ˇ!0ߎD HRT9SK!љܛS~^Lb2*?WP `}rU_o3 aMblc],2f8AzOz덝'?APW1zw齵x&TRݼ#ש֒[sm ~A^ $ς"~yzGueᶏNY,{uaib檋K>Y/$6Ė{("iZ4+"m;֦*?S&r%& S 40M1sX28J-/8 &)v\⁤U1"3rl&sE̲WpYV\}2zKmS`ub៴H@m~tqjc`9*Ig)Z;N&7)?F"s2ٟTLQyE̙BxZUswJ+/ewX`h]og .Džw y+{[Xؼf]-λ&K3- Z~%n*?(`)DR)P9ЇB4ϝ3ws |}sDHޯ2e<܄3EևbJD;c \x-La'iLA~\G,g$J Q2IP@D?)`J˔.H?)#aeRR$0¤uaވKm\A#9W!1֋UbΕ|\*r.^^.s,7b˜ ';>HWzρ>0f%GR@ԜLwJ;3`w9Bv>lcN4=jpy}?c͑W>r#cpB`2p` C<}oN%)-g[M=OvMa> stream GPL Ghostscript 9.50 2021-10-18T16:49:44+02:00 2021-10-18T16:49:44+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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DdYLG{rendstream endobj 240 0 obj << /Filter /FlateDecode /Length 150 >> stream xU;1 {'0q_N@ -ׇE٬W.,?慅:c8]k  I1 7g`tBw2SZJffBPUR=uw$֓TS>HԖ!56w/ûC endstream endobj 241 0 obj << /Type /XRef /Length 213 /Filter /FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 242 /ID [<7a63efb148d31ecc15134fda3894aefa>] >> stream xcb&F~0 $8J$/ҋii$'Zd RDH`=d"9^H R1DgAF (qĖ,`3G9&u@$v)h ۸D%H![ۄ*lb`WmA$O ؜ - f (` endstream endobj startxref 201317 %%EOF HSAUR3/inst/doc/Ch_analysis_of_variance.Rnw0000644000175000017500000004721114133304452020360 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analysis of Variance} %%\VignetteDepends{wordcloud} \setcounter{chapter}{4} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("wordcloud") @ \chapter[Analysis of Variance]{Analysis of Variance: Weight Gain, Foster Feeding in Rats, Water Hardness, and Male Egyptian Skulls \label{ANOVA}} \section{Introduction} \section{Analysis of Variance} \section{Analysis Using \R{}} \subsection{Weight Gain in Rats \label{ANOVA:rats}} Before applying analysis of variance to the data in Table~\ref{ANOVA-weightgain-tab} we should try to summarize the main features of the data by calculating means and standard deviations and by producing some hopefully informative graphs. The data is available in the \Rclass{data.frame} \Robject{weightgain}. The following \R{} code produces the required summary statistics <>= data("weightgain", package = "HSAUR3") tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), mean) tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), sd) @ \begin{figure} \begin{center} <>= plot.design(weightgain) @ \caption{Plot of mean weight gain for each level of the two factors. \label{ANOVA-weightgain-fig}} \end{center} \end{figure} To apply analysis of variance to the data we can use the \Rcmd{aov} function in \R{} and then the \Rcmd{summary} method to give us the usual analysis of variance table. The model \Rclass{formula} specifies a two-way layout with interaction terms, where the first factor is \Robject{source}, and the second factor is \Robject{type}. <>= wg_aov <- aov(weightgain ~ source * type, data = weightgain) @ \renewcommand{\nextcaption}{\R{} output of the ANOVA fit for the \Robject{weightgain} data. \label{ANOVA-weightgain-output}} \SchunkLabel <>= summary(wg_aov) @ \SchunkRaw \begin{figure} \begin{center} <>= interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain) @ <>= interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain, legend = FALSE) legend(1.5, 95, legend = levels(weightgain$source), title = "weightgain$source", lty = c(2,1), bty = "n") @ \caption{Interaction plot of type and source. \label{ANOVA-weightgain-fig2}} \end{center} \end{figure} The estimates of the intercept and the main and interaction effects can be extracted from the model fit by <>= coef(wg_aov) @ Note that the model was fitted with the restrictions $\gamma_1 = 0$ (corresponding to \Rlevel{Beef}) and $\beta_1 = 0$ (corresponding to \Rlevel{High}) because treatment contrasts were used as default as can be seen from <>= options("contrasts") @ Thus, the coefficient for \Robject{source} of $\Sexpr{coef(wg_aov)[2]}$ can be interpreted as an estimate of the difference $\gamma_2 - \gamma_1$. Alternatively, we can use the restriction $\sum_i \gamma_i = 0$ by <>= coef(aov(weightgain ~ source + type + source:type, data = weightgain, contrasts = list(source = contr.sum))) @ \subsection{Foster Feeding of Rats of Different Genotype} As in the previous subsection we will begin the analysis of the foster feeding data in Table~\ref{ANOVA-foster-tab} with a plot of the mean litter weight for the different genotypes of mother and litter (see Figure~\ref{ANOVA-foster-fig}). The data are in the \Rclass{data.frame} \Robject{foster} <>= data("foster", package = "HSAUR3") @ \begin{figure} \begin{center} <>= plot.design(foster) @ \caption{Plot of mean litter weight for each level of the two factors for the \Robject{foster} data. \label{ANOVA-foster-fig}} \end{center} \end{figure} We can derive the two analyses of variance tables for the foster feeding example by applying the \R{} code <>= summary(aov(weight ~ litgen * motgen, data = foster)) @ to give <>= summary(aov(weight ~ litgen * motgen, data = foster)) @ and then the code <>= summary(aov(weight ~ motgen * litgen, data = foster)) @ to give <>= summary(aov(weight ~ motgen * litgen, data = foster)) @ There are (small) differences in the sum of squares for the two main effects and, consequently, in the associated $F$-tests and $p$-values. \index{F-tests@$F$-tests} This would not be true if in the previous example in Subsection~\ref{ANOVA:rats} we had used the code <>= summary(aov(weightgain ~ type * source, data = weightgain)) @ instead of the code which produced Figure~\ref{ANOVA-weightgain-output} (readers should confirm that this is the case). We can investigate the effect of genotype B on litter weight in more detail by the use of \stress{multiple comparison procedures} \index{Multiple comparison procedures|(} \citep[see][and \Sexpr{ch("SIMC")}]{HSAUR:Everitt1996}. Such procedures allow a comparison of all pairs of levels of a factor whilst maintaining the nominal significance level at its specified value and producing adjusted confidence intervals for mean differences. One such procedure is called \stress{Tukey honest significant differences} \index{Tukey honest significant differences} suggested by \cite{HSAUR:Tukey1953}; see \cite{HSAUR:HochbergTamhane1987} also. Here, we are interested in simultaneous confidence intervals for the weight differences between all four genotypes of the mother. First, an ANOVA model is fitted <>= foster_aov <- aov(weight ~ litgen * motgen, data = foster) @ which serves as the basis of the multiple comparisons, here with all pair-wise differences by <>= foster_hsd <- TukeyHSD(foster_aov, "motgen") foster_hsd @ A convenient \Rcmd{plot} method exists for this object and we can get a graphical representation of the multiple confidence intervals as shown in Figure~\ref{ANOVA-foster-mc}. It appears that there is only evidence for a difference in the B and J genotypes. Note that the particular method implemented in \Rcmd{TukeyHSD} is applicable only to balanced and mildly unbalanced designs (which is the case here). Alternative approaches, applicable to unbalanced designs and more general research questions, will be introduced and discussed in \Sexpr{ch("SIMC")}. \begin{figure} \begin{center} <>= plot(foster_hsd) @ \caption{Graphical presentation of multiple comparison results for the \Robject{foster} feeding data. \label{ANOVA-foster-mc}} \end{center} \end{figure} \index{Multiple comparison procedures|)} \subsection{Water Hardness and Mortality} The water hardness and mortality data for $61$ large towns in England and Wales (see Table~2.3) was analyzed in \Sexpr{ch("SI")} and here we will extend the analysis by an assessment of the differences of both hardness and mortality in the North or South. The hypothesis that the two-dimensional mean-vector of water hardness and mortality is the same for cities in the North and the South can be tested by \stress{Hotelling-Lawley} test in a multivariate analysis of variance framework. The \R{} function \Rcmd{manova} can be used to fit such a model and the corresponding \Rcmd{summary} method performs the test specified by the \Rcmd{test} argument <>= data("water", package = "HSAUR3") summary(manova(cbind(hardness, mortality) ~ location, data = water), test = "Hotelling-Lawley") @ The \Rcmd{cbind} statement in the left-hand side of the formula indicates that a \stress{multivariate} response variable is to be modeled. \index{cbind function in formula@\texttt{cbind} function in \textit{formula}} The $p$-value associated with the \stress{Hotelling-Lawley} statistic is very small and there is strong evidence that the mean vectors of the two variables are not the same in the two regions. Looking at the sample means <>= tapply(water$hardness, water$location, mean) tapply(water$mortality, water$location, mean) @ we see large differences in the two regions both in water hardness and mortality, where low mortality is associated with hard water in the South and high mortality with soft water in the North (see Figure~\ref{SI-water-sp} also). \subsection{Male Egyptian Skulls} \index{Multivariate analysis of variance (MANOVA)|(} We can begin by looking at a table of mean values for the four measurements within each of the five epochs. The measurements are available in the \Rclass{data.frame} \Robject{skulls} and we can compute the means over all epochs by <>= data("skulls", package = "HSAUR3") means <- aggregate(skulls[,c("mb", "bh", "bl", "nh")], list(epoch = skulls$epoch), mean) means @ It may also be useful to look at these means graphically and this could be done in a variety of ways. Here we construct a scatterplot matrix of the means using the code attached to Figure~\ref{ANOVA-skulls-fig}. %% %% now uses wordcloud::textplot but xlim/ylim needs to be increased %% \begin{figure} \begin{center} <>= pairs(means[,-1], panel = function(x, y) { textplot(x, y, levels(skulls$epoch), new = FALSE, cex = 0.8) }) @ \caption{Scatterplot matrix of epoch means for Egyptian \Robject{skulls} data. \label{ANOVA-skulls-fig}} \end{center} \end{figure} There appear to be quite large differences between the epoch means, at least on some of the four measurements. We can now test for a difference more formally by using MANOVA with the following \R{} code to apply each of the four possible test criteria mentioned earlier; <>= skulls_manova <- manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls) summary(skulls_manova, test = "Pillai") summary(skulls_manova, test = "Wilks") summary(skulls_manova, test = "Hotelling-Lawley") summary(skulls_manova, test = "Roy") @ The $p$-value associated with each four test criteria is very small and there is strong evidence that the skull measurements differ between the five epochs. We might now move on to investigate which epochs differ and on which variables. We can look at the univariate $F$-tests \index{F-tests@$F$-tests} for each of the four variables by using the code <>= summary.aov(skulls_manova) @ We see that the results for the maximum breadths (\Robject{mb}) and basialiveolar length (\Robject{bl}) are highly significant, with those for the other two variables, in particular for nasal heights (\Robject{nh}), suggesting little evidence of a difference. To look at the pairwise multivariate tests (any of the four test criteria are equivalent in the case of a one-way layout with two levels only) we can use the \Rcmd{summary} method and \Rcmd{manova} function as follows: <>= summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c3300BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c1850BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c200BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "cAD150"))) @ To keep the overall significance level for the set of all pairwise multivariate tests under some control (and still maintain a reasonable power), \cite{HSAUR:Stevens2001} recommends setting the nominal level $\alpha = 0.15$ and carrying out each test at the $\alpha / m$ level where $m$ is the number of tests performed. The results of the four pairwise tests suggest that as the epochs become further separated in time the four skull measurements become increasingly distinct. \index{Multivariate analysis of variance (MANOVA)|)} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_bayesian_inference.R0000644000175000017500000002605514133304507017451 0ustar nileshnilesh### R code from vignette source 'Ch_bayesian_inference.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: BI-Smoking_Mueller1940-tab ################################################### data("Smoking_Mueller1940", package = "HSAUR3") toLatex(HSAURtable(Smoking_Mueller1940), caption = paste("Smoking and lung cancer case-control study by M\\\"uller (1940).", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-15 (moderate), 16-25 (heavy), 26-35 (very heavy),", "and more than 35 (extreme)."), label = "BI-Smoking_Mueller1940-tab") ################################################### ### code chunk number 4: BI-Smoking_SchairerSchoeniger1944-tab ################################################### x <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) toLatex(HSAURtable(x, xname = "Smoking_SchairerSchoeniger1944"), caption = paste("Smoking and lung cancer case-control study by Schairer and Sch\\\"oniger (1944). Cancer other than lung cancer omitted.", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-5 (moderate), 6-10 (medium), 11-20 (heavy),", "and more than 20 (very heavy)."), label = "BI-Smoking_SchairerSchoeniger1944-tab") ################################################### ### code chunk number 5: BI-Smoking_Wassink1945-tab ################################################### data("Smoking_Wassink1945", package = "HSAUR3") toLatex(HSAURtable(Smoking_Wassink1945), caption = paste("Smoking and lung cancer case-control study by Wassink (1945).", "Smoking categories correspond to the categories used by M\\\"uller (1940)."), label = "BI-Smoking_Wassink1945-tab") ################################################### ### code chunk number 6: BI-Smoking_DollHill1950-tab ################################################### data("Smoking_DollHill1950", package = "HSAUR3") x <- as.table(Smoking_DollHill1950[,,"Male", drop = FALSE]) toLatex(HSAURtable(x, xname = "Smoking_DollHill1950"), caption = paste("Smoking and lung cancer case-control study (only males) by Doll and Hill (1950).", "The labels for the smoking categories give the number of cigarettes smoked every day."), label = "BI-Smoking_DollHill1950-tab") ################################################### ### code chunk number 7: BI-M-it ################################################### library("coin") set.seed(29) independence_test(Smoking_Mueller1940, teststat = "quad", distribution = approximate(100000)) ################################################### ### code chunk number 8: BI-M40-linit ################################################### ssc <- c(0, 1 + 14 / 2, 16 + 9 / 2, 26 + 9 / 2, 40) independence_test(Smoking_Mueller1940, teststat = "quad", scores = list(Smoking = ssc), distribution = approximate(100000)) ################################################### ### code chunk number 9: BI-expconfint ################################################### eci <- function(model) cbind("Odds (Ratio)" = exp(coef(model)), exp(confint(model))) ################################################### ### code chunk number 10: BI-M40-logreg ################################################### smoking <- ordered(rownames(Smoking_Mueller1940), levels = rownames(Smoking_Mueller1940)) contrasts(smoking) <- "contr.treatment" eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) ################################################### ### code chunk number 11: BI-M40-logreg-split ################################################### K <- diag(nlevels(smoking) - 1) K[lower.tri(K)] <- 1 contrasts(smoking) <- rbind(0, K) eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) ################################################### ### code chunk number 12: BI-SS44-it ################################################### xSS44 <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) ap <- approximate(100000) pvalue(independence_test(xSS44, teststat = "quad", distribution = ap)) pvalue(independence_test(Smoking_Wassink1945, teststat = "quad", distribution = ap)) xDH50 <- as.table(Smoking_DollHill1950[,, "Male"]) pvalue(independence_test(xDH50, teststat = "quad", distribution = ap)) ################################################### ### code chunk number 13: BI-data-M ################################################### (M <- rbind(Smoking_Mueller1940[1:2,], colSums(Smoking_Mueller1940[3:5,]))) ################################################### ### code chunk number 14: BI-data-SS ################################################### SS <- Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")] (SS <- rbind(SS[1,], colSums(SS[2:3,]), colSums(SS[4:5,]))) ################################################### ### code chunk number 15: BI-data-WDH ################################################### (W <- rbind(Smoking_Wassink1945[1:2,], colSums(Smoking_Wassink1945[3:4,]))) DH <- Smoking_DollHill1950[,, "Male"] (DH <- rbind(DH[1,], colSums(DH[2:3,]), colSums(DH[4:6,]))) ################################################### ### code chunk number 16: BI-data-all ################################################### smk <- c("Nonsmoker", "Moderate smoker", "Heavy smoker") x <- expand.grid(Smoking = ordered(smk, levels = smk), Diagnosis = factor(c("Lung cancer", "Control")), Study = c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945", "DollHill1950")) x$weights <- c(as.vector(M), as.vector(SS), as.vector(W), as.vector(DH)) ################################################### ### code chunk number 17: BI-data-contrasts ################################################### contrasts(x$Smoking) <- "contr.treatment" x <- x[rep(1:nrow(x), x$weights),] ################################################### ### code chunk number 18: BI-models ################################################### models <- lapply(levels(x$Study), function(s) glm(Diagnosis ~ Smoking, data = x, family = binomial(), subset = Study == s)) names(models) <- levels(x$Study) ################################################### ### code chunk number 19: BI-M40 ################################################### eci(models[["Mueller1940"]]) ################################################### ### code chunk number 20: BI-SS44 ################################################### eci(models[["SchairerSchoeniger1944"]]) ################################################### ### code chunk number 21: BI-M40-SS44 ################################################### mM40_SS44 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944")) eci(mM40_SS44) ################################################### ### code chunk number 22: BI-M40-SS44-W45-ML ################################################### eci(models[["Wassink1945"]]) ################################################### ### code chunk number 23: BI-M40-SS44-W45 ################################################### mM40_SS44_W45 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945")) eci(mM40_SS44_W45) ################################################### ### code chunk number 24: BI-DH50 ################################################### eci(models[["DollHill1950"]]) ################################################### ### code chunk number 25: BI-all ################################################### m_all <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial()) eci(m_all) ################################################### ### code chunk number 26: BI-all-round ################################################### r <- eci(m_all) xM <- round(r["SmokingModerate smoker", 2:3], 1) xH <- round(r["SmokingHeavy smoker", 2:3], 1) ################################################### ### code chunk number 27: BI-results ################################################### K <- diag(nlevels(x$Smoking) - 1) K[lower.tri(K)] <- 1 contrasts(x$Smoking) <- rbind(0, K) eci(glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial())) ################################################### ### code chunk number 28: BI-meta-data ################################################### y <- xtabs(~ Study + Smoking + Diagnosis, data = x) ntrtM <- margin.table(y, 1:2)[,"Moderate smoker"] nctrl <- margin.table(y, 1:2)[,"Nonsmoker"] ptrtM <- y[,"Moderate smoker","Lung cancer"] pctrl <- y[,"Nonsmoker","Lung cancer"] ntrtH <- margin.table(y, 1:2)[,"Heavy smoker"] ptrtH <- y[,"Heavy smoker","Lung cancer"] ################################################### ### code chunk number 29: BI-meta-data ################################################### library("rmeta") meta.MH(ntrt = ntrtM, nctrl = nctrl, ptrt = ptrtM, pctrl = pctrl) meta.MH(ntrt = ntrtH, nctrl = nctrl, ptrt = ptrtH, pctrl = pctrl) HSAUR3/inst/doc/Ch_analysing_longitudinal_dataI.pdf0000644000175000017500000033336014133304605022047 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 4109 /Filter /FlateDecode /N 86 /First 708 >> stream x[[w6~_MN F{=%c;IyP$F]J @JH6ݍ" `0$ be)14cCf!Y-KXCW+U2$n⑲x_&EIaP̤M0.a*4UF 3%TJ W@Fx hI `Q`413**dQ` їXHlR +V[2\#fW,5>+X|jUR_8@r*B%" ̀:fIHMF"X1)i.Cw@Dn.QP$;Dr]01 0@@@1mՌY @Vh1Eu m1shh EXY@gYǘ Ab F0 SKj`Gc@1d8NK;C E#㏌h2*F,C_/i6K`f3FGw){?ͯO?9&g|Q32f6gts=OGEGEʞC5"N!ÿW2}Ǿd yzǯ?ɂ=C4<<,)xs^b1gwKbq Y1] {,bp_x4evͮA=S ;d=^h/_0 p΀o_x=7C ~gM򂀫r<<xx`7eXg8'I6_0M=+"_@09Z 2$aNc؇EZ2_ _?ڍq;tABT`I%I`tJk HV,VW @>gYdIvV[}z ¾VӟѺƄ1Ѭp,K6ooV[~-M[7Lt[d+ѩJɉI('88I-_9%|Ŋ2Fg^-R7!uN~0Z6NJ8qf4'Cpnz͡n SV ~_IqC@ZvէCm ! dUXGFYXQ F%?dh읿6bajctzDa;F I+;6=جiv}NbtAIg|G_KG>|<7<> Ư '>|sR~a|_Bj |NGI*h~Lkǝ¿K2+O;:O5%tMUIJG5Ec! _^$JsۓSq)[v 7kU^Mf6|β\F2R$ÕC>ZȦq4磱2BOiЖI>J_-rP+t%DJ}%^WMbB-J5?5np\Ld-ԣk8)E!+=8qND"a$r67EqTwwߟS4xyt*>HUPeoNÐqnld]Ja벒%9\Coϧ#ߢ+ITFpÔH3t JL" )z^»$R)k.%|@Sx!d-&}`ꇳrqNviVgifi壽vmjXª;}۽o}˜m咽Q)DͤApc_yͭg|_0 NI4o3"*)cʺb>tWp[אO8WXniP+UDY% %k䫃cURi7 HkcD6 `u64p N٧ UW]lYtDXΧIzgSRhXE '*FGɧ*iVRR&s-4z2Hq@ +!eSPR+`#5RVcmH(05R`3l.G{F=Cc%9ߨG yM=jAiXvUuZ7$eu_#_%jk:(U#)}[GtiSp=7zM5fcNv_2~NK}klkb;o.ѭTyؗ mp#-fW3^$ >/ݜWJ:-to` 1[C#<ƽ,Kg)P,+,CнKčv'E(\gY׭ˎWuޡ}-VHb%4Uj:^tҩ{t8ϗgdz%ӌhsm}VIu.Gsqj-Oǫ6vgš0`;KW#W5.T î0NV_~[QTԬ/ShYWKW+3kK7]'* u7&{W^ /] {$jcLwչUku3TZht҈Dd"MKPItnqJGrHL[ieTNoK4~vTNXhJ_?uՆҖy|i+3K[:-vM"-mm+&vϧzԻ~(DQxV*YE#mK۱1A=I耴۶7qL~7>FG$PqjZE2PtIe|W沃U\*DLѶl@(PtAA%6p&H4Zy|!.;Bm' 7H{@I D,z NF>L'":C? 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Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Simultaneous Inference and Multiple Comparisons} %%\VignetteDepends{lme4,multcomp,coin,sandwich} \setcounter{chapter}{14} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("multcomp") library("coin") library("sandwich") library("lme4") @ \chapter[Simultaneous Inference and Multiple Comparisons]{Simultaneous Inference and Multiple Comparisons: Genetic Components of Alcoholism, Deer Browsing Intensities, and Cloud Seeding \label{SIMC}} \section{Introduction} \section{Simultaneous Inference and Multiple Comparisons} \section{Analysis Using \R{}} \subsection{Genetic Components of Alcoholism} We start with a graphical display of the data. Three parallel boxplots shown in Figure~\ref{SIMC-alpha-data-figure} indicate increasing expression levels of alpha synuclein mRNA for longer \textit{NACP}-REP1 alleles. %%\setkeys{Gin}{width=0.6\textwidth} \begin{figure}[t] \begin{center} <>= n <- table(alpha$alength) levels(alpha$alength) <- abbreviate(levels(alpha$alength), 4) plot(elevel ~ alength, data = alpha, varwidth = TRUE, ylab = "Expression Level", xlab = "NACP-REP1 Allele Length") axis(3, at = 1:3, labels = paste("n = ", n)) @ \caption{Distribution of levels of expressed alpha synuclein mRNA in three groups defined by the \textit{NACP}-REP1 allele lengths. \label{SIMC-alpha-data-figure}} \end{center} \end{figure} \index{Tukey honest significant differences|(} In order to model this relationship, we start fitting a simple one-way ANOVA model of the form $y_{ij} = \mu + \gamma_i + \varepsilon_{ij}$ to the data with independent normal errors $\varepsilon_{ij} \sim \N(0, \sigma^2)$, $j \in \{\text{short}, \text{intermediate}, \text{long}\}$, and $i = 1, \dots, n_j$. The parameters $\mu + \gamma_\text{short}$, $\mu + \gamma_\text{intermediate}$ and $\mu + \gamma_\text{long}$ can be interpreted as the mean expression levels in the corresponding groups. As already discussed in \Sexpr{ch("ANOVA")}, this model description is overparameterized. A standard approach is to consider a suitable re-parameterization. The so-called ``treatment contrast'' vector $% \theta = (\mu, \gamma_\text{intermediate} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{short})$ (the default re-parameterization used as elemental parameters in \R{}) is one possibility and is equivalent to imposing the restriction $\gamma_\text{short} = 0$. In addition, we define all comparisons among our three groups by choosing $\K$ such that $\K \theta$ contains all three group differences (Tukey's all-pairwise comparisons): %%' \begin{eqnarray*} \K_\text{Tukey} = \left( \begin{array}{rrr} 0 & 1 & 0 \\%% 0 & 0 & 1 \\%% 0 & -1 & 1% \end{array} \right) \end{eqnarray*} with parameters of interest \begin{eqnarray*} \vartheta_\text{Tukey} = \K_\text{Tukey} \theta = (\gamma_\text{intermediate} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{short}, \gamma_\text{long} - \gamma_\text{intermediate}). \end{eqnarray*} The function \Rcmd{glht} (for generalized linear hypothesis) from package \Rpackage{multcomp} \citep{PKG:multcomp,HSAUR:HothornBretzWestfall2008} takes the fitted \Rclass{aov} object and a description of the matrix $\K$. Here, we use the \Rcmd{mcp} function to set up the matrix of all pairwise differences for the model parameters associated with factor \Robject{alength}: <>= library("multcomp") amod <- aov(elevel ~ alength, data = alpha) amod_glht <- glht(amod, linfct = mcp(alength = "Tukey")) @ The matrix $\K$ reads <>= amod_glht$linfct @ The \Robject{amod\_glht} object now contains information about the estimated linear function $\hat{\vartheta}$ and their covariance matrix which can be inspected via the \Rcmd{coef} and \Rcmd{vcov} methods: <>= coef(amod_glht) vcov(amod_glht) @ The \Rcmd{summary} and \Rcmd{confint} methods can be used to compute a summary statistic including adjusted $p$-values and simultaneous confidence intervals, respectively: <>= confint(amod_glht) summary(amod_glht) @ Because of the variance heterogeneity that can be observed in Figure~\ref{SIMC-alpha-data-figure}, one might be concerned with the validity of the above results stating that there is no difference between any combination of the three allele lengths. A sandwich estimator might be more appropriate in this situation, and the \Rarg{vcov} argument can be used to specify a function to compute some alternative covariance estimator as follows: <>= amod_glht_sw <- glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich) summary(amod_glht_sw) @ We use the \Rcmd{sandwich} function from package \Rpackage{sandwich} \citep{PKG:sandwich, HSAUR:Zeileis2006} which provides us with a heteroscedasticity-consistent estimator of the covariance matrix. This result is more in line with previously published findings for this study obtained from non-parametric test procedures such as the Kruskal-Wallis test. A comparison of the simultaneous confidence intervals calculated based on the ordinary and sandwich estimator is given in Figure~\ref{SIMC-alpha-confint-plot}. %%\setkeys{Gin}{width=0.95\textwidth} \begin{figure}[h] \begin{center} <>= par(mai = par("mai") * c(1, 2.1, 1, 0.5)) layout(matrix(1:2, ncol = 2)) ci1 <- confint(glht(amod, linfct = mcp(alength = "Tukey"))) ci2 <- confint(glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich)) ox <- expression(paste("Tukey (ordinary ", bold(S)[n], ")")) sx <- expression(paste("Tukey (sandwich ", bold(S)[n], ")")) plot(ci1, xlim = c(-0.6, 2.6), main = ox, xlab = "Difference", ylim = c(0.5, 3.5)) plot(ci2, xlim = c(-0.6, 2.6), main = sx, xlab = "Difference", ylim = c(0.5, 3.5)) @ \caption{Simultaneous confidence intervals for the \Robject{alpha} data based on the ordinary covariance matrix (left) and a sandwich estimator (right). \label{SIMC-alpha-confint-plot}} \end{center} \end{figure} It should be noted that this data set is heavily unbalanced; see Figure~\ref{SIMC-alpha-data-figure}, and therefore the results obtained from function \Rcmd{TukeyHSD} might be less accurate. \index{Tukey honest significant differences|)} \subsection{Deer Browsing} \index{Generalized linear mixed model|(} Since we have to take the spatial structure of the deer browsing data into account, we cannot simply use a logistic regression model as introduced in \Sexpr{ch("GLM")}. One possibility is to apply a mixed logistic regression model \citep[using package \Rpackage{lme4},][]{PKG:lme4} with random intercept accounting for the spatial variation of the trees. These models have already been discussed in \Sexpr{ch("ALDII")}. For each plot nested within a set of five plots oriented on a 100m transect (the location of the transect is determined by a predefined equally spaced lattice of the area under test), a random intercept is included in the model. Essentially, trees that are close to each other are handled like repeated measurements in a longitudinal analysis. We are interested in probability estimates and confidence intervals for each tree species. Each of the five fixed parameters of the model corresponds to one species (in absence of a global intercept term); therefore, $\K = \text{diag}(5)$ is the linear function we are interested in: <>= trees513 <- subset(trees513, !species %in% c("fir", "ash/maple/elm/lime", "softwood (other)")) trees513$species <- trees513$species[,drop = TRUE] levels(trees513$species)[nlevels(trees513$species)] <- "hardwood" @ <>= mmod <- glmer(damage ~ species - 1 + (1 | lattice / plot), data = trees513, family = binomial()) K <- diag(length(fixef(mmod))) K @ In order to help interpretation, the names of the tree species and the corresponding sample sizes (computed via \Rcmd{table}) are added to $\K$ as row names; this information will carry through all subsequent steps of our analysis: <>= colnames(K) <- rownames(K) <- paste(gsub("species", "", names(fixef(mmod))), " (", table(trees513$species), ")", sep = "") K @ Based on $\K$, we first compute simultaneous confidence intervals for $\K \theta$ and transform these into probabilities. Note that $\left(1 + \exp(- \hat{\vartheta})\right)^{-1}$ (cf.~Equation~\ref{GLM:logitexp}) is the vector of estimated probabilities; simultaneous confidence intervals can be transformed to the probability scale in the same way: <>= ci <- confint(glht(mmod, linfct = K)) ci$confint <- 1 - binomial()$linkinv(ci$confint) ci$confint[,2:3] <- ci$confint[,3:2] @ The result is shown in Figure~\ref{SIMC-trees-plot}. Browsing is more frequent in hardwood but especially small oak trees are severely at risk. Consequently, the local authorities increased the number of roe deers to be harvested in the following years. %%The large confidence interval for ash, maple, elm and lime %%trees is caused by the small sample size. %%\setkeys{Gin}{width=0.8\textwidth} \begin{figure}[t] \begin{center} <>= plot(ci, xlab = "Probability of Damage Caused by Browsing", xlim = c(0, 0.5), main = "", ylim = c(0.5, 5.5)) @ \caption{Probability of damage caused by roe deer browsing for five tree species. Sample sizes are given in brackets. \label{SIMC-trees-plot}} \end{center} \end{figure} \index{Generalized linear mixed model|)} \subsection{Cloud Seeding} \index{Confidence band|(} In \Sexpr{ch("MLR")} we studied the dependency of rainfall on S-Ne values by means of linear models. Because the number of observations is small, an additional assessment of the variability of the fitted regression lines is interesting. Here, we are interested in a confidence band around some estimated regression line, i.e., a confidence region which covers the true but unknown regression line with probability greater or equal $1 - \alpha$. It is straightforward to compute \stress{pointwise} confidence intervals but we have to make sure that the type I error is controlled for all $x$ values simultaneously. Consider the simple linear regression model \begin{eqnarray*} \text{rainfall}_i = \beta_0 + \beta_1 \text{sne}_i + \varepsilon_i \end{eqnarray*} where we are interested in a confidence band for the predicted rainfall, i.e., the values $\hat{\beta}_0 + \hat{\beta}_1 \text{sne}_i$ for some observations $\text{sne}_i$. (Note that the estimates $\hat{\beta}_0$ and $\hat{\beta}_1$ are random variables.) We can formulate the problem as a linear combination of the regression coefficients by multiplying a matrix $\K$ to a grid of S-Ne values (ranging from $1.5$ to $4.5$, say) from the left to the elemental parameters $\theta = (\beta_0, \beta_1)$: \begin{eqnarray*} \K \theta = \left( \begin{array}{rr} 1 & 1.50 \\%% 1 & 1.75 \\%% \vdots & \vdots \\%% 1 & 4.25 \\%% 1 & 4.50 % \end{array} \right)\theta = (\beta_0 + \beta_1 1.50, \beta_0 + \beta_1 1.75, \dots, \beta_0 + \beta_1 4.50) = \vartheta. \end{eqnarray*} Simultaneous confidence intervals for all the parameters of interest $\vartheta$ form a confidence band for the estimated regression line. We implement this idea for the \Robject{clouds} data writing a small reusable function as follows: <>= confband <- function(subset, main) { mod <- lm(rainfall ~ sne, data = clouds, subset = subset) sne_grid <- seq(from = 1.5, to = 4.5, by = 0.25) K <- cbind(1, sne_grid) sne_ci <- confint(glht(mod, linfct = K)) plot(rainfall ~ sne, data = clouds, subset = subset, xlab = "S-Ne criterion", main = main, xlim = range(clouds$sne), ylim = range(clouds$rainfall)) abline(mod) lines(sne_grid, sne_ci$confint[,2], lty = 2) lines(sne_grid, sne_ci$confint[,3], lty = 2) } @ The function \Rcmd{confband} basically fits a linear model using \Rcmd{lm} to a subset of the data, sets up the matrix $\K$ as shown above and nicely plots both the regression line and the confidence band. Now, this function can be reused to produce plots similar to Figure~\ref{MLR-clouds-lmplot} separately for days with and without cloud seeding in Figure~\ref{SIMC-clouds-lmplot}. For the days without seeding, there is more uncertainty about the true regression line compared to the days with cloud seeding. Clearly, this is caused by the larger variability of the observations in the left part of the figure. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) confband(clouds$seeding == "no", main = "No seeding") confband(clouds$seeding == "yes", main = "Seeding") @ \caption{Regression relationship between S-Ne criterion and rainfall with and without seeding. The confidence bands cover the area within the dashed curves. \label{SIMC-clouds-lmplot}} \end{center} \end{figure} \index{Confidence band|)} \section{Summary of Findings} \begin{description} \item[Genetic components of alcoholism] We were interested in studying all pairwise differences in expression levels for three groups of subjects defined by allele length. Overall, there seem to be different expression levels for short and long alleles but no difference between these two groups and the intermediate group. \item[Deer browsing] For a number of tree species, the simultaneous confidence intervals for the probability of browsing damage show that there is rather precise information about browsing damage for spruce and pine with more variability for the broad-leaf species. For oak, more than $\Sexpr{round(ci$confint["oak (1258)", 2], 2)}\%$ of the trees are damaged. \item[Cloud seeding] Confidence bands for the estimated effects help to identify days where the uncertainty about rainfall is largest. \end{description} \section{Final Comments} Multiple comparisons in linear models have been in use for a long time. The \Rpackage{multcomp} package extends much of the theory to a broad class of parametric and semi-parametric statistical models, which allows for a unified treatment of multiple comparisons and other simultaneous inference procedures in generalized linear models, mixed models, models for censored data, robust models, etc. Honest decisions based on simultaneous inference procedures maintaining a pre-specified familywise error rate (at least asymptotically) can be derived from almost all classical and modern statistical models. The technical details and more examples can be found in \cite{HSAUR:HothornBretzWestfall2008} and the package vignettes of package \Rpackage{multcomp} \citep{PKG:multcomp}. \section*{Exercises} \begin{description} \exercise Compare the results of \Rcmd{glht} and \Rcmd{TukeyHSD} on the \Robject{alpha} data. \exercise Consider the linear model fitted to the clouds data as summarized in Figure~\ref{MLR-clouds-summary}. Set up a matrix $\K$ corresponding to the global null hypothesis that all interaction terms present in the model are zero. Test both the global hypothesis and all hypotheses corresponding to each of the interaction terms. Which interaction remains significant after adjustment for multiple testing? \exercise For the logistic regression model presented in Figure~\ref{GLM-womensrole-summary-2} perform a multiplicity adjusted test on all regression coefficients (except for the intercept) being zero. Do the conclusions drawn in \Sexpr{ch("GLM")} remain valid? \end{description} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_conditional_inference.R0000644000175000017500000001631314133304517020156 0ustar nileshnilesh### R code from vignette source 'Ch_conditional_inference.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: CI-roomwidth-ties ################################################### data("roomwidth", package = "HSAUR3") nobs <- table(roomwidth$unit) ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - length(unique(x))) library("coin") ################################################### ### code chunk number 4: CI-roomwidth-data ################################################### data("roomwidth", package = "HSAUR3") convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) feet <- roomwidth$unit == "feet" meter <- !feet y <- roomwidth$width * convert ################################################### ### code chunk number 5: CI-roomwidth-teststat ################################################### T <- mean(y[feet]) - mean(y[meter]) T ################################################### ### code chunk number 6: CI-roomwidth-permutation ################################################### meandiffs <- double(9999) for (i in 1:length(meandiffs)) { sy <- sample(y) meandiffs[i] <- mean(sy[feet]) - mean(sy[meter]) } ################################################### ### code chunk number 7: CI-roomwidth-plot ################################################### hist(meandiffs) abline(v = T, lty = 2) abline(v = -T, lty = 2) ################################################### ### code chunk number 8: CI-roomwidth-pvalue ################################################### greater <- abs(meandiffs) > abs(T) mean(greater) ################################################### ### code chunk number 9: CI-roomwidth-pvalue ################################################### binom.test(sum(greater), length(greater))$conf.int ################################################### ### code chunk number 10: CI-roomwidth-coin ################################################### library("coin") independence_test(y ~ unit, data = roomwidth, distribution = exact()) ################################################### ### code chunk number 11: CI-roomwidth-coin ################################################### wilcox_test(y ~ unit, data = roomwidth, distribution = exact()) ################################################### ### code chunk number 12: CI-suicides-ft ################################################### data("suicides", package = "HSAUR3") fisher.test(suicides) ################################################### ### code chunk number 13: CI-suicides-chisq ################################################### ftp <- round(fisher.test(suicides)$p.value, 3) ctp <- round(chisq.test(suicides)$p.value, 3) ################################################### ### code chunk number 14: CI-Lanza-data ################################################### data("Lanza", package = "HSAUR3") xtabs(~ treatment + classification + study, data = Lanza) ################################################### ### code chunk number 15: CI-width ################################################### options(width = 65) ################################################### ### code chunk number 16: CI-Lanza-singleI ################################################### library("coin") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "I") ################################################### ### code chunk number 17: CI-Lanza-singleII ################################################### cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II") ################################################### ### code chunk number 18: CI-Lanza-singleIIa ################################################### p <- cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II", distribution = approximate(B = 19999)) pvalue(p) ################################################### ### code chunk number 19: CI-Lanza-singleIII-IV ################################################### cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "III") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "IV") ################################################### ### code chunk number 20: CI-Lanza-all ################################################### cmh_test(classification ~ treatment | study, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30))) ################################################### ### code chunk number 21: CI-anomalies ################################################### anomalies <- c(235, 23, 3, 0, 41, 35, 8, 0, 20, 11, 11, 1, 2, 1, 3, 1) anomalies <- as.table(matrix(anomalies, ncol = 4, dimnames = list(MD = 0:3, RA = 0:3))) anomalies ################################################### ### code chunk number 22: CI-anomalies-mh ################################################### mh_test(anomalies) ################################################### ### code chunk number 23: CI-anomalies-ordered ################################################### mh_test(anomalies, scores = list(response = c(0, 1, 2, 3))) HSAUR3/inst/doc/Ch_density_estimation.Rnw0000644000175000017500000004716314133304452020122 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Density Estimation} %%\VignetteDepends{flexmix,KernSmooth,boot} \setcounter{chapter}{7} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} <>= x <- library("KernSmooth") x <- library("flexmix") x <- library("boot") @ \chapter[Density Estimation]{Density Estimation: Erupting Geysers and Star Clusters \label{DE}} \section{Introduction} \section{Density Estimation} The three kernel functions are implemented in \R{} as shown in lines 1--3 of Figure~\ref{DE-kernel-fig}. For some grid \Robject{x}, the kernel functions are plotted using the \R{} statements in lines 5--11 (Figure~\ref{DE-kernel-fig}). \numberSinput \begin{figure} \begin{center} <>= rec <- function(x) (abs(x) < 1) * 0.5 tri <- function(x) (abs(x) < 1) * (1 - abs(x)) gauss <- function(x) 1/sqrt(2*pi) * exp(-(x^2)/2) x <- seq(from = -3, to = 3, by = 0.001) plot(x, rec(x), type = "l", ylim = c(0,1), lty = 1, ylab = expression(K(x))) lines(x, tri(x), lty = 2) lines(x, gauss(x), lty = 3) legend(-3, 0.8, legend = c("Rectangular", "Triangular", "Gaussian"), lty = 1:3, title = "kernel functions", bty = "n") @ \caption{Three commonly used kernel functions. \label{DE-kernel-fig}} \end{center} \end{figure} \rawSinput <>= w <- options("width")$w options(width = 66) @ The kernel estimator $\hat{f}$ is a sum of `bumps' placed at the observations. %' The kernel function determines the shape of the bumps while the window width $h$ determines their width. \index{Windows, in kernel density estimation} Figure~\ref{DE-bumps} \citep[redrawn from a similar plot in][]{HSAUR:Silverman1986} shows the individual bumps $n^{-1}h^{-1} K((x - x_i) / h)$, as well as the estimate $\hat{f}$ obtained by adding them up for an artificial set of data points <>= x <- c(0, 1, 1.1, 1.5, 1.9, 2.8, 2.9, 3.5) n <- length(x) @ For a grid <>= xgrid <- seq(from = min(x) - 1, to = max(x) + 1, by = 0.01) @ on the real line, we can compute the contribution of each measurement in \Robject{x}, with $h = 0.4$, by the Gaussian kernel (defined in Figure~\ref{DE-kernel-fig}, line 3) as follows; <>= h <- 0.4 bumps <- sapply(x, function(a) gauss((xgrid - a)/h)/(n * h)) @ A plot of the individual bumps and their sum, the kernel density estimate $\hat{f}$, is shown in Figure~\ref{DE-bumps}. <>= options(width = w) @ \numberSinput \begin{figure} \begin{center} <>= plot(xgrid, rowSums(bumps), ylab = expression(hat(f)(x)), type = "l", xlab = "x", lwd = 2) rug(x, lwd = 2) out <- apply(bumps, 2, function(b) lines(xgrid, b)) @ \caption{Kernel estimate showing the contributions of Gaussian kernels evaluated for the individual observations with bandwidth $h = 0.4$. \label{DE-bumps}} \end{center} \end{figure} \rawSinput \begin{figure} \begin{center} <>= epa <- function(x, y) ((x^2 + y^2) < 1) * 2/pi * (1 - x^2 - y^2) x <- seq(from = -1.1, to = 1.1, by = 0.05) epavals <- sapply(x, function(a) epa(a, x)) persp(x = x, y = x, z = epavals, xlab = "x", ylab = "y", zlab = expression(K(x, y)), theta = -35, axes = TRUE, box = TRUE) @ \caption{Epanechnikov kernel for a grid between $(-1.1, -1.1)$ and $(1.1, 1.1)$. \label{DE-epakernel-fig}} \end{center} \end{figure} \section{Analysis Using \R{}} \numberSinput \begin{figure} \begin{center} <>= data("faithful", package = "datasets") x <- faithful$waiting layout(matrix(1:3, ncol = 3)) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Gaussian kernel", border = "gray") lines(density(x, width = 12), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Rectangular kernel", border = "gray") lines(density(x, width = 12, window = "rectangular"), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Triangular kernel", border = "gray") lines(density(x, width = 12, window = "triangular"), lwd = 2) rug(x) @ \caption{Density estimates of the geyser eruption data imposed on a histogram of the data. \label{DE:faithfuldens}} \end{center} \end{figure} \rawSinput \begin{figure} \begin{center} <>= library("KernSmooth") data("CYGOB1", package = "HSAUR3") CYGOB1d <- bkde2D(CYGOB1, bandwidth = sapply(CYGOB1, dpik)) contour(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity") @ \caption{A contour plot of the bivariate density estimate of the \Robject{CYGOB1} data, i.e., a two-dimensional graphical display for a three-dimensional problem. \label{DE:CYGOB12Dcontour}} \end{center} \end{figure} \begin{figure} \begin{center} <>= persp(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity", zlab = "estimated density", theta = -35, axes = TRUE, box = TRUE) @ \caption{The bivariate density estimate of the \Robject{CYGOB1} data, here shown in a three-dimensional fashion using the \Rcmd{persp} function. \label{DE:CYGOB12Dpersp}} \end{center} \end{figure} \subsection{A Parametric Density Estimate for the Old Faithful Data \label{DE-waiting}} <>= logL <- function(param, x) { d1 <- dnorm(x, mean = param[2], sd = param[3]) d2 <- dnorm(x, mean = param[4], sd = param[5]) -sum(log(param[1] * d1 + (1 - param[1]) * d2)) } startparam <- c(p = 0.5, mu1 = 50, sd1 = 3, mu2 = 80, sd2 = 3) opp <- optim(startparam, logL, x = faithful$waiting, method = "L-BFGS-B", lower = c(0.01, rep(1, 4)), upper = c(0.99, rep(200, 4))) @ \newpage <>= opp @ <>= print(opp[names(opp) != "message"]) @ Of course, optimizing the appropriate likelihood `by hand' %' is not very convenient. In fact, (at least) two packages offer high-level functionality for estimating mixture models. The first one is package \Rpackage{mclust} \citep{PKG:mclust} implementing the methodology described in \cite{HSAUR:FraleyRaftery2002}. Here, a Bayesian information criterion (BIC) is applied to choose the form of the mixture model: \index{Bayesian Information Criterion (BIC)} <>= library("mclust") @ <>= library("mclust") mc <- Mclust(faithful$waiting) mc @ and the estimated means are <>= mc$parameters$mean @ with estimated standard deviation (found to be equal within both groups) <>= sqrt(mc$parameters$variance$sigmasq) @ The proportion is $\hat{p} = \Sexpr{round(mc$parameters$pro[1], 2)}$. The second package is called \Rpackage{flexmix} whose functionality is described by \cite{HSAUR:Leisch2004}. A mixture of two normals can be fitted using <>= library("flexmix") fl <- flexmix(waiting ~ 1, data = faithful, k = 2) @ with $\hat{p} = \Sexpr{round(fl@prior, 2)}$ and estimated parameters <>= parameters(fl, component = 1) parameters(fl, component = 2) @ \begin{figure} \begin{center} <>= opar <- as.list(opp$par) rx <- seq(from = 40, to = 110, by = 0.1) d1 <- dnorm(rx, mean = opar$mu1, sd = opar$sd1) d2 <- dnorm(rx, mean = opar$mu2, sd = opar$sd2) f <- opar$p * d1 + (1 - opar$p) * d2 hist(x, probability = TRUE, xlab = "Waiting times (in min.)", border = "gray", xlim = range(rx), ylim = c(0, 0.06), main = "") lines(rx, f, lwd = 2) lines(rx, dnorm(rx, mean = mean(x), sd = sd(x)), lty = 2, lwd = 2) legend(50, 0.06, lty = 1:2, bty = "n", legend = c("Fitted two-component mixture density", "Fitted single normal density")) @ \caption{Fitted normal density and two-component normal mixture for geyser eruption data. \label{DE:2Dplot}} \end{center} \end{figure} \index{Bootstrap approach|(} We can get standard errors for the five parameter estimates by using a bootstrap approach \citep[see][]{HSAUR:EfronTibshirani1993}. The original data are slightly perturbed by drawing $n$ out of $n$ observations \stress{with replacement} and those artificial replications of the original data are called \stress{bootstrap samples}. Now, we can fit the mixture for each bootstrap sample and assess the variability of the estimates, for example using confidence intervals. \index{Confidence interval!derived from bootstrap samples} Some suitable \R{} code based on the \Rcmd{Mclust} function follows. First, we define a function that, for a bootstrap sample \Robject{indx}, fits a two-component mixture model and returns $\hat{p}$ and the estimated means (note that we need to make sure that we always get an estimate of $p$, not $1 - p$): <>= library("boot") fit <- function(x, indx) { a <- Mclust(x[indx], minG = 2, maxG = 2, modelNames="E")$parameters if (a$pro[1] < 0.5) return(c(p = a$pro[1], mu1 = a$mean[1], mu2 = a$mean[2])) return(c(p = 1 - a$pro[1], mu1 = a$mean[2], mu2 = a$mean[1])) } @ The function \Rcmd{fit} can now be fed into the \Rcmd{boot} function \citep{PKG:boot} for bootstrapping (here $1000$ bootstrap samples are drawn) \begin{Schunk} \begin{Sinput} R> bootpara <- boot(faithful$waiting, fit, R = 1000) \end{Sinput} \end{Schunk} <>= bootparafile <- system.file("cache", "DE-bootpara.rda", package = "HSAUR3") if (file.exists(bootparafile)) { load(bootparafile) } else { bootpara <- boot(faithful$waiting, fit, R = 1000) } @ We assess the variability of our estimates $\hat{p}$ by means of adjusted bootstrap percentile (BCa) confidence intervals, which for $\hat{p}$ can be obtained from <>= boot.ci(bootpara, type = "bca", index = 1) @ We see that there is a reasonable variability in the mixture model; however, the means in the two components are rather stable, as can be seen from <>= boot.ci(bootpara, type = "bca", index = 2) @ for $\hat{\mu}_1$ and for $\hat{\mu}_2$ from <>= boot.ci(bootpara, type = "bca", index = 3) @ Finally, we show a graphical representation of both the bootstrap distribution of the mean estimates \stress{and} the corresponding confidence intervals. For convenience, we define a function for plotting, namely <>= bootplot <- function(b, index, main = "") { dens <- density(b$t[,index]) ci <- boot.ci(b, type = "bca", index = index)$bca[4:5] est <- b$t0[index] plot(dens, main = main) y <- max(dens$y) / 10 segments(ci[1], y, ci[2], y, lty = 2) points(ci[1], y, pch = "(") points(ci[2], y, pch = ")") points(est, y, pch = 19) } @ The element \Robject{t} of an object created by \Rcmd{boot} contains the bootstrap replications of our estimates, i.e., the values computed by \Rcmd{fit} for each of the $1000$ bootstrap samples of the geyser data. First, we plot a simple density estimate and then construct a line representing the confidence interval. We apply this function to the bootstrap distributions of our estimates $\hat{\mu}_1$ and $\hat{\mu}_2$ in Figure~\ref{DE-bootplot}. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) bootplot(bootpara, 2, main = expression(mu[1])) bootplot(bootpara, 3, main = expression(mu[2])) @ \caption{Bootstrap distribution and confidence intervals for the mean estimates of a two-component mixture for the geyser data. \label{DE-bootplot}} \end{center} \end{figure} \index{Bootstrap approach|)} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_quantile_regression.pdf0000644000175000017500000062030514133304612020265 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 4033 /Filter /FlateDecode /N 61 /First 488 >> stream x;w6?qF A2Mz--6Yt(vY{{@R(9S }A&@ 1D@1A [ Y@69C"aqDe1D(" uLB"LsLJm(mx ӑ?$2Ni"PL%Ę .ۆBfJd66ԁf 9$ Ȧ9|Oa$p(s1(Ð@v@< G(rY|?b1KLrʹ! d-7 8p8ѰG'PG rLpf"5!c!HfӀ0ĢYa/rn`V_*0>NCŕsоL j4c"+WFY/#\D]x{Es#?(:z֙ !6aba2Ui;wȝ?A3zSz; pP<0(V B3A%B.BN`:+D+A}JmL3LhD~-β[:Pli`Qoї۽zuʠZA#I₫_RUX%-H\3" G"nbşܓX<|A$0o͸7A3a]"|$;6#9 cJP Уw1l`Ȳ ¸f<{ܰA=I@წŐ[oh8U$xH,e U*WK%9:N^B~"n9.M^sxJr$GaGp K^N (zizo'nS5]`apo #Jr{ S4RgjCKTo/F3JNӌfHh ւ^-SԄ ˦`R,dpmyU axLc:G8os髨~1ތ Y0ŪZ)HXݹ?=rPY w^܇78ނ]< 2.b{E2?)/xյk>ʜCR(PֲX2&D7NvS%-Aހo rWkrڿ~^TkЉ*;ߠ5%%֤?F IP=ڂ$Lȃst'*}%LMo4D'dE=.vFP׏[(58U3T ibTiZ5\J\*(F 2Q]` g d •3Rn aK&wT}Q_ȺݴcrY r}0BPf¯S~ؑ>R}s =f{r!DCf܈ɈGvntXe:&&.)k26^}]ٿ#S32Mt4d DBxs>hGꦺ[0.v+/a:G~}tC<OGuCyϋj>~ŠT$5ÞZt-KɠJ}.UpTh&=کSir + ;k!IF`ʲѴ*5*|(=\4j6k`5#d2doWf"hdߧwK?YM㳥d-zkۺ&57u5-ZFxl@Eb(zLE^YE^RuKl*4*.k#\Ciq]4(h'"+2+rJ@VUEd{jK隉Z;$gY1G +];ˍ]"s  ,g25y28+_ޗҪV䛖y1.dK%+XOL-HVy,h[enp|%J@\]]be|`Nʁxhpy0`ڢWb1|Dgu6 CՀi5X5TW Bk0P]Xu0 T@h`Ձ L LJ!tQG}s̱{qVݡ:֬Ys']6aa:!6)zCF. Ŷmq֭[wI'_Oްa)rꩧvvvvuuuwwoܸq```ӦMCCC###ccc7o[lٺum۶o߾cǎ;wڵkgϞN;O?3\ם, b󼩩陙ݻo߾R4;;[sssðRDQTV8p3<:9IJj`,ցh`j@5`p VԀj4 :ցh`j@5`p V@R@4050 B+s=;/ /./K/.˯+򪫮ꫯk뮻oono[on;{x|zyG}{ǟx'|򩧞z駟yg}{_x_|^z_yW_}^{x7|zyw}{??>?O?>Ͽ/򫯾믿o~_~?hOvt˦riwh4NB2w[3`FB"RM[9ILw/>Z*V-5.k: ĪΊ첒Vd3ÅvX,7q…h)y!B 9n@CiDZeũb.TQu-d(M}TRfLsTQ?ÎO7v"qc Vm=$ncႺ%cs}~yd0WN6D~:gVΔg-'X` a93OwBy`"F_C:H!9f̡02)ϙplK7Ԋ劒[S1&ža-bHIPR1f+h/耀e?5偭eW!Gk #R{@N-OWkbB(^_>)vNZHPѤ~.#>+ iMmoendstream endobj 63 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:46+02:00 2021-10-18T16:49:46+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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V~-[ueK3)?C&Q1~j8:N-q^è".Dh-|-{+[K24ph'YݳRg4ㅳYLf!*ohBW(Jf9hG+%4[I 5A-$K> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 160 /ID [<31d0afc5d78ce9ba3ae73d6fb5219666><807e07c6c47e180ab3240a33fc2bb4f5>] >> stream xcb&F~0 $8JҜ `vf W^!OP?(̙HA%xDrHɼDJH :dW9>6s؂P)x DGA$~`r d64FAd&ع n endstream endobj startxref 204554 %%EOF HSAUR3/inst/doc/Ch_simple_inference.Rnw0000644000175000017500000005240414133304452017510 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Simple Inference} %%\VignetteDepends{vcd} \setcounter{chapter}{2} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Simple Inference]{Simple Inference: Guessing Lengths, Wave Energy, Water Hardness, Piston Rings, and Rearrests of Juveniles \label{SI}} \section{Introduction} <>= library("vcd") if (!interactive()) { print.htest <- function (x, digits = 4, quote = TRUE, prefix = "", ...) { cat("\n") cat(strwrap(x$method, prefix = "\t"), sep = "\n") cat("\n") cat("data: ", x$data.name, "\n") out <- character() if (!is.null(x$statistic)) out <- c(out, paste(names(x$statistic), "=", format(round(x$statistic, 4)))) if (!is.null(x$parameter)) out <- c(out, paste(names(x$parameter), "=", format(round(x$parameter, 3)))) if (!is.null(x$p.value)) { fp <- format.pval(x$p.value, digits = digits) out <- c(out, paste("p-value", if (substr(fp, 1, 1) == "<") fp else paste("=", fp))) } cat(strwrap(paste(out, collapse = ", ")), sep = "\n") if (!is.null(x$conf.int)) { cat(format(100 * attr(x$conf.int, "conf.level")), "percent confidence interval:\n", format(c(x$conf.int[1], x$conf.int[2])), "\n") } if (!is.null(x$estimate)) { cat("sample estimates:\n") print(x$estimate, ...) } cat("\n") invisible(x) } } @ \section{Statistical Tests} \section{Analysis Using \R{}} \subsection{Estimating the Width of a Room} The data shown in Table~\ref{SI-rw-tab} are available as \Robject{roomwidth} \Rclass{data.frame} from the \Rpackage{HSAUR3} package and can be attached by using <>= data("roomwidth", package = "HSAUR3") @ If we convert the estimates of the room width in meters into feet by multiplying each by $3.28$ then we would like to test the hypothesis that the mean of the population of `metre' estimates is equal to the mean %' of the population of `feet' estimates. We shall do this first %' by using an independent samples $t$-test, but first it is good practice to check, informally at least, the normality and equal variance assumptions. Here we can use a combination of numerical and graphical approaches. The first step should be to convert the meter estimates into feet by a factor <>= convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) @ which equals one for all feet measurements and $3.28$ for the measurements in meters. Now, we get the usual summary statistics and standard deviations of each set of estimates using <>= tapply(roomwidth$width * convert, roomwidth$unit, summary) tapply(roomwidth$width * convert, roomwidth$unit, sd) @ where \Rcmd{tapply} applies \Rcmd{summary}, or \Rcmd{sd}, to the converted widths for both groups of measurements given by \Robject{roomwidth\$unit}. A boxplot of each set of estimates might be useful and is depicted in Figure~\ref{SI-rw-bxp}. The \Rcmd{layout} function (line 1 in Figure~\ref{SI-rw-bxp}) divides the plotting area into three parts. The \Rcmd{boxplot} function produces a boxplot in the upper part and the two \Rcmd{qqnorm} statements in lines 7 and 10 set up the normal probability plots that can be used to assess the normality assumption of the $t$-test. \index{Normal probability plot} \numberSinput \begin{figure} \begin{center} <>= layout(matrix(c(1,2,1,3), nrow = 2, ncol = 2, byrow = FALSE)) boxplot(I(width * convert) ~ unit, data = roomwidth, ylab = "Estimated width (feet)", varwidth = TRUE, names = c("Estimates in feet", "Estimates in meters (converted to feet)")) feet <- roomwidth$unit == "feet" qqnorm(roomwidth$width[feet], ylab = "Estimated width (feet)") qqline(roomwidth$width[feet]) qqnorm(roomwidth$width[!feet], ylab = "Estimated width (meters)") qqline(roomwidth$width[!feet]) @ \caption{Boxplots of estimates of room width in feet and meters (after conversion to feet) and normal probability plots of estimates of room width made in feet and in meters. \label{SI-rw-bxp}} \end{center} \end{figure} \rawSinput The boxplots indicate that both sets of estimates contain a number of outliers and also that the estimates made in meters are skewed and more variable than those made in feet, a point underlined by the numerical summary statistics above. Both normal probability plots depart from linearity, suggesting that the distributions of both sets of estimates are not normal. The presence of outliers, the apparently different variances and the evidence of non-normality all suggest caution in applying the $t$-test, but for the moment we shall apply the usual version of the test using the \Rcmd{t.test} function in \R{}. The two-sample test problem is specified by a \Rclass{formula}, here by <>= I(width * convert) ~ unit @ where the response, \Robject{width}, on the left-hand side needs to be converted first and, because the star has a special meaning in formulae as will be explained in \Sexpr{ch("ANOVA")}, the conversion needs to be embedded by \texttt{I}. The factor \Robject{unit} on the right-hand side specifies the two groups to be compared. <>= tt <- t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) @ \renewcommand{\nextcaption}{\R{} output of the independent samples $t$-test for the \Robject{roomwidth} data. \label{SI-roomwidth-tt-fig}} \SchunkLabel <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = TRUE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the independent samples Welch test for the \Robject{roomwidth} data. \label{SI-roomwidth-welch-fig}} \SchunkLabel <>= t.test(I(width * convert) ~ unit, data = roomwidth, var.equal = FALSE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the Wilcoxon rank sum test for the \Robject{roomwidth} data. \label{SI-roomwidth-wilcox-fig}} \SchunkLabel <>= wilcox.test(I(width * convert) ~ unit, data = roomwidth, conf.int = TRUE) @ \SchunkRaw <>= pwt <- round(wilcox.test(I(width * convert) ~ unit, data = roomwidth)$p.value, 3) @ \subsection{Wave Energy Device Mooring} The data from Table~\ref{SI-m-tab} are available as \Rclass{data.frame} \Robject{waves} <>= data("waves", package = "HSAUR3") @ and requires the use of a matched pairs $t$-test to answer the question of interest. This test assumes that the differences between the matched observations have a normal distribution so we can begin by checking this assumption by constructing a boxplot and a normal probability plot -- see Figure~\ref{SI-w-bxp}. \begin{figure} \begin{center} <>= mooringdiff <- waves$method1 - waves$method2 layout(matrix(1:2, ncol = 2)) boxplot(mooringdiff, ylab = "Differences (Newton meters)", main = "Boxplot") abline(h = 0, lty = 2) qqnorm(mooringdiff, ylab = "Differences (Newton meters)") qqline(mooringdiff) @ \caption{Boxplot and normal probability plot for differences between the two mooring methods. \label{SI-w-bxp}} \end{center} \end{figure} \renewcommand{\nextcaption}{\R{} output of the paired $t$-test for the \Robject{waves} data. \label{SI-waves-tt-fig}} \SchunkLabel <>= t.test(mooringdiff) @ \SchunkRaw <>= pwt <- round(wilcox.test(mooringdiff)$p.value, 3) @ \renewcommand{\nextcaption}{\R{} output of the Wilcoxon signed rank test for the \Robject{waves} data. \label{SI-waves-ws-fig}} \SchunkLabel <>= wilcox.test(mooringdiff) @ \SchunkRaw \subsection{Mortality and Water Hardness} There is a wide range of analyses we could apply to the data in Table~\ref{SI-w-tab} available from <>= data("water", package = "HSAUR3") @ But to begin we will construct a scatterplot of the data enhanced somewhat by the addition of information about the marginal distributions of water hardness (calcium concentration) and mortality, and by adding the estimated linear regression fit (see \Sexpr{ch("MLR")}) for mortality on hardness. The plot and the required \R{} code are given along with Figure~\ref{SI-water-sp}. In line 1 of Figure~\ref{SI-water-sp}, we divide the plotting region into four areas of different size. The scatterplot (line 3) uses a plotting symbol depending on the location of the city (by the \Rarg{pch} argument); a legend for the location is added in line 6. We add a least squares fit (see \Sexpr{ch("MLR")}) to the scatterplot and, finally, depict the marginal distributions by means of a boxplot and a histogram. The scatterplot shows that as hardness increases mortality decreases, and the histogram for the water hardness shows it has a rather skewed distribution. \numberSinput \begin{figure} \begin{center} <>= nf <- layout(matrix(c(2, 0, 1, 3), 2, 2, byrow = TRUE), c(2, 1), c(1, 2), TRUE) psymb <- as.numeric(water$location) plot(mortality ~ hardness, data = water, pch = psymb) abline(lm(mortality ~ hardness, data = water)) legend("topright", legend = levels(water$location), pch = c(1,2), bty = "n") hist(water$hardness) boxplot(water$mortality) @ \caption{Enhanced scatterplot of water hardness and mortality, showing both the joint and the marginal distributions and, in addition, the location of the city by different plotting symbols. \label{SI-water-sp}} \end{center} \end{figure} \rawSinput \renewcommand{\nextcaption}{\R{} output of Pearsons' correlation coefficient %' for the \Robject{water} data. \label{SI-water-c-fig}} \SchunkLabel <>= cor.test(~ mortality + hardness, data = water) @ \SchunkRaw <>= cr <- round(cor.test(~ mortality + hardness, data = water)$estimate, 3) @ \subsection{Piston-ring Failures} <>= chisqt <- chisq.test(pistonrings) @ \renewcommand{\nextcaption}{\R{} output of the chi-squared test for the \Robject{pistonrings} data. \label{SI-pr-x2-fig}} \SchunkLabel <>= data("pistonrings", package = "HSAUR3") chisq.test(pistonrings) @ \SchunkRaw Rather than looking at the simple differences of observed and expected values for each cell which would be unsatisfactory since a difference of fixed size is clearly more important for smaller samples, it is preferable to consider a \stress{standardized residual} \index{Standardized residual, for chi-squared tests} given by dividing the observed minus the expected difference by the square root of the appropriate expected value. The $X^2$ statistic for assessing independence is simply the sum, over all the cells in the table, of the squares of these terms. We can find these values extracting the \Robject{residuals} element of the object returned by the \Rcmd{chisq.test} function <>= chisq.test(pistonrings)$residuals @ A graphical representation of these residuals is called an \stress{association plot} \index{Association plot} and is available via the \Rcmd{assoc} function from package \Rpackage{vcd} \citep{PKG:vcd} applied to the contingency table of the two categorical variables. Figure~\ref{SI-assoc-plot} depicts the residuals for the piston ring data. The deviations from independence are largest for C1 and C4 compressors in the center and south leg. \begin{figure} \begin{center} <>= library("vcd") assoc(pistonrings) @ \caption{Association plot of the residuals for the \Robject{pistonrings} data. \label{SI-assoc-plot}} \end{center} \end{figure} \subsection{Rearrests of Juveniles} The data in Table~\ref{SI-r-tab} are available as \Rclass{table} object via <>= data("rearrests", package = "HSAUR3") rearrests @ <>= mcs <- round(mcnemar.test(rearrests, correct = FALSE)$statistic, 2) @ and in \Robject{rearrests} the counts in the four cells refer to the matched pairs of subjects; for example, in $\Sexpr{rearrests[1,1]}$ pairs both members of the pair were rearrested. Here we need to use McNemar's %' test to assess whether rearrest is associated with the type of court where the juvenile was tried. We can use the \R{} function \Rcmd{mcnemar.test}. The test statistic shown in Figure~\ref{SI-ra-mc-fig} is $\Sexpr{mcs}$ with a single degree of freedom -- the associated $p$-value is extremely small and there is strong evidence that type of court and the probability of rearrest are related. It appears that trial at a juvenile court is less likely to result in rearrest (see Exercise~3.4). % An exact version of McNemar's test %%' can be obtained by testing whether $b$ and $c$ are equal using a binomial test (see Figure~\ref{SI-ra-mcbin-fig}). \renewcommand{\nextcaption}{\R{} output of McNemar's test %' for the \Robject{rearrests} data. \label{SI-ra-mc-fig}} \SchunkLabel <>= mcnemar.test(rearrests, correct = FALSE) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of an exact version of McNemar's test %' for the \Robject{rearrests} data computed via a binomial test. \label{SI-ra-mcbin-fig}} \SchunkLabel <>= binom.test(rearrests[2], n = sum(rearrests[c(2,3)])) @ \SchunkRaw \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_cluster_analysis.R0000644000175000017500000001636414133304511017221 0ustar nileshnilesh### R code from vignette source 'Ch_cluster_analysis.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: thissetup ################################################### library("mclust") library("mvtnorm") mai <- par("mai") options(SweaveHooks = list(rmai = function() { par(mai = mai * c(1,1,1,2))})) data("pottery", package = "HSAUR3") ################################################### ### code chunk number 4: CA-pottery-dist ################################################### pottery_dist <- dist(pottery[, colnames(pottery) != "kiln"]) library("lattice") levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number") ################################################### ### code chunk number 5: CA-pottery-distplot ################################################### trellis.par.set(standard.theme(color = FALSE)) plot(levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number")) ################################################### ### code chunk number 6: CA-pottery-hclust ################################################### pottery_single <- hclust(pottery_dist, method = "single") pottery_complete <- hclust(pottery_dist, method = "complete") pottery_average <- hclust(pottery_dist, method = "average") layout(matrix(1:3, ncol = 3)) plot(pottery_single, main = "Single Linkage", sub = "", xlab = "") plot(pottery_complete, main = "Complete Linkage", sub = "", xlab = "") plot(pottery_average, main = "Average Linkage", sub = "", xlab = "") ################################################### ### code chunk number 7: pottery-cluster ################################################### pottery_cluster <- cutree(pottery_average, h = 4) xtabs(~ pottery_cluster + kiln, data = pottery) ################################################### ### code chunk number 8: CA-planets-scatter ################################################### getOption("SweaveHooks")[["rmai"]]() data("planets", package = "HSAUR3") library("scatterplot3d") scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, pch = 16, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, scale.y = 0.7, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") ################################################### ### code chunk number 9: CA-planet-ss ################################################### rge <- apply(planets, 2, max) - apply(planets, 2, min) planet.dat <- sweep(planets, 2, rge, FUN = "/") n <- nrow(planet.dat) wss <- rep(0, 10) wss[1] <- (n - 1) * sum(apply(planet.dat, 2, var)) for (i in 2:10) wss[i] <- sum(kmeans(planet.dat, centers = i)$withinss) plot(1:10, wss, type = "b", xlab = "Number of groups", ylab = "Within groups sum of squares") ################################################### ### code chunk number 10: CA-planets-kmeans3 ################################################### planet_kmeans3 <- kmeans(planet.dat, centers = 3) table(planet_kmeans3$cluster) ################################################### ### code chunk number 11: CA-planets-ccent ################################################### ccent <- function(cl) { f <- function(i) colMeans(planets[cl == i,]) x <- sapply(sort(unique(cl)), f) colnames(x) <- sort(unique(cl)) return(x) } ################################################### ### code chunk number 12: CA-planets--kmeans3-ccent ################################################### ccent(planet_kmeans3$cluster) ################################################### ### code chunk number 13: CA-planets-kmeans5 ################################################### planet_kmeans5 <- kmeans(planet.dat, centers = 5) table(planet_kmeans5$cluster) ccent(planet_kmeans5$cluster) ################################################### ### code chunk number 14: CA-planets-mclust ################################################### library("mclust") planet_mclust <- Mclust(planet.dat) ################################################### ### code chunk number 15: CA-planets-mclust-plot ################################################### plot(planet_mclust, planet.dat, what = "BIC", col = "black", ylab = "-BIC", ylim = c(0, 350)) ################################################### ### code chunk number 16: CA-planets-mclust-print ################################################### print(planet_mclust) ################################################### ### code chunk number 17: CA-planets-mclust-scatter ################################################### clPairs(planet.dat, classification = planet_mclust$classification, symbols = 1:3, col = "black") ################################################### ### code chunk number 18: CA-planets-mclust-scatterclust ################################################### getOption("SweaveHooks")[["rmai"]]() scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, scale.y = 0.7, pch = planet_mclust$classification, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") ################################################### ### code chunk number 19: CA-planets-mclust-mu ################################################### table(planet_mclust$classification) ccent(planet_mclust$classification) HSAUR3/inst/doc/Ch_meta_analysis.pdf0000644000175000017500000023234214133304611017033 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3992 /Filter /FlateDecode /N 87 /First 716 >> stream x[mS۸~v:wNgBmiwCH x6qh#ىe;`hv˶|$=$&hC$JED-1D[A,$ I00R \aR$Es7 aCL@Yq`J0~#(-a1$֘ }(&4PHrkJW GbkQ\3,͋tJr/Y Ibp+v󳬘- k$$}^dlMs<^<<1g?>=`¿#x"";<*fLyc:SK<5`8n?3^Q@F "X?Hb6pk"Ew_ؗB3GiW0G$_Ϲ@0=.AЗiOQ"$Zb25xFJJ)/5/~8E`Týu&&`Z89D C_T5gmrӟ7 #2HoU$k'iKRS붤MJ65IZbT*g Rn Ibb],뢱ɣjІVFV-P"JV9^\L֐l8jb碶|.#|v~;>Bvv@"zFS7 }p8xlhtQwl5+4j; #|KV3v[FűY5?l\\Y!h<7=O:6?!g  Ꟁ4 u {Cl0bRs~(a?La -D.;񽱟)j׽4N/(IOݦ;tݧG-=zJ{Q>ɧtLSf<_Kzy6 ^S):7tJsOS aSh%(9s-giJ9][|4ح9D +ƁNh+ s[*$5 vx6zbl5ӣlɢl]ZkҚO;'?@q@ħ[yR!yP!K0 k JeMR5 e}O!Ҩ=¬0`4WOݽ70t?!k̛ LW?s}tMv`=6kH~Re>w'0k$m C6؄=gNAQK=F-mKePmEqBM WO!z^. sŎZp?2js,wi@rUzu~?sBzY[+[ ezۮܾ}@Kw+rw9u^>)xul+nюZ` zz]Txu ;yʛ ,q\ ]:'?Of$QQ~s3{p??fa0I/ ߚ9`Up!u:Y2FLт~Пow:k!/%ٖ- T-R+;?x%?1l͈,Z5::Mu7w$AcuAJP"FMWwDIQ {r Nv[7D;U暫l={g=}KnS{Ye8_OSzn+uYF4/9*ct8e]dq L ۋp%-),FwO&z{tִt>\kmm~[E: Z0%[Ll>g6-.O*]V݉&8nrCS MC]3p7c'Lee>]E puwplHOkg!dK3'xt e\7BVQյ-KսIqOTWv[QլwtάѪ)7PV(^:MM*Xt.XŗW$>~:;v+9w6pWz&.y[U>c'Mp8㦕ߌKJ1YmRdv鬊 a*4|.j沱#*dSHŀ՞*U(m.v;xH]|!PV%-wi\yv9]YxgraQc+c?Q-X z@}n&OHٶVVEw,4u] JS"ֆx$Xzo~eǷn :hD!t,z lO6bGvbkF_eo`O"::9tsY[?Px7[]xutrsqͧ:ضzy qFr&hn\ğ.u. ڦ%|kx.`ً^\Hi,']GT7bA X!yiIddnamdjN)JHK$*fY-˷RU) 'i$BM8,\lG &a4)`ǜ6> stream GPL Ghostscript 9.50 2021-10-18T16:49:45+02:00 2021-10-18T16:49:45+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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/FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 160 /ID [<5488b63a1c39e5be77053421c86fb696>] >> stream xcb&F~0 $8J҄~ f 7ᣡMЖ6$(E@$)̾"9ހH RvB R@ DM"W-`f?;fdEy6+B8ޙ%A$;^Bɪ "ׂH~0f {%d endstream endobj startxref 111600 %%EOF HSAUR3/inst/doc/Ch_density_estimation.R0000644000175000017500000002553414133304524017553 0ustar nileshnilesh### R code from vignette source 'Ch_density_estimation.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: DE-setup ################################################### x <- library("KernSmooth") x <- library("flexmix") x <- library("boot") ################################################### ### code chunk number 4: DE-kernel-figs ################################################### rec <- function(x) (abs(x) < 1) * 0.5 tri <- function(x) (abs(x) < 1) * (1 - abs(x)) gauss <- function(x) 1/sqrt(2*pi) * exp(-(x^2)/2) x <- seq(from = -3, to = 3, by = 0.001) plot(x, rec(x), type = "l", ylim = c(0,1), lty = 1, ylab = expression(K(x))) lines(x, tri(x), lty = 2) lines(x, gauss(x), lty = 3) legend(-3, 0.8, legend = c("Rectangular", "Triangular", "Gaussian"), lty = 1:3, title = "kernel functions", bty = "n") ################################################### ### code chunk number 5: DE-options ################################################### w <- options("width")$w options(width = 66) ################################################### ### code chunk number 6: DE-x-bumps-data ################################################### x <- c(0, 1, 1.1, 1.5, 1.9, 2.8, 2.9, 3.5) n <- length(x) ################################################### ### code chunk number 7: DE-x-bumps-gaussian ################################################### xgrid <- seq(from = min(x) - 1, to = max(x) + 1, by = 0.01) ################################################### ### code chunk number 8: DE-x-bumps-bumps ################################################### h <- 0.4 bumps <- sapply(x, function(a) gauss((xgrid - a)/h)/(n * h)) ################################################### ### code chunk number 9: DE-reoptions ################################################### options(width = w) ################################################### ### code chunk number 10: DE-x-bumps ################################################### getOption("SweaveHooks")[["leftpar"]]() plot(xgrid, rowSums(bumps), ylab = expression(hat(f)(x)), type = "l", xlab = "x", lwd = 2) rug(x, lwd = 2) out <- apply(bumps, 2, function(b) lines(xgrid, b)) ################################################### ### code chunk number 11: DE-epakernel-fig ################################################### epa <- function(x, y) ((x^2 + y^2) < 1) * 2/pi * (1 - x^2 - y^2) x <- seq(from = -1.1, to = 1.1, by = 0.05) epavals <- sapply(x, function(a) epa(a, x)) persp(x = x, y = x, z = epavals, xlab = "x", ylab = "y", zlab = expression(K(x, y)), theta = -35, axes = TRUE, box = TRUE) ################################################### ### code chunk number 12: DE-faithful-density ################################################### data("faithful", package = "datasets") x <- faithful$waiting layout(matrix(1:3, ncol = 3)) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Gaussian kernel", border = "gray") lines(density(x, width = 12), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Rectangular kernel", border = "gray") lines(density(x, width = 12, window = "rectangular"), lwd = 2) rug(x) hist(x, xlab = "Waiting times (in min.)", ylab = "Frequency", probability = TRUE, main = "Triangular kernel", border = "gray") lines(density(x, width = 12, window = "triangular"), lwd = 2) rug(x) ################################################### ### code chunk number 13: DE-CYGOB1-contour ################################################### library("KernSmooth") data("CYGOB1", package = "HSAUR3") CYGOB1d <- bkde2D(CYGOB1, bandwidth = sapply(CYGOB1, dpik)) contour(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity") ################################################### ### code chunk number 14: DE-CYGOB1-persp ################################################### persp(x = CYGOB1d$x1, y = CYGOB1d$x2, z = CYGOB1d$fhat, xlab = "log surface temperature", ylab = "log light intensity", zlab = "estimated density", theta = -35, axes = TRUE, box = TRUE) ################################################### ### code chunk number 15: DE-faithful-optim ################################################### logL <- function(param, x) { d1 <- dnorm(x, mean = param[2], sd = param[3]) d2 <- dnorm(x, mean = param[4], sd = param[5]) -sum(log(param[1] * d1 + (1 - param[1]) * d2)) } startparam <- c(p = 0.5, mu1 = 50, sd1 = 3, mu2 = 80, sd2 = 3) opp <- optim(startparam, logL, x = faithful$waiting, method = "L-BFGS-B", lower = c(0.01, rep(1, 4)), upper = c(0.99, rep(200, 4))) ################################################### ### code chunk number 16: DE-faithful-optim-print-null ################################################### opp ################################################### ### code chunk number 17: DE-faithful-optim-print ################################################### print(opp[names(opp) != "message"]) ################################################### ### code chunk number 18: DE-attach-mclust ################################################### library("mclust") ################################################### ### code chunk number 19: DE-faithful-mclust ################################################### library("mclust") mc <- Mclust(faithful$waiting) mc ################################################### ### code chunk number 20: DE-faithful-mclust-mu ################################################### mc$parameters$mean ################################################### ### code chunk number 21: DE-faithful-mclust-para ################################################### sqrt(mc$parameters$variance$sigmasq) ################################################### ### code chunk number 22: DE-faithful-flexmix ################################################### library("flexmix") fl <- flexmix(waiting ~ 1, data = faithful, k = 2) ################################################### ### code chunk number 23: DE-faithful-flexmix-parameters ################################################### parameters(fl, component = 1) parameters(fl, component = 2) ################################################### ### code chunk number 24: DE-faithful-2Dplot ################################################### opar <- as.list(opp$par) rx <- seq(from = 40, to = 110, by = 0.1) d1 <- dnorm(rx, mean = opar$mu1, sd = opar$sd1) d2 <- dnorm(rx, mean = opar$mu2, sd = opar$sd2) f <- opar$p * d1 + (1 - opar$p) * d2 hist(x, probability = TRUE, xlab = "Waiting times (in min.)", border = "gray", xlim = range(rx), ylim = c(0, 0.06), main = "") lines(rx, f, lwd = 2) lines(rx, dnorm(rx, mean = mean(x), sd = sd(x)), lty = 2, lwd = 2) legend(50, 0.06, lty = 1:2, bty = "n", legend = c("Fitted two-component mixture density", "Fitted single normal density")) ################################################### ### code chunk number 25: DE-faithful-boot ################################################### library("boot") fit <- function(x, indx) { a <- Mclust(x[indx], minG = 2, maxG = 2, modelNames="E")$parameters if (a$pro[1] < 0.5) return(c(p = a$pro[1], mu1 = a$mean[1], mu2 = a$mean[2])) return(c(p = 1 - a$pro[1], mu1 = a$mean[2], mu2 = a$mean[1])) } ################################################### ### code chunk number 26: DE-faithful-bootrun ################################################### bootparafile <- system.file("cache", "DE-bootpara.rda", package = "HSAUR3") if (file.exists(bootparafile)) { load(bootparafile) } else { bootpara <- boot(faithful$waiting, fit, R = 1000) } ################################################### ### code chunk number 27: DE-faithful-p-ci ################################################### boot.ci(bootpara, type = "bca", index = 1) ################################################### ### code chunk number 28: DE-faithful-mu1-ci ################################################### boot.ci(bootpara, type = "bca", index = 2) ################################################### ### code chunk number 29: DE-faithful-mu2-ci ################################################### boot.ci(bootpara, type = "bca", index = 3) ################################################### ### code chunk number 30: DE-bootplot ################################################### bootplot <- function(b, index, main = "") { dens <- density(b$t[,index]) ci <- boot.ci(b, type = "bca", index = index)$bca[4:5] est <- b$t0[index] plot(dens, main = main) y <- max(dens$y) / 10 segments(ci[1], y, ci[2], y, lty = 2) points(ci[1], y, pch = "(") points(ci[2], y, pch = ")") points(est, y, pch = 19) } ################################################### ### code chunk number 31: DE-faithful-boot-plot ################################################### layout(matrix(1:2, ncol = 2)) bootplot(bootpara, 2, main = expression(mu[1])) bootplot(bootpara, 3, main = expression(mu[2])) HSAUR3/inst/doc/Ch_quantile_regression.Rnw0000644000175000017500000006432514133304452020270 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Quantile Regression} %%\VignetteDepends{lattice,quantreg} \setcounter{chapter}{11} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 80} <>= library("lattice") trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7), box.rectangle = list(col=1), plot.line = list(col = 1, lwd = 1), box.umbrella = list(lty=1, col=1), strip.background = list(col = "white"))) ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) data("db", package = "gamlss.data") nboys <- with(db, sum(age > 2)) @ \chapter[Quantile Regression]{Quantile Regression: Head Circumference for Age\label{QR}} \section{Introduction} \section{Quantile Regression} \section{Analysis Using \R{}} We begin with a graphical inspection of the influence of age on head circumference by means of a scatterplot. Plotting all pairs of age and head circumference in one panel gives more weight to the teens and 20s, so we produce one plot for younger boys between two and nine years old and one additional plot for boys older than nine years (or $>108$ months, to be precise). The \Rcmd{cut} function is very convenient for constructing a factor representing these two groups <>= summary(db) db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) @ which can then be used as a conditioning variable for conditional scatterplots produced with the \Rcmd{xyplot} function \citep[package \Rpackage{lattice}]{PKG:lattice}. Because we draw $\Sexpr{nboys}$ points in total, we use transparent shading (via \Rcmd{rgb(.1, .1, .1, .1)}) in order to obtain a clearer picture for the more populated areas in the plot. \begin{figure} \begin{center} <>= db$cut <- cut(db$age, breaks = c(2, 9, 23), labels = c("2-9 yrs", "9-23 yrs")) xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", scales = list(x = list(relation = "free")), layout = c(2, 1), pch = 19, col = rgb(.1, .1, .1, .1)) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys. \label{QR-db-plot}} \end{center} \end{figure} Figure~\ref{QR-db-plot}, as expected, shows that head circumference increases with age. It also shows that there is considerable variation and also quite a number of extremely large or small head circumferences in the respective age cohorts. It should be noted that each point corresponds to one boy participating in the study due to its cross-sectional study design. No longitudinal measurements (cf.~Chapter~\ref{ALDI}) were taken and we can safely assume independence between observations. We start with a simple linear model, computed separately for the younger and older boys, for regressing the mean head circumference on age <>= (lm2.9 <- lm(head ~ age, data = db, subset = age < 9)) (lm9.23 <- lm(head ~ age, data = db, subset = age > 9)) @ This approach is equivalent to fitting two intercepts and two slopes in the joint model <>= (lm_mod <- lm(head ~ age:I(age < 9) + I(age < 9) - 1, data = db)) @ while omitting the global intercept. Because the median of the normal distribution is equal to its mean, the two models can be interpreted as conditional median models under the normal assumption. The model states that within one year, the head circumference increases by $\Sexpr{round(coef(lm_mod)["age:I(age < 9)TRUE"], 3)}$ cm for boys less than nine years old and by $\Sexpr{round(coef(lm_mod)["age:I(age < 9)FALSE"], 3)}$ for older boys. We now relax this distributional assumption and compute a median regression model using the \Rcmd{rq} function from package \Rpackage{quantreg} \citep{PKG:quantreg}: <>= library("quantreg") (rq_med2.9 <- rq(head ~ age, data = db, tau = 0.5, subset = age < 9)) (rq_med9.23 <- rq(head ~ age, data = db, tau = 0.5, subset = age > 9)) @ When we construct confidence intervals for the intercept and slope parameters from both models for the younger boys <>= cbind(coef(lm2.9)[1], confint(lm2.9, parm = "(Intercept)")) cbind(coef(lm2.9)[2], confint(lm2.9, parm = "age")) summary(rq_med2.9, se = "rank") @ we see that the two intercepts are almost identical but there seems to be a larger slope parameter for age in the median regression model. For the older boys, we get the confidence intervals via <>= cbind(coef(lm9.23)[1], confint(lm9.23, parm = "(Intercept)")) cbind(coef(lm9.23)[2], confint(lm9.23, parm = "age")) summary(rq_med9.23, se = "rank") @ with again almost identical intercepts and only a slightly increased slope for age in the median regression model. Since one of our aims was the construction of growth curves, we first use the linear models regressing head circumference on age to plot such curves. Based on the two normal linear models, we can compute the quantiles of head circumference for age. For the following values of $\tau$ <>= tau <- c(.01, .1, .25, .5, .75, .9, .99) @ and a grid of age values <>= gage <- c(2:9, 9:23) i <- 1:8 @ (the index \Rcmd{i} denoting younger boys), we compute the standard prediction intervals \index{Prediction interval} taking the randomness of the estimated intercept, slope, and variance parameters into account. We first set up a data frame with our grid of age values and then use the \Rcmd{predict} function for a linear model to compute prediction intervals, here with a coverage of $50\%$. The lower limit of such a $50\%$ prediction interval is equivalent to the conditional $25\%$ quantile for the given age and the upper limit corresponds to the $75\%$ quantile. The conditional mean is also reported and is equivalent to the conditional median: <>= idf <- data.frame(age = gage[i]) p <- predict(lm2.9, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p @ We now proceed with $80\%$ prediction intervals for constructing the $10\%$ and $90\%$ quantiles, and with $98\%$ prediction intervals corresponding to the $1\%$ and $99\%$ quantiles and repeat the exercise also for the older boys: <>= p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm2.9, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") p2.9 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] idf <- data.frame(age = gage[-i]) p <- predict(lm9.23, newdata = idf, level = 0.5, interval = "prediction") colnames(p) <- c("0.5", "0.25", "0.75") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.8, interval = "prediction")[,-1]) colnames(p)[4:5] <- c("0.1", "0.9") p <- cbind(p, predict(lm9.23, newdata = idf, level = 0.98, interval = "prediction")[,-1]) colnames(p)[6:7] <- c("0.01", "0.99") @ We now reorder the columns of this table and get the following conditional quantiles, estimated under the normal assumption of head circumference: <>= p9.23 <- p[, c("0.01", "0.1", "0.25", "0.5", "0.75", "0.9", "0.99")] round((q2.23 <- rbind(p2.9, p9.23)), 3) @ We can now superimpose these conditional quantiles on our scatterplot. To do this, we need to write our own little panel function that produces the scatterplot using the \Rcmd{panel.xyplot} function and then adds the just computed conditional quantiles by means of the \Rcmd{panel.lines} function called for every column of $\Robject{q2.23}$. Figure~\ref{QR-db-lm-plot} shows parallel lines owing to the fact that the linear model assumes an error variance independent from age; this is the so-called variance homogeneity. Compared to a plot with only a single (mean) regression line, we plotted a whole bunch of conditional distributions here, one for each value of age. Of course, we did so under extremely simplifying assumptions like linearity and variance homogeneity that we're going to drop now. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), q2.23[nrow(q2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), q2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed normal quantiles. \label{QR-db-lm-plot}} \end{center} \end{figure} For the production of a nonparametric version of our growth curves, we start with fitting not only one but multiple quantile regression models, one for each value of $\tau$. We start with the younger boys <>= (rq2.9 <- rq(head ~ age, data = db, tau = tau, subset = age < 9)) @ and continue with the older boys <>= (rq9.23 <- rq(head ~ age, data = db, tau = tau, subset = age > 9)) @ Naturally, the intercept parameters vary but there is also a considerable variation in the slopes, with the largest value for the $1\%$ quantile regression model for younger boys. The parameters $\beta_\tau$ have to be interpreted with care. In general, they cannot be interpreted on an individual-specific level. A boy who happens to be at the $\tau \times 100\%$ quantile of head circumference conditional on his age would not be at the same quantile anymore when he gets older. When knowing $\beta_\tau$, the only conclusion that can be drawn is how the $\tau \times 100\%$ quantile of a population with a specific age differs from the $\tau \times 100\%$ quantile of a population with a different age. Because the linear functions estimated by linear quantile regression, here in model \Robject{rq9.23}, directly correspond to the conditional quantiles of interest, we can use the \Rcmd{predict} function to compute the estimated conditional quantiles: <>= p2.23 <- rbind(predict(rq2.9, newdata = data.frame(age = gage[i])), predict(rq9.23, newdata = data.frame(age = gage[-i]))) @ It is important to note that these numbers were obtained without assuming anything about the continuous distribution of head circumference given any age. Again, we produce a scatterplot with superimposed quantiles, this time each line corresponds to a specific model. For the sake of comparison with the linear model, we add the linear model quantiles as dashed lines to Figure~\ref{QR-db-rq-plot}. For the older boys, there seems to be almost no difference but the more extreme $1\%$ and $99\%$ quantiles for the younger boys differ considerably. So, at least for the younger boys, we might want to allow for age-specific variability in the distribution of head circumference. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) if (max(x) <= 9) { apply(q2.23, 2, function(x) panel.lines(gage[i], x[i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[i], x[i])) } else { apply(q2.23, 2, function(x) panel.lines(gage[-i], x[-i], lty = 2)) apply(p2.23, 2, function(x) panel.lines(gage[-i], x[-i])) } panel.text(rep(max(db$age), length(tau)), p2.23[nrow(p2.23),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p2.23[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed regression quantiles (solid lines) and normal quantiles (dashed lines). \label{QR-db-rq-plot}} \end{center} \end{figure} Still, with the quantile regression models shown in Figure~\ref{QR-db-rq-plot} we assume that the quantiles of head circumference depend on age in a linear way. Additive quantile regression is one way to approach the estimation of non-linear quantile functions. By considering two different models for younger and older boys, we allowed for a certain type of non-linear function in the results shown so far. Additive quantile regression should be able to deal with this problem and we therefore fit these models to all boys simultaneously. For our different choices of $\tau$, we fit one additive quantile regression model using the \Rcmd{rqss} function from the \Rpackage{quantreg} and allow smooth quantile functions of age via the \Rcmd{qss} function in the right-hand side of the model formula. Note that we transformed age by the third root prior to model fitting. This does not affect the model since it is a monotone transformation, however, it helps to avoid fitting a function with large derivatives for very young boys resulting in a low penalty parameter $\lambda$: <>= rqssmod <- vector(mode = "list", length = length(tau)) db$lage <- with(db, age^(1/3)) for (i in 1:length(tau)) rqssmod[[i]] <- rqss(head ~ qss(lage, lambda = 1), data = db, tau = tau[i]) @ For the analysis of the head circumference, we choose a penalty parameter $\lambda = 1$, which is the default for the \Rcmd{qss} function. Simply using the default without a careful hyperparameter tuning, for example using crossvalidation or similar procedures, is almost always a mistake. By visual inspection (Figure~\ref{QR-db-rqss-plot}) we find this choice appropriate but ask the readers to make a second guess (Exercise 3). For a finer grid of age values, we compute the conditional quantiles from the \Rcmd{predict} function: <>= gage <- seq(from = min(db$age), to = max(db$age), length = 50) p <- sapply(1:length(tau), function(i) { predict(rqssmod[[i]], newdata = data.frame(lage = gage^(1/3))) }) @ Using very similar code as for plotting linear quantiles, we produce again a scatterplot of age and head circumference but this time overlaid with non-linear regression quantiles. Given that the results from the linear models presented in Figure~\ref{QR-db-rq-plot} looked pretty convincing, the quantile curves in Figure~\ref{QR-db-rqss-plot} shed a surprising new light on the data. For the younger boys, we expected to see a larger variability than for boys between two and three years old, but in fact the distribution seems to be more complex. The distribution seems to be positively skewed with a heavy lower tail and the degree of skewness varies with age (note that the median is almost linear for boys older than four years). Also in the right part of Figure~\ref{QR-db-rqss-plot}, we see an age-varying skewness, although less pronounced as for the younger boys. The median increases up to 16 years but then the growth rate is much smaller. This does not seem to be the case for the $1\%, 10\%, 90\%$, and $99\%$ quantiles. Note that the discontinuity in the quantiles between the two age groups is only due to the overlapping abscissae. However, the deviations between the growth curves obtained from a linear model under normality assumption on the one hand and quantile regression on the other hand as shown in Figures~\ref{QR-db-rq-plot} and \ref{QR-db-rqss-plot} are hardly dramatic for the head circumference data. \begin{figure} \begin{center} <>= pfun <- function(x, y, ...) { panel.xyplot(x = x, y = y, ...) apply(p, 2, function(x) panel.lines(gage, x)) panel.text(rep(max(db$age), length(tau)), p[nrow(p),], label = tau, cex = 0.9) panel.text(rep(min(db$age), length(tau)), p[1,], label = tau, cex = 0.9) } xyplot(head ~ age | cut, data = db, xlab = "Age (years)", ylab = "Head circumference (cm)", pch = 19, scales = list(x = list(relation = "free")), layout = c(2, 1), col = rgb(.1, .1, .1, .1), panel = pfun) @ \caption{Scatterplot of age and head circumference for $\Sexpr{nboys}$ Dutch boys with superimposed non-linear regression quantiles. \label{QR-db-rqss-plot}} \end{center} \end{figure} \section{Summary of Findings} We can conclude that the whole distribution of head circumference changes with age and that assumptions like symmetry and variance homogeneity might be questionable for such type of analysis. One alternative to the estimation of conditional quantiles is the estimation of conditional distributions. One very interesting parametric approach are generalized additive models for location, scale, and shape \citep[GAMLSS,][]{HSAUR:RigbyStasinopoulos2005}. In \cite{HSAUR:StasinopoulosRigby2007}, an analysis of the age and head circumference by means of the \Rpackage{gamlss} package can be found. One practical problem associated with contemporary methods in quantile regression is quantile crossing. Because we fitted one quantile regression model for each of the quantiles of interest, we cannot guarantee that the conditional quantile functions are monotone, so the $90\%$ quantile may well be larger than the $95\%$ quantile in some cases. Postprocessing of the estimated quantile curves may help in this situation \citep{HSAUR:DetteVolgushev2008}. \section{Final Comments} When estimating regression models, we have to be aware of the implications of model assumptions when interpreting the results. Symmetry, linearity, and variance homogeneity are among the strongest but common assumptions. Quantile regression, both in its linear and additive formulation, is an intellectually stimulating and practically very useful framework where such assumptions can be relaxed. At a more basic level, one should always ask \stress{Am I really interested in the mean?} before using the regression models discussed in other chapters of this book. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_errata.pdf0000644000175000017500000002671314133304607015470 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 1311 /Filter /FlateDecode /N 25 /First 180 >> stream xWn8}߯MPl(R"%-qnN[&A[[G*$m~)Y$5a6Ϝy ) _*p I*E!)OQD* ({EqN\C<̣II\$hC" aSLBXJ$cA>r/ZFvlo_iq1kJ3]x7L`U;*_Sq6˼i^Fg48$ӠH&tM1]ĤyvM{' OpW'~7rVd{jEV?|ϋyI{]|=w~ΗyiY~5H Ͽ`'֫Ut5E%\c0">/A rd%SF͖@hNY>t,ˤ +#.bA d8|klܩl1:tnO(eSu/D"zJRPh LU{>_oSl, 0#-q4=6Y?Cr:b .@qS6dv؜iIdwlRXrVfaߑةCxdas![p[-+ =}r~\Ύ(-m6qnrHvd캾oz/78l2\w*dGY>NzWop|7GYn4n0폊PVJUO6>Ǿ%6r/~V*byZTÆ:`K X |^N6"Qk pt $ uA? 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euS0P=XVXoi> stream x}CMR82vz-B@^o   eb_mqCopyright (c) 1997, 2009 American Mathematical Society (), with Reserved Font Name CMR8.CMR8Computer Modern3vťbڽQ"DfVT@htkpozc,MI%ڧϋ1# :Q?f{ku؎׃$Ena}{mltNx~}vCoa  7 כ endstream endobj 36 0 obj << /Type /XRef /Length 62 /Filter /FlateDecode /DecodeParms << /Columns 4 /Predictor 12 >> /W [ 1 2 1 ] /Info 3 0 R /Root 2 0 R /Size 37 /ID [<59d6ce360e23cfc430af27faa1d5dfdb>] >> stream xcb&F~ c?L .`" n xHp o g ۳ endstream endobj startxref 11390 %%EOF HSAUR3/inst/doc/Ch_introduction_to_R.R0000644000175000017500000005170714133304540017343 0ustar nileshnilesh### R code from vignette source 'Ch_introduction_to_R.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: AItR-welcome ################################################### HSAUR3:::Rwelcome() ################################################### ### code chunk number 4: AItR-promt ################################################### options(prompt = "> ") ################################################### ### code chunk number 5: AItR-welcome ################################################### options(prompt = "R> ") ################################################### ### code chunk number 6: AItR-firstex ################################################### x <- sqrt(25) + 2 ################################################### ### code chunk number 7: AItR-firstex-print ################################################### x ################################################### ### code chunk number 8: AItR-firstex-print ################################################### print(x) ################################################### ### code chunk number 9: AItR-recommended ################################################### colwidth <- 4 ip <- installed.packages(priority = "high") pkgs <- unique(ip[,"Package"]) pkgs <- paste("\\Rpackage{", pkgs, "}", sep = "") nrows <- ceiling(length(pkgs) / colwidth) pkgs <- c(pkgs, rep("", colwidth * nrows - length(pkgs))) cat(paste(c("\\begin{tabular}{", paste(rep("l", colwidth), collapse=""), "}"), collapse = ""), "\n", file = "tables/rec.tex", append = FALSE) for (i in 1:nrows) { cat(paste(pkgs[(1:colwidth) + (i-1)*colwidth], collapse = " & "), file = "tables/rec.tex", append = TRUE) cat("\\\\ \n", file = "tables/rec.tex", append = TRUE) } cat("\\end{tabular}\n", file = "tables/rec.tex", append = TRUE) rm(ip, nrows) ################################################### ### code chunk number 10: AItR-CRAN ################################################### cp <- available.packages(contriburl = "http://CRAN.r-project.org/src/contrib") ncp <- sum(!rownames(cp) %in% pkgs) rm(cp, pkgs) ################################################### ### code chunk number 11: AItR-rm ################################################### rm(ncp, colwidth, i) ################################################### ### code chunk number 12: AItR-install-packages (eval = FALSE) ################################################### ## install.packages("sandwich") ################################################### ### code chunk number 13: AItR-library (eval = FALSE) ################################################### ## library("sandwich") ################################################### ### code chunk number 14: AItR-help (eval = FALSE) ################################################### ## help("mean") ################################################### ### code chunk number 15: AItR-help-lib (eval = FALSE) ################################################### ## help(package = "sandwich") ################################################### ### code chunk number 16: AItR-help-lib (eval = FALSE) ################################################### ## vignette("sandwich", package = "sandwich") ################################################### ### code chunk number 17: AItR-Forbes2000 ################################################### data("Forbes2000", package = "HSAUR3") ls() ################################################### ### code chunk number 18: AItR-Forbes2000-ls ################################################### x <- c("x", "Forbes2000") print(x) ################################################### ### code chunk number 19: AItR-Forbes2000-print (eval = FALSE) ################################################### ## print(Forbes2000) ################################################### ### code chunk number 20: AItR-Forbes2000-print ################################################### print(Forbes2000[1:3,]) cat("...\n") ################################################### ### code chunk number 21: AItR-Forbes2000-str (eval = FALSE) ################################################### ## str(Forbes2000) ################################################### ### code chunk number 22: AItR-Forbes2000-str ################################################### str(Forbes2000, vec.len = 2, strict.width = "cut", width = 60) ################################################### ### code chunk number 23: AItR-Forbes2000-help (eval = FALSE) ################################################### ## help("Forbes2000") ################################################### ### code chunk number 24: AItR-Forbes2000-df ################################################### class(Forbes2000) ################################################### ### code chunk number 25: AItR-Forbes2000-dim ################################################### dim(Forbes2000) ################################################### ### code chunk number 26: AItR-Forbes2000-nrow-ncol ################################################### nrow(Forbes2000) ncol(Forbes2000) ################################################### ### code chunk number 27: AItR-Forbes2000-names ################################################### names(Forbes2000) ################################################### ### code chunk number 28: AItR-Forbes2000-rank ################################################### class(Forbes2000[,"rank"]) ################################################### ### code chunk number 29: AItR-Forbes2000-length ################################################### length(Forbes2000[,"rank"]) ################################################### ### code chunk number 30: AItR-Forbes2000-one-to-three ################################################### 1:3 c(1,2,3) seq(from = 1, to = 3, by = 1) ################################################### ### code chunk number 31: AItR-Forbes2000-name ################################################### class(Forbes2000[,"name"]) length(Forbes2000[,"name"]) ################################################### ### code chunk number 32: AItR-Forbes2000-first ################################################### Forbes2000[,"name"][1] ################################################### ### code chunk number 33: AItR-Forbes2000-category ################################################### class(Forbes2000[,"category"]) ################################################### ### code chunk number 34: AItR-Forbes2000-nlevels ################################################### nlevels(Forbes2000[,"category"]) ################################################### ### code chunk number 35: AItR-Forbes2000-levels (eval = FALSE) ################################################### ## levels(Forbes2000[,"category"]) ################################################### ### code chunk number 36: AItR-Forbes2000-levels ################################################### levels(Forbes2000[,"category"])[1:3] cat("...\n") ################################################### ### code chunk number 37: AItR-Forbes2000-table (eval = FALSE) ################################################### ## table(Forbes2000[,"category"]) ################################################### ### code chunk number 38: AItR-Forbes2000-table ################################################### table(Forbes2000[,"category"])[1:3] cat("...\n") ################################################### ### code chunk number 39: AItR-Forbes2000-sales ################################################### class(Forbes2000[,"sales"]) ################################################### ### code chunk number 40: AItR-Forbes2000-numsum ################################################### median(Forbes2000[,"sales"]) mean(Forbes2000[,"sales"]) range(Forbes2000[,"sales"]) ################################################### ### code chunk number 41: AItR-Forbes2000-summary ################################################### summary(Forbes2000[,"sales"]) ################################################### ### code chunk number 42: AItR-Forbes2000-files ################################################### pkgpath <- system.file(package = "HSAUR2") mywd <- getwd() filep <- file.path(pkgpath, "rawdata") setwd(filep) ################################################### ### code chunk number 43: AItR-Forbes2000-read.table ################################################### csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1) ################################################### ### code chunk number 44: AItR-Forbes2000-csv-names ################################################### class(csvForbes2000[,"name"]) ################################################### ### code chunk number 45: AItR-Forbes2000-read.table2 ################################################### csvForbes2000 <- read.table("Forbes2000.csv", header = TRUE, sep = ",", row.names = 1, colClasses = c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric")) class(csvForbes2000[,"name"]) ################################################### ### code chunk number 46: AItR-Forbes2000-all.equal ################################################### all.equal(csvForbes2000, Forbes2000) ################################################### ### code chunk number 47: AItR-Forbes2000-classes ################################################### classes <- c("character", "integer", "character", "factor", "factor", "numeric", "numeric", "numeric", "numeric") length(classes) class(classes) ################################################### ### code chunk number 48: AItR-Forbes2000-RODBC (eval = FALSE) ################################################### ## library("RODBC") ## cnct <- odbcConnectExcel("Forbes2000.xls") ## sqlQuery(cnct, "select * from \"Forbes2000\\$\"") ################################################### ### code chunk number 49: AItR-Forbes2000-RODBC ################################################### setwd(mywd) ################################################### ### code chunk number 50: AItR-Forbes2000-write.table ################################################### write.table(Forbes2000, file = "Forbes2000.csv", sep = ",", col.names = NA) ################################################### ### code chunk number 51: AItR-Forbes2000-save ################################################### save(Forbes2000, file = "Forbes2000.rda") ################################################### ### code chunk number 52: AItR-Forbes2000-list ################################################### list.files(pattern = "\\.rda") ################################################### ### code chunk number 53: AItR-Forbes2000-load ################################################### load("Forbes2000.rda") ################################################### ### code chunk number 54: AItR-Forbes2000-vector-companies ################################################### companies <- Forbes2000[,"name"] ################################################### ### code chunk number 55: AItR-Forbes2000-vector-indexing ################################################### companies[1] ################################################### ### code chunk number 56: AItR-Forbes2000-vector-indexing ################################################### 1:3 companies[1:3] ################################################### ### code chunk number 57: AItR-Forbes2000-vector-negative-indexing ################################################### companies[-(4:2000)] ################################################### ### code chunk number 58: AItR-Forbes2000-top-three ################################################### Forbes2000[1:3, c("name", "sales", "profits", "assets")] ################################################### ### code chunk number 59: AItR-Forbes2000-list-extract ################################################### companies <- Forbes2000$name ################################################### ### code chunk number 60: AItR-Forbes2000-vector-companies ################################################### companies <- Forbes2000[,"name"] ################################################### ### code chunk number 61: AItR-Forbes2000-sales ################################################### order_sales <- order(Forbes2000$sales) ################################################### ### code chunk number 62: AItR-Forbes2000-sales-small ################################################### companies[order_sales[1:3]] ################################################### ### code chunk number 63: AItR-Forbes2000-order ################################################### Forbes2000[order_sales[c(2000, 1999, 1998)], c("name", "sales", "profits", "assets")] ################################################### ### code chunk number 64: AItR-Forbes2000-logical ################################################### Forbes2000[Forbes2000$assets > 1000, c("name", "sales", "profits", "assets")] ################################################### ### code chunk number 65: AItR-Forbes2000-logical2 ################################################### table(Forbes2000$assets > 1000) ################################################### ### code chunk number 66: AItR-Forbes2000-NA ################################################### na_profits <- is.na(Forbes2000$profits) table(na_profits) Forbes2000[na_profits, c("name", "sales", "profits", "assets")] ################################################### ### code chunk number 67: AItR-Forbes2000-complete-cases ################################################### table(complete.cases(Forbes2000)) ################################################### ### code chunk number 68: AItR-Forbes2000-UK ################################################### UKcomp <- subset(Forbes2000, country == "United Kingdom") dim(UKcomp) ################################################### ### code chunk number 69: AItR-Forbes2000-summary ################################################### summary(Forbes2000) ################################################### ### code chunk number 70: AItR-Forbes2000-summary-output ################################################### summary(Forbes2000) ################################################### ### code chunk number 71: AItR-Forbes2000-lapply (eval = FALSE) ################################################### ## lapply(Forbes2000, summary) ################################################### ### code chunk number 72: AItR-Forbes2000-tapply-category ################################################### mprofits <- tapply(Forbes2000$profits, Forbes2000$category, median, na.rm = TRUE) ################################################### ### code chunk number 73: AItR-Forbes2000-medianNA ################################################### median(Forbes2000$profits) ################################################### ### code chunk number 74: AItR-Forbes2000-mprofits ################################################### rev(sort(mprofits))[1:3] ################################################### ### code chunk number 75: AItR-Forbes2000-medianNA ################################################### median(Forbes2000$profits, na.rm = TRUE) ################################################### ### code chunk number 76: AItR-iqr ################################################### iqr <- function(x) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE) return(diff(q)) } ################################################### ### code chunk number 77: AItR-iqr-test ################################################### xdata <- rnorm(100) iqr(xdata) IQR(xdata) ################################################### ### code chunk number 78: AItR-iqr-test (eval = FALSE) ################################################### ## xdata[1] <- NA ## iqr(xdata) ################################################### ### code chunk number 79: AItR-iqr-test-results ################################################### xdata[1] <- NA cat(try(iqr(xdata))) ################################################### ### code chunk number 80: AItR-iqr ################################################### iqr <- function(x, ...) { q <- quantile(x, prob = c(0.25, 0.75), names = FALSE, ...) return(diff(q)) } iqr(xdata, na.rm = TRUE) IQR(xdata, na.rm = TRUE) ################################################### ### code chunk number 81: AItR-Forbes2000-iqr ################################################### iqr(Forbes2000$profits, na.rm = TRUE) ################################################### ### code chunk number 82: AItR-Forbes2000-tapply-category-iqr ################################################### iqr_profits <- tapply(Forbes2000$profits, Forbes2000$category, iqr, na.rm = TRUE) ################################################### ### code chunk number 83: AItR-Forbes2000-variability ################################################### levels(Forbes2000$category)[which.min(iqr_profits)] levels(Forbes2000$category)[which.max(iqr_profits)] ################################################### ### code chunk number 84: AItR-Forbes2000-for ################################################### bcat <- Forbes2000$category iqr_profits2 <- numeric(nlevels(bcat)) names(iqr_profits2) <- levels(bcat) for (cat in levels(bcat)) { catprofit <- subset(Forbes2000, category == cat)$profit this_iqr <- iqr(catprofit, na.rm = TRUE) iqr_profits2[levels(bcat) == cat] <- this_iqr } ################################################### ### code chunk number 85: AItR-Forbes2000-marketvalue ################################################### layout(matrix(1:2, nrow = 2)) hist(Forbes2000$marketvalue) hist(log(Forbes2000$marketvalue)) ################################################### ### code chunk number 86: AItR-Forbes2000-formula ################################################### fm <- marketvalue ~ sales class(fm) ################################################### ### code chunk number 87: AItR-Forbes2000-marketvalue-sales ################################################### plot(log(marketvalue) ~ log(sales), data = Forbes2000, pch = ".") ################################################### ### code chunk number 88: AItR-Forbes2000-marketvalue-sales-shading ################################################### plot(log(marketvalue) ~ log(sales), data = Forbes2000, col = rgb(0,0,0,0.1), pch = 16) ################################################### ### code chunk number 89: AItR-Forbes2000-country-plot ################################################### tmp <- subset(Forbes2000, country %in% c("United Kingdom", "Germany", "India", "Turkey")) tmp$country <- tmp$country[,drop = TRUE] plot(log(marketvalue) ~ country, data = tmp, ylab = "log(marketvalue)", varwidth = TRUE) ################################################### ### code chunk number 90: AItR-analysis1 ################################################### file.create("analysis.R") ################################################### ### code chunk number 91: AItR-analysis2 (eval = FALSE) ################################################### ## source("analysis.R", echo = TRUE) ################################################### ### code chunk number 92: AItR-analysis3 ################################################### file.remove("analysis.R") HSAUR3/inst/doc/Ch_gam.R0000644000175000017500000001710714133304530014376 0ustar nileshnilesh### R code from vignette source 'Ch_gam.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: packages ################################################### library("mgcv") library("mboost") library("rpart") library("wordcloud") ################################################### ### code chunk number 4: GAM-men1500m-plot ################################################### plot(time ~ year, data = men1500m, xlab = "Year", ylab = "Winning time (sec)") ################################################### ### code chunk number 5: GAM-men1500m-lm ################################################### men1500m1900 <- subset(men1500m, year >= 1900) men1500m_lm <- lm(time ~ year, data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") abline(men1500m_lm) ################################################### ### code chunk number 6: GAM-men1500m-smooth ################################################### x <- men1500m1900$year y <- men1500m1900$time men1500m_lowess <- lowess(x, y) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m_lowess, lty = 2) men1500m_cubic <- gam(y ~ s(x, bs = "cr")) lines(x, predict(men1500m_cubic), lty = 3) ################################################### ### code chunk number 7: GAM-men1500m-quad ################################################### men1500m_lm2 <- lm(time ~ year + I(year^2), data = men1500m1900) plot(time ~ year, data = men1500m1900, xlab = "Year", ylab = "Winning time (sec)") lines(men1500m1900$year, predict(men1500m_lm2)) ################################################### ### code chunk number 8: GAM-men1500m-pred ################################################### predict(men1500m_lm, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") predict(men1500m_lm2, newdata = data.frame(year = c(2008, 2012)), interval = "confidence") ################################################### ### code chunk number 9: GAM-USairpollution-boost ################################################### library("mboost") USair_boost <- gamboost(SO2 ~ ., data = USairpollution) USair_aic <- AIC(USair_boost) USair_aic ################################################### ### code chunk number 10: GAM-USairpollution-boostplot ################################################### USair_gam <- USair_boost[mstop(USair_aic)] layout(matrix(1:6, ncol = 3)) plot(USair_gam, ask = FALSE) ################################################### ### code chunk number 11: GAM-USairpollution-residplot ################################################### SO2hat <- predict(USair_gam) SO2 <- USairpollution$SO2 plot(SO2hat, SO2 - SO2hat, type = "n", xlim = c(-20, max(SO2hat) * 1.1), ylim = range(SO2 - SO2hat) * c(2, 1)) textplot(SO2hat, SO2 - SO2hat, rownames(USairpollution), show.lines = FALSE, new = FALSE) abline(h = 0, lty = 2, col = "grey") ################################################### ### code chunk number 12: GAM-kyphosis-plot ################################################### layout(matrix(1:3, nrow = 1)) spineplot(Kyphosis ~ Age, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Number, data = kyphosis, ylevels = c("present", "absent")) spineplot(Kyphosis ~ Start, data = kyphosis, ylevels = c("present", "absent")) ################################################### ### code chunk number 13: GAM-kyphosis-gam ################################################### (kyphosis_gam <- gam(Kyphosis ~ s(Age, bs = "cr") + s(Number, bs = "cr", k = 3) + s(Start, bs = "cr", k = 3), family = binomial, data = kyphosis)) ################################################### ### code chunk number 14: GAM-kyphosis-gamplot ################################################### trans <- function(x) binomial()$linkinv(x) layout(matrix(1:3, nrow = 1)) plot(kyphosis_gam, select = 1, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 2, shade = TRUE, trans = trans) plot(kyphosis_gam, select = 3, shade = TRUE, trans = trans) ################################################### ### code chunk number 15: GAM-womensrole-gam ################################################### data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ s(education, by = gender) womensrole_gam <- gam(fm1, data = womensrole, family = binomial()) ################################################### ### code chunk number 16: GAM-womensrole-gamplot ################################################### layout(matrix(1:2, nrow = 1)) plot(womensrole_gam, select = 1, shade = TRUE) plot(womensrole_gam, select = 1, shade = TRUE) ################################################### ### code chunk number 17: GAM-plot-setup ################################################### myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } ################################################### ### code chunk number 18: GAM-womensrole-probplot ################################################### myplot(predict(womensrole_gam, type = "response")) HSAUR3/inst/doc/Ch_logistic_regression_glm.Rnw0000644000175000017500000011117014133304452021111 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Logistic Regression and Generalized Linear Models} %%\VignetteDepends{survival,MASS,multcomp,lattice} \setcounter{chapter}{6} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Logistic Regression and Generalized Linear Models]{Logistic Regression and Generalized Linear Models: Blood Screening, Women's Role in %' Society, Colonic Polyps, Driving and Back Pain, and Happiness in China \label{GLM}} \section{Introduction} \section{Logistic Regression and Generalized Linear Models} \section{Analysis Using \R{}} \subsection{ESR and Plasma Proteins} \begin{figure} \begin{center} <>= data("plasma", package = "HSAUR3") layout(matrix(1:2, ncol = 2)) cdplot(ESR ~ fibrinogen, data = plasma) cdplot(ESR ~ globulin, data = plasma) @ \caption{Conditional density plots of the erythrocyte sedimentation rate (ESR) given fibrinogen and globulin. \label{GLM:plasma1}} \end{center} \end{figure} We can now fit a logistic regression model to the data using the \Rcmd{glm} function. We start with a model that includes only a single explanatory variable, \Robject{fibrinogen}. The code to fit the model is <>= plasma_glm_1 <- glm(ESR ~ fibrinogen, data = plasma, family = binomial()) @ The formula implicitly defines a parameter for the global mean (the intercept term) as discussed in \Sexpr{ch("ANOVA")} and \Sexpr{ch("MLR")}. The distribution of the response is defined by the \Robject{family} argument, a binomial distribution in our case. \index{family argument@\Rcmd{family} argument} \index{Binomial distribution} (The default link function when the binomial family is requested is the logistic function.) \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to ESR and fibrigonen. \label{GLM-plasma-summary-1}} \SchunkLabel <>= summary(plasma_glm_1) @ \SchunkRaw From the results in Figure~\ref{GLM-plasma-summary-1} we see that the regression coefficient for fibrinogen is significant at the $5\%$ level. An increase of one unit in this variable increases the log-odds in favor of an ESR value greater than $20$ by an estimated $\Sexpr{round(coef(plasma_glm_1)["fibrinogen"], 2)}$ with 95\% confidence interval <>= ci <- confint(plasma_glm_1)["fibrinogen",] @ <>= confint(plasma_glm_1, parm = "fibrinogen") @ <>= print(ci) @ These values are more helpful if converted to the corresponding values for the odds themselves by exponentiating the estimate <>= exp(coef(plasma_glm_1)["fibrinogen"]) @ and the confidence interval <>= ci <- exp(confint(plasma_glm_1, parm = "fibrinogen")) @ <>= exp(confint(plasma_glm_1, parm = "fibrinogen")) @ <>= print(ci) @ The confidence interval is very wide because there are few observations overall and very few where the ESR value is greater than $20$. Nevertheless it seems likely that increased values of fibrinogen lead to a greater probability of an ESR value greater than $20$. We can now fit a logistic regression model that includes both explanatory variables using the code <>= plasma_glm_2 <- glm(ESR ~ fibrinogen + globulin, data = plasma, family = binomial()) @ and the output of the \Rcmd{summary} method is shown in Figure \ref{GLM-plasma-summary-2}. \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to ESR and both globulin and fibrinogen. \label{GLM-plasma-summary-2}} \SchunkLabel <>= summary(plasma_glm_2) @ \SchunkRaw <>= plasma_anova <- anova(plasma_glm_1, plasma_glm_2, test = "Chisq") @ The coefficient for gamma globulin is not significantly different from zero. Subtracting the residual deviance of the second model from the corresponding value for the first model we get a value of $\Sexpr{round(plasma_anova$Deviance[2], 2)}$. Tested using a $\chi^2$-distribution with a single degree of freedom this is not significant at the 5\% level and so we conclude that gamma globulin is not associated with ESR level. In \R{}, the task of comparing the two nested models can be performed using the \Rcmd{anova} function <>= anova(plasma_glm_1, plasma_glm_2, test = "Chisq") @ Nevertheless we shall use the predicted values from the second model and plot them against the values of \stress{both} explanatory variables using a \stress{bubbleplot} to illustrate the use of the \Rcmd{symbols} function. \index{Bubbleplot} The estimated conditional probability of a ESR value larger $20$ for all observations can be computed, following formula (\ref{GLM:logitexp}), by <>= prob <- predict(plasma_glm_2, type = "response") @ and now we can assign a larger circle to observations with larger probability as shown in Figure~\ref{GLM:bubble}. The plot clearly shows the increasing probability of an ESR value above $20$ (larger circles) as the values of fibrinogen, and to a lesser extent, gamma globulin, increase. \begin{figure} \begin{center} <>= plot(globulin ~ fibrinogen, data = plasma, xlim = c(2, 6), ylim = c(25, 55), pch = ".") symbols(plasma$fibrinogen, plasma$globulin, circles = prob, add = TRUE) @ \caption{Bubbleplot of fitted values for a logistic regression model fitted to the \Robject{plasma} data. \label{GLM:bubble}} \end{center} \end{figure} \subsection{Women's Role in Society} %' Originally the data in Table~\ref{GLM-womensrole-tab} would have been in a completely equivalent form to the data in Table~\ref{GLM-plasma-tab} data, but here the individual observations have been grouped into counts of numbers of agreements and disagreements for the two explanatory variables, \Robject{gender} and \Robject{education}. To fit a logistic regression model to such grouped data using the \Rcmd{glm} function we need to specify the number of agreements and disagreements as a two-column matrix on the left-hand side of the model formula. We first fit a model that includes the two explanatory variables using the code <>= data("womensrole", package = "HSAUR3") fm1 <- cbind(agree, disagree) ~ gender + education womensrole_glm_1 <- glm(fm1, data = womensrole, family = binomial()) @ \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to the \Robject{womensrole} data. \label{GLM-womensrole-summary-1}} \SchunkLabel <>= summary(womensrole_glm_1) @ \SchunkRaw From the \Rcmd{summary} output in Figure~\ref{GLM-womensrole-summary-1} it appears that education has a highly significant part to play in predicting whether a respondent will agree with the statement read to them, but the respondent's %' gender is apparently unimportant. As years of education increase the probability of agreeing with the statement declines. We now are going to construct a plot comparing the observed proportions of agreeing with those fitted by our fitted model. Because we will reuse this plot for another fitted object later on, we define a function which plots years of education against some fitted probabilities, e.g., <>= role.fitted1 <- predict(womensrole_glm_1, type = "response") @ and labels each observation with the person's gender: %%' \numberSinput <>= myplot <- function(role.fitted) { f <- womensrole$gender == "Female" plot(womensrole$education, role.fitted, type = "n", ylab = "Probability of agreeing", xlab = "Education", ylim = c(0,1)) lines(womensrole$education[!f], role.fitted[!f], lty = 1) lines(womensrole$education[f], role.fitted[f], lty = 2) lgtxt <- c("Fitted (Males)", "Fitted (Females)") legend("topright", lgtxt, lty = 1:2, bty = "n") y <- womensrole$agree / (womensrole$agree + womensrole$disagree) size <- womensrole$agree + womensrole$disagree size <- size - min(size) size <- (size / max(size)) * 3 + 1 text(womensrole$education, y, ifelse(f, "\\VE", "\\MA"), family = "HersheySerif", cex = size) } @ \rawSinput \begin{figure} \begin{center} <>= myplot(role.fitted1) @ \caption{Fitted (from \Robject{womensrole\_glm\_1}) and observed probabilities of agreeing for the \Robject{womensrole} data. The size of the symbols is proportional to the sample size. \label{GLM-role1plot}} \end{center} \end{figure} In lines 3--5 of function \Rcmd{myplot}, an empty scatterplot of education and fitted probabilities (\Rcmd{type = "n"}) is set up, basically to set the scene for the following plotting actions. Then, two lines are drawn (using function \Rcmd{lines} in lines 6 and 7), one for males (with line type 1) and one for females (with line type 2, i.e., a dashed line), where the logical vector \Robject{f} describes both genders. In line 9 a legend is added. Finally, in lines 12 onwards we plot `observed' values, i.e., the frequencies of agreeing in each of the groups (\Robject{y} as computed in lines 10 and 11) and use the Venus and Mars symbols to indicate gender. The size of the plotted symbol is proportional to the numbers of observations in the corresponding group of gender and years of education. The two curves for males and females in Figure~\ref{GLM-role1plot} are almost the same reflecting the non-significant value of the regression coefficient for gender in \Robject{womensrole\_glm\_1}. But the observed values plotted on Figure~\ref{GLM-role1plot} suggest that there might be an interaction of education and gender, a possibility that can be investigated by applying a further logistic regression model using \index{Interaction} <>= fm2 <- cbind(agree,disagree) ~ gender * education womensrole_glm_2 <- glm(fm2, data = womensrole, family = binomial()) @ The \Robject{gender} and \Robject{education} interaction term is seen to be highly significant, as can be seen from the \Rcmd{summary} output in Figure~\ref{GLM-womensrole-summary-2}. \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the logistic regression model fitted to the \Robject{womensrole} data. \label{GLM-womensrole-summary-2}} \SchunkLabel <>= summary(womensrole_glm_2) @ \SchunkRaw \begin{figure} \begin{center} <>= role.fitted2 <- predict(womensrole_glm_2, type = "response") myplot(role.fitted2) @ \caption{Fitted (from \Robject{womensrole\_glm\_2}) and observed probabilities of agreeing for the \Robject{womensrole} data. \label{GLM-role2plot}} \end{center} \end{figure} We can obtain a plot of deviance residuals plotted against fitted values using the following code above Figure~\ref{GLM:devplot}. \begin{figure} \begin{center} <>= res <- residuals(womensrole_glm_2, type = "deviance") plot(predict(womensrole_glm_2), res, xlab="Fitted values", ylab = "Residuals", ylim = max(abs(res)) * c(-1,1)) abline(h = 0, lty = 2) @ \caption{Plot of deviance residuals from logistic regression model fitted to the \Robject{womensrole} data. \label{GLM:devplot}} \end{center} \end{figure} The residuals fall into a horizontal band between $-2$ and $2$. This pattern does not suggest a poor fit for any particular observation or subset of observations. \subsection{Colonic Polyps} The data on colonic polyps in Table~\ref{GLM-polyps-tab} involves \stress{count} data. We could try to model this using multiple regression but there are two problems. The first is that a response that is a count can take only positive values, and secondly such a variable is unlikely to have a normal distribution. Instead we will apply a GLM with a log link function, ensuring that fitted values are positive, and a Poisson error distribution, i.e., \index{Poisson error distribution} \index{Poisson regression} \begin{eqnarray*} \P(y) = \frac{e^{-\lambda}\lambda^y}{y!}. \end{eqnarray*} This type of GLM is often known as \stress{Poisson regression}. We can apply the model using <>= data("polyps", package = "HSAUR3") polyps_glm_1 <- glm(number ~ treat + age, data = polyps, family = poisson()) @ (The default link function when the Poisson family is requested is the log function.) \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the Poisson regression model fitted to the \Robject{polyps} data. \label{GLM-polyps-summary-1}} \SchunkLabel <>= summary(polyps_glm_1) @ \SchunkRaw We can deal with overdispersion by using a procedure known as \stress{quasi-likelihood}, \index{Quasi-likelihood} which allows the estimation of model parameters without fully knowing the error distribution of the response variable. \cite{HSAUR:McCullaghNelder1989} give full details of the quasi-likelihood approach. In many respects it simply allows for the estimation of $\phi$ from the data rather than defining it to be unity for the binomial and Poisson distributions. We can apply quasi-likelihood estimation to the colonic polyps data using the following \R{} code <>= polyps_glm_2 <- glm(number ~ treat + age, data = polyps, family = quasipoisson()) summary(polyps_glm_2) @ The regression coefficients for both explanatory variables remain significant but their estimated standard errors are now much greater than the values given in Figure~\ref{GLM-polyps-summary-1}. A possible reason for overdispersion in these data is that polyps do not occur independently of one another, but instead may `cluster' together. %' \index{Overdispersion|)} \subsection{Driving and Back Pain} A frequently used design in medicine is the matched case-control study in which each patient suffering from a particular condition of interest included in the study is matched to one or more people without the condition. The most commonly used matching variables are age, ethnic group, mental status, etc. A design with $m$ controls per case is known as a $1:m$ matched study. In many cases $m$ will be one, and it is the $1:1$ matched study that we shall concentrate on here where we analyze the data on low back pain given in Table~\ref{GLM-backpain-tab}. To begin we shall describe the form of the logistic model appropriate for case-control studies in the simplest case where there is only one binary explanatory variable. With matched pairs data the form of the logistic model involves the probability, $\varphi$, that in matched pair number $i$, for a given value of the explanatory variable the member of the pair is a case. Specifically the model is \begin{eqnarray*} \text{logit}(\varphi_i) = \alpha_i + \beta x. \end{eqnarray*} The odds that a subject with $x=1$ is a case equals $\exp(\beta)$ times the odds that a subject with $x=0$ is a case. The model generalizes to the situation where there are $q$ explanatory variables as \begin{eqnarray*} \text{logit}(\varphi_i) = \alpha_i + \beta_1 x_1 + \beta_2 x_2 + \dots \beta_q x_q. \end{eqnarray*} Typically one $x$ is an explanatory variable of real interest, such as past exposure to a risk factor, with the others being used as a form of statistical control in addition to the variables already controlled by virtue of using them to form matched pairs. This is the case in our back pain example where it is the effect of car driving on lower back pain that is of most interest. The problem with the model above is that the number of parameters increases at the same rate as the sample size with the consequence that maximum likelihood estimation is no longer viable. We can overcome this problem if we regard the parameters $\alpha_i$ as of little interest and so are willing to forgo their estimation. If we do, we can then create a \stress{conditional likelihood function} that will yield maximum likelihood estimators of the coefficients, $\beta_1, \dots, \beta_q$, that are consistent and asymptotically normally distributed. The mathematics behind this are described in \cite{HSAUR:Collett2003}. The model can be fitted using the \Rcmd{clogit} function from package \Rpackage{survival}; the results are shown in Figure~\ref{GLM-backpain-print}. <>= library("survival") backpain_glm <- clogit(I(status == "case") ~ driver + suburban + strata(ID), data = backpain) @ The response has to be a logical (\Rcmd{TRUE} for cases) and the \Rcmd{strata} command specifies the matched pairs. \renewcommand{\nextcaption}{\R{} output of the \Robject{print} method for the conditional logistic regression model fitted to the \Robject{backpain} data. \label{GLM-backpain-print}} \SchunkLabel <>= print(backpain_glm) @ \SchunkRaw The estimate of the odds ratio of a herniated disc occurring in a driver relative to a nondriver is $\Sexpr{round(exp(coef(backpain_glm)[1]),2)}$ with a $95\%$ confidence interval of $\Sexpr{paste("(", paste(round(exp(confint(backpain_glm)[1,]), 2), collapse = ","),")", sep = "")}$. Conditional on residence we can say that the risk of a herniated disc occurring in a driver is about twice that of a nondriver. There is no evidence that where a person lives affects the risk of lower back pain. \subsection{Happiness in China} We model the probability distribution of reported happiness using a proportional odds model. In \R{}, the function \Rcmd{polr} from the \Rpackage{MASS} package \citep{HSAUR:VenablesRipley2002, PKG:MASS} implements such models, but in a slightly different form as explained in Section~\ref{GLM:polr}. The model we are going to fit reads \begin{eqnarray*} \log\left(\frac{\P(y \le k | x_1, \dots, x_q)}{\P(y > k | x_1, \dots, x_q)}\right) & = & \zeta_k - (\beta_1 x_1 + \dots + \beta_q x_q) \end{eqnarray*} and we have to take care when interpreting the signs of the estimated regression coefficients. Another issue needs our attention before we start. Three of the explanatory variables are itself ordered (\Robject{R\_edu}, the level of education of the responding woman; \Robject{R\_health}, the health status of the responding woman in the last year; and \Robject{A\_edu}, the level of education of the woman's partner). For unordered factors, the default treatment contrasts, see Chapters~\ref{ANOVA}, \ref{MLR}, and \ref{SIMC}, compares the effect of each level to the first level. This coding does not take the ordinal nature of an ordered factor into account. One more appropriate coding is called \stress{Helmert} contrasts. \index{Helmert constrast} Here, we compare each level $k$ to the average of the preceding levels, i.e., the second level to the first, the third to the average of the first and the second, and so on (these contrasts are also sometimes called \stress{reverse Helmert contrasts}). The \Rcmd{option} function can be used to specify the default contrasts for unordered (we don't change the default \Robject{contr.treatment} option) and ordered factors. The returned \Robject{opts} variable stores the options before manipulation and can be used to conveniently restore them after we fitted the proportional odds model: <>= library("MASS") opts <- options(contrasts = c("contr.treatment", "contr.helmert")) CHFLS_polr <- polr(R_happy ~ ., data = CHFLS, Hess = TRUE) options(opts) @ \renewcommand{\nextcaption}{\R{} output of the \Robject{summary} method for the proportional odds model fitted to the \Robject{CHFLS} data. \label{GLM-CHFLS-polr-summary}} \SchunkLabel <>= summary(CHFLS_polr) @ \SchunkRaw As (almost) always, the \Rcmd{summary} function can be used to display the fitted model, see Figure~\ref{GLM-CHFLS-polr-summary}. The largest absolute values of the $t$-statistics are associated with the self-reported health variable. To interpret the results correctly, we first make sure to understand the definition of the Helmert contrasts. <>= H <- with(CHFLS, contr.helmert(table(R_health))) rownames(H) <- levels(CHFLS$R_health) colnames(H) <- paste(levels(CHFLS$R_health)[-1], "- avg") H @ Let's focus on the probability of being very unhappy. A positive regression coefficient for the first contrast of health means that the probability of being very unhappy is smaller (because of the sign switch in the regression coefficients) for women that reported their health as not good compared to women that reported a poor health. Thus, the results given in Figure~\ref{GLM-CHFLS-polr-summary} indicate that better health leads to happier women, a finding that sits well with our expectations. The other effects are less clear to interpret, also because formal inference is difficult and no $p$-values are displayed in the summary output of Figure~\ref{GLM-CHFLS-polr-summary}. As a remedy, making use of the asymptotic distribution of maximum-likelihood-based estimators, we use the \Rcmd{cftest} function from the \Rpackage{multcomp} package \citep{PKG:multcomp} to compute normal $p$-values assuming that the estimated regression coefficients follow a normal limiting distribution (which is, for \Sexpr{nrow(CHFLS) - 3} observations, not completely unrealistic); the results are given in Figure~\ref{GLM-CHFLS-polr-cftest}. %% mess with the output function <>= library("multcomp") op <- options(digits = 2) cf <- cftest(CHFLS_polr) cftest <- function(x, digits = max(3, getOption("digits") - 3)) { x <- cf cat("\n\t", "Simultaneous Tests for General Linear Hypotheses\n\n") if (!is.null(x$type)) cat("Multiple Comparisons of Means:", x$type, "Contrasts\n\n\n") call <- if (isS4(x$model)) x$model@call else x$model$call if (!is.null(call)) { cat("Fit: ") print(call) cat("\n") } pq <- x$test mtests <- cbind(pq$coefficients, pq$sigma, pq$tstat, pq$pvalues) error <- attr(pq$pvalues, "error") pname <- switch(x$alternativ, less = paste("Pr(<", ifelse(x$df == 0, "z", "t"), ")", sep = ""), greater = paste("Pr(>", ifelse(x$df == 0, "z", "t"), ")", sep = ""), two.sided = paste("Pr(>|", ifelse(x$df == 0, "z", "t"), "|)", sep = "")) colnames(mtests) <- c("Estimate", "Std. Error", ifelse(x$df == 0, "z value", "t value"), pname) type <- pq$type if (!is.null(error) && error > .Machine$double.eps) { sig <- which.min(abs(1/error - (10^(1:10)))) sig <- 1/(10^sig) } else { sig <- .Machine$double.eps } cat("Linear Hypotheses:\n") alt <- switch(x$alternative, two.sided = "==", less = ">=", greater = "<=") rownames(mtests) <- rownames(mtests) printCoefmat(mtests, digits = digits, has.Pvalue = TRUE, P.values = TRUE, eps.Pvalue = sig) switch(type, univariate = cat("(Univariate p values reported)"), `single-step` = cat("(Adjusted p values reported -- single-step method)"), Shaffer = cat("(Adjusted p values reported -- Shaffer method)"), Westfall = cat("(Adjusted p values reported -- Westfall method)"), cat("(Adjusted p values reported --", type, "method)")) cat("\n\n") invisible(x) } @ \renewcommand{\nextcaption}{\R{} output of the \Robject{cftest} function for the proportional odds model fitted to the \Robject{CHFLS} data. \label{GLM-CHFLS-polr-cftest}} \SchunkLabel <>= library("multcomp") cftest(CHFLS_polr) @ \SchunkRaw <>= options(op) @ There seem to be geographical differences and also older and larger women seem to be happier. Other than that, education and income don't seem to contribute much in this model. One remarkable thing about the proportional odds model is that, similar to the quantile regression models presented in Chapter~\ref{QR}, it directly formulates a regression problem in terms of conditional distributions, not only conditional means (the same is trivially true for the binary case in logistic regression). Consequently, the model allows making distributional predictions, in other words, we can infer the predicted distribution or density of happiness in a woman with certain values for the explanatory variables that entered the model. To do so, we focus on the woman corresponding to the first row of the data set: \clearpage <>= CHFLS[1,] @ and repeat these values as often as there are levels in the \Robject{R\_health} factor, and each row is assigned one of these levels <>= nd <- CHFLS[rep(1, nlevels(CHFLS$R_health)),] nd$R_health <- ordered(levels(nd$R_health), labels = levels(nd$R_health)) @ We can now use the \Rcmd{predict} function to compute the density of the response variable \Rcmd{R\_happy} for each of these five hypothetical women: <>= (dens <- predict(CHFLS_polr, newdata = nd, type = "probs")) @ From each row, we get the predicted probability that the self-reported happiness will correspond to the levels shown in the column name. These densities, one for each row in \Robject{nd} and therefore for each level of health, can now be plotted, for example using a conditional barchart, see Figure~\ref{GLM-CHFLS-pred-plot}. We clearly see that better health is associated with greater happiness. \begin{figure} \begin{center} <>= library("lattice") D <- expand.grid(R_health = nd$R_health, R_happy = ordered(LETTERS[1:4])) D$dens <- as.vector(dens) barchart(dens ~ R_happy | R_health, data = D, ylab = "Density", xlab = "Happiness",) @ \caption{Predicted distribution of happiness for hypothetical women with health conditions rating from poor to excellent, with the remaining explanatory variables being the same as for the woman corresponding to the first row in the \Robject{CHFLS} data frame. The levels of happiness have been abbreviated (A: very unhappy, B: not too happy, C: somewhat happy; D: very happy). \label{GLM-CHFLS-pred-plot}} \end{center} \end{figure} We'll present an alternative and maybe simpler model in Chapter~\ref{RP}. \section{Summary of Findings} <>= ci <- round(exp(confint(plasma_glm_1, parm = "fibrinogen")), 2) ci <- paste("(", paste(ci, collapse = ","), ")", sep = "") @ \begin{description} \item[Blood screening] Application of logistic regression shows that an increase of one unit in the fibrinogen value produces approximately a six fold increase in the odds of an ESR value greater than $20$. However, because the number of observations is small the corresponding $95\%$ confidence interval for the odds is rather wide namely, $\Sexpr{ci}$. Gamma globulin values do not help in the prediction of ESR values greater than $20$ over and above the fibrinogen values. \item[Women's role in society] Modeling the probability of agreeing with the statement about women's role in society using logistic regression demonstrates that it is the interaction of education and gender which is of most importance; for fewer years of education women have a higher probability of agreeing with the statement than men, but when the years of education exceed about ten then this situation reverses. \item[Colonic polyps] Fitting a Poisson regression allowing for overdispersion shows that the drug treatment is effective in reducing the number of polyps with age having only a marginal effect. \item[Driving and back pain] Application of conditional logistic regression shows that the odds ratio of a herniated disc occurring in a driver relative to a nondriver is $\Sexpr{round(exp(coef(backpain_glm)[1]),2)}$ with a $95\%$ confidence interval of $\Sexpr{paste("(", paste(round(exp(confint(backpain_glm)[1,]), 2), collapse = ","),")", sep = "")}$. There is no evidence that where a person lives affects the risk of suffering lower back pain. \item[Happiness in China] Better health is associated with greater happiness -- what a surprise! \end{description} \section{Final Comments} Generalized linear models provide a very powerful and flexible framework for the application of regression models to a variety of non-normal response variables, for example, logistic regression to binary responses and Poisson regression to count data. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_conditional_inference.pdf0000644000175000017500000020154514133304606020530 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3539 /Filter /FlateDecode /N 75 /First 612 >> stream x[mS۸~m;Fl֝[(BvCH 64qh~#ىe';ƱdGst^$XTBH$ K,bJ O1b0ß1="DQ 2d~̗Lx! RDiLDLhPhۣ>y_L,/Щ @|a<Ũ3)$j&c %t f ! 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%1e%.J)%5\?^B&#_10ͯHˆ`v`FP8wF0q_D4aT`$F"E!ZDVn f5X(rVCf>ZMhuѺXĹ])r^M͵s>Z/' ^]+לb)E$Il}@5C55IX:4u1{>oXʡȻ|}Q~U\ \w3Ҏ)PR!S7ŨnLmo0 yb&|u4Yd6|t꛻&P[ݷB/+R_̳9c='q.9RY}?a\DLF:ji5 q|~S% @R8 P?CU(0߀A`wpiBs) Ja S/mc BݏIn3,4x"c#VS =wNHFS$|!OGp=Y 5a|BUP)m:._Z^$?m5gendstream endobj 103 0 obj << /Type /XRef /Length 125 /Filter /FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 104 /ID [<5f73563f7488f2c336227b365ec7e4ca><39b867397bd87ffc0bae7d9fe2177884>] >> stream xcb&F~0 $8JI?6 }?(@$> D2@$=) "@4u6 X$DwHU ,+"\ Yֻ!.` $Y0  endstream endobj startxref 66006 %%EOF HSAUR3/inst/doc/Ch_missing_values.R0000644000175000017500000001625414133304547016674 0ustar nileshnilesh### R code from vignette source 'Ch_missing_values.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: MV-bp-tab ################################################### data("bp", package = "HSAUR3") toLatex(HSAURtable(bp), pcol = 2, caption = paste("Blood pressure data."), label = "MV-bp-tab") ################################################### ### code chunk number 4: MV-bp-NA ################################################### sapply(bp, function(x) sum(is.na(x))) ################################################### ### code chunk number 5: MV-bp-msd-cc ################################################### summary(bp$recovtime, na.rm = TRUE) ################################################### ### code chunk number 6: MV-bp-sd-cc ################################################### sd(bp$recovtime, na.rm = TRUE) ################################################### ### code chunk number 7: MV-bp-cor-cc ################################################### with(bp, cor(bloodp, recovtime, use = "complete.obs")) with(bp, cor(logdose, recovtime, use = "complete.obs")) ################################################### ### code chunk number 8: MV-bp-pairs-cc ################################################### layout(matrix(1:3, nrow = 1)) plot(bloodp ~ logdose, data = bp) plot(recovtime ~ bloodp, data = bp) plot(recovtime ~ logdose, data = bp) ################################################### ### code chunk number 9: MV-bp-lm-cc ################################################### summary(lm(recovtime ~ bloodp + logdose, data = bp)) ################################################### ### code chunk number 10: MV-bp-mice-pkg ################################################### library("mice") ################################################### ### code chunk number 11: MV-bp-mice ################################################### imp <- mice(bp, method = "mean", m = 1, maxit = 1) ################################################### ### code chunk number 12: MV-bp-imp-summary ################################################### with(imp, summary(recovtime)) ################################################### ### code chunk number 13: MV-bp-imp-sd ################################################### with(imp, sd(recovtime)) ################################################### ### code chunk number 14: MV-bp-imp-cor ################################################### with(imp, cor(bloodp, recovtime)) with(imp, cor(logdose, recovtime)) ################################################### ### code chunk number 15: MV-bp-pairs-imp ################################################### layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) ################################################### ### code chunk number 16: MV-bp-lm-imp ################################################### with(imp, summary(lm(recovtime ~ bloodp + logdose))) ################################################### ### code chunk number 17: MV-bp-mice ################################################### imp_ppm <- mice(bp, m = 10, method = "pmm", print = FALSE, seed = 1) ################################################### ### code chunk number 18: MV-bp-pairs-mice ################################################### layout(matrix(1:2, nrow = 1)) plot(recovtime ~ bloodp, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) plot(recovtime ~ logdose, data = complete(imp_ppm), pch = is.na(bp$recovtime) + 1) legend("topleft", pch = 1:2, bty = "n", legend = c("original", "imputed")) ################################################### ### code chunk number 19: MV-bp-mice-out ################################################### summary(unlist(with(imp_ppm, mean(recovtime))$analyses)) summary(unlist(with(imp_ppm, sd(recovtime))$analyses)) ################################################### ### code chunk number 20: MV-bp-mice-cor ################################################### summary(unlist(with(imp_ppm, cor(bloodp, recovtime))$analyses)) summary(unlist(with(imp_ppm, cor(logdose, recovtime))$analyses)) ################################################### ### code chunk number 21: MV-bp-mice-lm ################################################### fit <- with(imp_ppm, lm(recovtime ~ bloodp + logdose)) ################################################### ### code chunk number 22: MV-bp-lm-mice ################################################### summary(pool(fit)) ################################################### ### code chunk number 23: MI-bp-t ################################################### with(bp, t.test(recovtime, mu = 27)) with(imp, t.test(recovtime, mu = 27))$analyses[[1]] ################################################### ### code chunk number 24: MI-mice-t ################################################### fit <- with(imp_ppm, lm(I(recovtime - 27) ~ 1)) summary(pool(fit)) ################################################### ### code chunk number 25: MI-UStemp-tab ################################################### data("UStemp", package = "HSAUR3") toLatex(HSAURtable(UStemp), caption = "Lowest temperatures in Fahrenheit recorded in various months for cities in the US.", label = "MI-UStemp-tab", rownames = TRUE) HSAUR3/inst/doc/Ch_analysing_longitudinal_dataI.Rnw0000644000175000017500000003373214133304452022044 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Analyzing Longitudinal Data I} %%\VignetteDepends{lme4,multcomp} \setcounter{chapter}{12} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("lme4") library("multcomp") residuals <- function(object) { y <- getME(object, 'y') y - fitted(object) } @ \chapter[Analyzing Longitudinal Data I]{Analyzing Longitudinal Data I: Computerized Delivery of Cognitive Behavioral Therapy -- Beat the Blues \label{ALDI}} \section{Introduction} \section{Analyzing Longitudinal Data} \section{Analysis Using \R{}} \begin{figure} \begin{center} <>= data("BtheB", package = "HSAUR3") layout(matrix(1:2, nrow = 1)) ylim <- range(BtheB[,grep("bdi", names(BtheB))], na.rm = TRUE) tau <- subset(BtheB, treatment == "TAU")[, grep("bdi", names(BtheB))] boxplot(tau, main = "Treated as Usual", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) btheb <- subset(BtheB, treatment == "BtheB")[, grep("bdi", names(BtheB))] boxplot(btheb, main = "Beat the Blues", ylab = "BDI", xlab = "Time (in months)", names = c(0, 2, 3, 5, 8), ylim = ylim) @ \caption{Boxplots for the repeated measures by treatment group for the \Robject{BtheB} data. \label{ALDI:boxplots}} \end{center} \end{figure} We shall fit both random intercept and random intercept and slope models to the data including the baseline BDI values (\Robject{pre.bdi}), \Robject{treatment} group, \Robject{drug}, and \Robject{length} as fixed effect covariates. Linear mixed effects models are fitted in \R{} by using the \Rcmd{lmer} function contained in the \Rpackage{lme4} package \citep{PKG:lme4,HSAUR:PinheiroBates2000,HSAUR:Bates2005}, but an essential first step is to rearrange the data from the `wide form' in which they appear in the \Robject{BtheB} data frame %%' into the `long form' in which each separate repeated measurement %%' and associated covariate values appear as a separate row in a \Rclass{data.frame}. This rearrangement can be made using the following code: <>= data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) @ such that the data are now in the form (here shown for the first three subjects) <>= subset(BtheB_long, subject %in% c("1", "2", "3")) @ The resulting \Rclass{data.frame} \Robject{BtheB\_long} contains a number of missing values \index{Missing values} and in applying the \Rcmd{lmer} function these will be dropped. But notice it is only the missing values that are removed, \stress{not} participants that have at least one missing value. All the available data is used in the model fitting process. The \Rcmd{lmer} function is used in a similar way to the \Rcmd{lm} function met in \Sexpr{ch("MLR")} with the addition of a random term to identify the source of the repeated measurements, here \Robject{subject}. We can fit the two models (\ref{ALDI:ModelA}) and (\ref{ALDI:ModelB}) and test which is most appropriate using <>= library("lme4") BtheB_lmer1 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (1 | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) BtheB_lmer2 <- lmer(bdi ~ bdi.pre + time + treatment + drug + length + (time | subject), data = BtheB_long, REML = FALSE, na.action = na.omit) anova(BtheB_lmer1, BtheB_lmer2) @ \renewcommand{\nextcaption}{\R{} output of the linear mixed-effects model fit for the \Robject{BtheB} data. \label{ALDI-BtheB-summary}} \SchunkLabel <>= summary(BtheB_lmer1) @ \SchunkRaw The \Rcmd{summary} method for \Rclass{lmer} objects doesn't print $p$-values for Gaussian mixed models because the degrees of freedom of the $t$ reference distribution are not obvious. However, one can rely on the asymptotic normal distribution for computing univariate $p$-values for the fixed effects using the \Rcmd{cftest} function from package \Rpackage{multcomp}. The asymptotic $p$-values are given in Figure~\ref{ALDI-BtheB-summary-p}. \renewcommand{\nextcaption}{\R{} output of the asymptotic $p$-values for linear mixed-effects model fit for the \Robject{BtheB} data. \label{ALDI-BtheB-summary-p}} \SchunkLabel <>= cftest(BtheB_lmer1) @ \SchunkRaw We can check the assumptions of the final model fitted to the \Robject{BtheB} data, i.e., the normality of the random effect terms and the residuals, by first using the \Rcmd{ranef} method to \stress{predict} the former and the \Rcmd{residuals} method to calculate the differences between the observed data values and the fitted values, and then using normal probability plots on each. How the random effects are predicted is explained briefly in Section~\ref{ALDI:predictrandom}. The necessary \R{} code to obtain the effects, residuals, and plots is shown with Figure~\ref{ALDI:qqplots}. There appear to be no large departures from linearity in either plot. \begin{figure} \begin{center} <>= layout(matrix(1:2, ncol = 2)) qint <- ranef(BtheB_lmer1)$subject[["(Intercept)"]] qres <- residuals(BtheB_lmer1) qqnorm(qint, ylab = "Estimated random intercepts", xlim = c(-3, 3), ylim = c(-20, 20), main = "Random intercepts") qqline(qint) qqnorm(qres, xlim = c(-3, 3), ylim = c(-20, 20), ylab = "Estimated residuals", main = "Residuals") qqline(qres) @ \caption{Quantile-quantile plots of predicted random intercepts and residuals for the random intercept model \Robject{BtheB\_lmer1} fitted to the \Robject{BtheB} data. \label{ALDI:qqplots}} \end{center} \end{figure} \begin{figure} \begin{center} <>= bdi <- BtheB[, grep("bdi", names(BtheB))] plot(1:4, rep(-0.5, 4), type = "n", axes = FALSE, ylim = c(0, 50), xlab = "Months", ylab = "BDI") axis(1, at = 1:4, labels = c(0, 2, 3, 5)) axis(2) for (i in 1:4) { dropout <- is.na(bdi[,i + 1]) points(rep(i, nrow(bdi)) + ifelse(dropout, 0.05, -0.05), jitter(bdi[,i]), pch = ifelse(dropout, 20, 1)) } @ \caption{Distribution of BDI values for patients that do (circles) and do not (bullets) attend the next scheduled visit. \label{ALDI-dropout}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_meta_analysis.Rnw0000644000175000017500000003654214133304452017037 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Meta-Analysis} %%\VignetteDepends{rmeta} \setcounter{chapter}{16} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Meta-Analysis]{Meta-Analysis: Nicotine Gum and Smoking Cessation and the Efficacy of BCG Vaccine in the Treatment of Tuberculosis \label{MA}} \section{Introduction} \section{Systematic Reviews and Meta-Analysis} \section{Analysis Using \R{}} The aim in collecting the results from the randomized trials of using nicotine gum to help smokers quit was to estimate the overall \stress{odds ratio}, the odds of quitting smoking for those given the gum, divided by the odds of quitting for those not receiving the gum. Following formula (\ref{MA:barY}), we can compute the pooled odds ratio as follows: <>= data("smoking", package = "HSAUR3") odds <- function(x) (x[1] * (x[4] - x[3])) / ((x[2] - x[1]) * x[3]) weight <- function(x) ((x[2] - x[1]) * x[3]) / sum(x) W <- apply(smoking, 1, weight) Y <- apply(smoking, 1, odds) sum(W * Y) / sum(W) @ Of course, the computations are more conveniently done using the functionality provided in package \Rpackage{rmeta}. The odds ratios and corresponding confidence intervals are computed by means of the \Rcmd{meta.MH} function for fixed effects meta-analysis as shown here <>= library("rmeta") smokingOR <- meta.MH(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking)) @ and the results can be inspected via a \Rcmd{summary} method -- see Figure~\ref{MA-smoking-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{smokingOR}. \label{MA-smoking-summary}} \SchunkLabel <>= summary(smokingOR) @ \SchunkRaw \begin{figure} \begin{center} <>= plot(smokingOR, ylab = "") @ \caption{Forest plot of observed effect sizes and $95\%$ confidence intervals for the nicotine gum studies. \label{MA:smokingplot}} \end{center} \end{figure} We shall use both the fixed effects and random effects approaches here so that we can compare results. For the fixed effects model (see Figure~\ref{MA-smoking-summary}) the estimated overall log-odds ratio is \Sexpr{round(smokingOR$logMH, 3)} with a standard error of \Sexpr{round(smokingOR$selogMH, 3)}. This leads to an estimate of the overall odds ratio of \Sexpr{round(exp(smokingOR$logMH), 3)}, with a 95\% confidence interval as given above. For the random effects model, which is fitted by applying function \Rcmd{meta.DSL} to the \Robject{smoking} data as follows \vspace{1cm} <>= (smokingDSL <- meta.DSL(smoking[["tt"]], smoking[["tc"]], smoking[["qt"]], smoking[["qc"]], names = rownames(smoking))) @ the corresponding estimate is \Sexpr{round(exp(smokingDSL$logDSL), 3)}. Both models suggest that there is clear evidence that nicotine gum increases the odds of quitting. The random effects confidence interval is considerably wider than that from the fixed effects model; here the test of homogeneity of the studies is not significant implying that we might use the fixed effects results. But the test is not particularly powerful and it is more sensible to assume a priori that heterogeneity is present and so we use the results from the random effects model. \section{Meta-Regression} The examination of heterogeneity of the effect sizes from the studies in a meta-analysis begins with the formal test for its presence, although in most meta-analyses such heterogeneity can almost be assumed to be present. There will be many possible sources of such heterogeneity and estimating how these various factors affect the observed effect sizes in the studies chosen is often of considerable interest and importance, indeed usually more important than the relatively simplistic use of meta-analysis to determine a single summary estimate of overall effect size. We can illustrate the process using the BCG vaccine data. We first find the estimate of the overall effect size from applying the fixed effects and the random effects models described previously: <>= data("BCG", package = "HSAUR3") BCG_OR <- meta.MH(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) BCG_DSL <- meta.DSL(BCG[["BCGVacc"]], BCG[["NoVacc"]], BCG[["BCGTB"]], BCG[["NoVaccTB"]], names = BCG$Study) @ The results are inspected using the \Rcmd{summary} method as shown in Figures~\ref{MA-BCGOR-summary} and \ref{MA-BCGDSL-summary}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_OR}. \label{MA-BCGOR-summary}} \SchunkLabel <>= summary(BCG_OR) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_DSL}. \label{MA-BCGDSL-summary}} \SchunkLabel <>= summary(BCG_DSL) @ \SchunkRaw To assess how the two covariates, latitude and year, relate to the observed effect sizes we shall use multiple linear regression but will weight each observation by $W_i = (\hat{\sigma}^2 + V_i^2)^{-1}, i = 1, \dots, 13$, where $\hat{\sigma}^2$ is the estimated between-study variance and $V_i^2$ is the estimated variance from the $i$th study. The required \R{} code to fit the linear model via weighted least squares is: \index{Meta-Analysis!weighted least squares regression} <>= studyweights <- 1 / (BCG_DSL$tau2 + BCG_DSL$selogs^2) y <- BCG_DSL$logs BCG_mod <- lm(y ~ Latitude + Year, data = BCG, weights = studyweights) @ and the results of the \Rcmd{summary} method are shown in Figure~\ref{MA-mod-summary}. There is some evidence that latitude is associated with observed effect size, the log-odds ratio becoming increasingly negative as latitude increases, as we can see from a scatterplot of the two variables with the added weighted regression fit seen in Figure~\ref{MA-BCG}. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{BCG\_mod}. \label{MA-mod-summary}} \SchunkLabel <>= summary(BCG_mod) @ \SchunkRaw \begin{figure} \begin{center} <>= plot(y ~ Latitude, data = BCG, ylab = "Estimated log-OR") abline(lm(y ~ Latitude, data = BCG, weights = studyweights)) @ \caption{Plot of observed effect size for the \Robject{BCG} vaccine data against latitude, with a weighted least squares regression fit shown in addition. \label{MA-BCG}} \end{center} \end{figure} \section{Publication Bias} \begin{figure} \begin{center} <>= set.seed(290875) sigma <- seq(from = 1/10, to = 1, length.out = 35) y <- rnorm(35) * sigma gr <- (y > -0.5) layout(matrix(1:2, ncol = 1)) plot(y, 1/sigma, xlab = "Effect size", ylab = "1 / standard error") plot(y[gr], 1/(sigma[gr]), xlim = range(y), xlab = "Effect size", ylab = "1 / standard error") @ \caption{Example funnel plots from simulated data. The asymmetry in the lower plot is a hint that a publication bias might be a problem. \label{MA-funnel}} \end{center} \end{figure} We can construct a funnel plot for the nicotine gum data using the \R{} code depicted with Figure~\ref{MA:funnel}. There does not appear to be any strong evidence of publication bias here. \begin{figure} \begin{center} <>= funnelplot(smokingDSL$logs, smokingDSL$selogs, summ = smokingDSL$logDSL, xlim = c(-1.7, 1.7)) abline(v = 0, lty = 2) @ \caption{Funnel plot for nicotine gum data. \label{MA:funnel}} \end{center} \end{figure} \index{Meta-analysis!funnel plots|)} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_survival_analysis.Rnw0000644000175000017500000004023614133304452017757 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Survival Analysis} %%\VignetteDepends{survival,coin,partykit} \setcounter{chapter}{10} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= x <- library("survival") x <- library("coin") x <- library("partykit") @ \chapter[Survival Analysis]{Survival Analysis: \\ Glioma Treatment and \\ Breast Cancer Survival \label{SA}} \section{Introduction} \section{Survival Analysis} \section{Analysis Using \R{}} \subsection{Glioma Radioimmunotherapy} \begin{figure} \begin{center} <>= data("glioma", package = "coin") library("survival") layout(matrix(1:2, ncol = 2)) g3 <- subset(glioma, histology == "Grade3") plot(survfit(Surv(time, event) ~ group, data = g3), main = "Grade III Glioma", lty = c(2, 1), ylab = "Probability", xlab = "Survival Time in Month", legend.text = c("Control", "Treated"), legend.bty = "n") g4 <- subset(glioma, histology == "GBM") plot(survfit(Surv(time, event) ~ group, data = g4), main = "Grade IV Glioma", ylab = "Probability", lty = c(2, 1), xlab = "Survival Time in Month", xlim = c(0, max(glioma$time) * 1.05)) @ \caption{Survival times comparing treated and control patients. \label{SA-glioma-plot}} \end{center} \end{figure} Figure~\ref{SA-glioma-plot} leads to the impression that patients treated with the novel radioimmunotherapy survive longer, regardless of the tumor type. In order to assess if this informal finding is reliable, we may perform a log-rank test via \index{Log-rank test} <>= survdiff(Surv(time, event) ~ group, data = g3) @ which indicates that the survival times are indeed different in both groups. However, the number of patients is rather limited and so it might be dangerous to rely on asymptotic tests. As shown in \Sexpr{ch("CI")}, conditioning on the data and computing the distribution of the test statistics without additional assumptions are one alternative. The function \Rcmd{surv\_test} from package \Rpackage{coin} \citep{HSAUR:Hothorn:2006:AmStat,PKG:coin} can be used to compute an exact conditional test answering the question whether the survival times differ for grade III patients. For all possible permutations of the groups on the censored response variable, the test statistic is computed and the fraction of whose being greater than the observed statistic defines the exact $p$-value: <>= library("coin") logrank_test(Surv(time, event) ~ group, data = g3, distribution = "exact") @ which, in this case, confirms the above results. The same exercise can be performed for patients with grade IV glioma <>= logrank_test(Surv(time, event) ~ group, data = g4, distribution = "exact") @ which shows a difference as well. However, it might be more appropriate to answer the question whether the novel therapy is superior for both groups of tumors simultaneously. This can be implemented by \stress{stratifying}, or \stress{blocking}, with respect to tumor grading: <>= logrank_test(Surv(time, event) ~ group | histology, data = glioma, distribution = approximate(B = 10000)) @ Here, we need to approximate the exact conditional distribution since the exact distribution is hard to compute. The result supports the initial impression implied by Figure~\ref{SA-glioma-plot}. \subsection{Breast Cancer Survival} Before fitting a Cox model to the \Robject{GBSG2} data, we again derive a Kaplan-Meier estimate of the survival function of the data, here stratified with respect to whether a patient received hormonal therapy or not (see Figure~\ref{SA-GBSG2-plot}). \begin{figure} \begin{center} <>= data("GBSG2", package = "TH.data") plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2), lty = 1:2, mark.time = FALSE, ylab = "Probability", xlab = "Survival Time in Days") legend(250, 0.2, legend = c("yes", "no"), lty = c(2, 1), title = "Hormonal Therapy", bty = "n") @ \caption{Kaplan-Meier estimates for breast cancer patients who either received hormonal therapy or not. \label{SA-GBSG2-plot}} \end{center} \end{figure} Fitting a Cox model follows roughly the same rules as shown for linear models in \Sexpr{ch("MLR")} with the exception that the response variable is again coded as a \Rclass{Surv} object. For the \Robject{GBSG2} data, the model is fitted via <>= GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2) @ and the results as given by the \Rcmd{summary} method are given in Figure~\ref{GBSG2-coxph-summary}. Since we are especially interested in the relative risk for patients who underwent hormonal therapy, we can compute an estimate of the relative risk and a corresponding confidence interval via <>= ci <- confint(GBSG2_coxph) exp(cbind(coef(GBSG2_coxph), ci))["horThyes",] @ This result implies that patients treated with hormonal therapy had a lower risk and thus survived longer compared to women who were not treated this way. \renewcommand{\nextcaption}{\R{} output of the \Rcmd{summary} method for \Robject{GBSG2\_coxph}. \label{GBSG2-coxph-summary}} \SchunkLabel <>= summary(GBSG2_coxph) @ \SchunkRaw Model checking and model selection for proportional hazards models are complicated by the fact that easy-to-use residuals, such as those discussed in \Sexpr{ch("MLR")} for linear regression models, are not available, but several possibilities do exist. A check of the proportional hazards assumption can be done by looking at the parameter estimates $\beta_1, \dots, \beta_q$ over time. We can safely assume proportional hazards when the estimates don't vary much over time. %' The null hypothesis of constant regression coefficients can be tested, both globally as well as for each covariate, by using the \Rcmd{cox.zph} function <>= GBSG2_zph <- cox.zph(GBSG2_coxph) GBSG2_zph @ There seems to be some evidence of time-varying effects, \index{Time-varying effects} especially for age and tumor grading. A graphical representation of the estimated regression coefficient over time is shown in Figure~\ref{SA-GBSG2-zph-plot}. We refer to \cite{HSAUR:TherneauGrambsch2000} for a detailed theoretical description of these topics. \begin{figure} \begin{center} <>= plot(GBSG2_zph, var = "age") @ \caption{Estimated regression coefficient for \Robject{age} depending on time for the \Robject{GBSG2} data. \label{SA-GBSG2-zph-plot}} \end{center} \end{figure} \begin{figure} \begin{center} <>= layout(matrix(1:3, ncol = 3)) res <- residuals(GBSG2_coxph) plot(res ~ age, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "Martingale Residuals") abline(h = 0, lty = 3) plot(res ~ pnodes, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) plot(res ~ log(progrec), data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) @ \caption{Martingale residuals for the \Robject{GBSG2} data. \label{SA-GBSG2-mart-plot}} \end{center} \end{figure} The tree-structured regression models applied to continuous and binary responses in \Sexpr{ch("RP")} are applicable to censored responses in survival analysis as well. Such a simple prognostic model with only a few terminal nodes might be helpful for relating the risk to certain subgroups of patients. Both \Rcmd{rpart} and the \Rcmd{ctree} function from package \Rpackage{partykit} can be applied to the GBSG2 data, where the conditional trees of the latter select cutpoints based on log-rank statistics \index{Conditional tree} <>= GBSG2_ctree <- ctree(Surv(time, cens) ~ ., data = GBSG2) @ and the \Rcmd{plot} method applied to this tree produces the graphical representation in Figure~\ref{SA-GBSG2-ctree-plot}. The number of positive lymph nodes (\Robject{pnodes}) is the most important variable in the tree, corresponding to the $p$-value associated with this variable in Cox's %%'s regression; see Figure~\ref{GBSG2-coxph-summary}. Women with not more than three positive lymph nodes who have undergone hormonal therapy seem to have the best prognosis whereas a large number of positive lymph nodes and a small value of the progesterone receptor indicates a bad prognosis. \begin{figure} \begin{center} <>= plot(GBSG2_ctree) @ \caption{Conditional inference tree for the \Robject{GBSG2} data with the survival function, estimated by Kaplan-Meier, shown for every subgroup of patients identified by the tree. \label{SA-GBSG2-ctree-plot}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_analysing_longitudinal_dataII.R0000644000175000017500000002543514133304472021613 0ustar nileshnilesh### R code from vignette source 'Ch_analysing_longitudinal_dataII.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: setup ################################################### options(digits = 3) if (!interactive()) { print.summary.gee <- function (x, digits = NULL, quote = FALSE, prefix = "", ...) { if (is.null(digits)) digits <- options()$digits else options(digits = digits) cat("...") cat("\nModel:\n") cat(" Link: ", x$model$link, "\n") cat(" Variance to Mean Relation:", x$model$varfun, "\n") if (!is.null(x$model$M)) cat(" Correlation Structure: ", x$model$corstr, ", M =", x$model$M, "\n") else cat(" Correlation Structure: ", x$model$corstr, "\n") cat("\n...") nas <- x$nas if (!is.null(nas) && any(nas)) cat("\n\nCoefficients: (", sum(nas), " not defined because of singularities)\n", sep = "") else cat("\n\nCoefficients:\n") print(x$coefficients, digits = digits) cat("\nEstimated Scale Parameter: ", format(round(x$scale, digits))) cat("\n...\n") invisible(x) } } ################################################### ### code chunk number 4: ALDII-gee ################################################### library("gee") ################################################### ### code chunk number 5: ALDII-BtheB-data ################################################### data("BtheB", package = "HSAUR3") BtheB$subject <- factor(rownames(BtheB)) nobs <- nrow(BtheB) BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m", "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long") BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4)) names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt" ################################################### ### code chunk number 6: ALDII-BtheB-geefit-indep ################################################### osub <- order(as.integer(BtheB_long$subject)) BtheB_long <- BtheB_long[osub,] btb_gee <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "independence") ################################################### ### code chunk number 7: ALDII-BtheB-geefit-ex ################################################### btb_gee1 <- gee(bdi ~ bdi.pre + trt + length + drug, data = BtheB_long, id = subject, family = gaussian, corstr = "exchangeable") ################################################### ### code chunk number 8: ALDII-BtheB-geesummary ################################################### summary(btb_gee) ################################################### ### code chunk number 9: ALDII-BtheB-gee1summary ################################################### summary(btb_gee1) ################################################### ### code chunk number 10: ALDII-respiratory-data ################################################### data("respiratory", package = "HSAUR3") resp <- subset(respiratory, month > "0") resp$baseline <- rep(subset(respiratory, month == "0")$status, rep(4, 111)) resp$nstat <- as.numeric(resp$status == "good") resp$month <- resp$month[, drop = TRUE] ################################################### ### code chunk number 11: ALDII-respiratory-names ################################################### names(resp)[names(resp) == "treatment"] <- "trt" levels(resp$trt)[2] <- "trt" ################################################### ### code chunk number 12: ALDII-respiratory-fit ################################################### resp_glm <- glm(status ~ centre + trt + gender + baseline + age, data = resp, family = "binomial") resp_gee1 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) resp_gee2 <- gee(nstat ~ centre + trt + gender + baseline + age, data = resp, family = "binomial", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) ################################################### ### code chunk number 13: ALDII-resp-glm-summary ################################################### summary(resp_glm) ################################################### ### code chunk number 14: ALDII-resp-gee1summary ################################################### summary(resp_gee1) ################################################### ### code chunk number 15: ALDII-resp-gee2-summary ################################################### summary(resp_gee2) ################################################### ### code chunk number 16: ALDII-resp-confint ################################################### se <- summary(resp_gee2)$coefficients["trttrt", "Robust S.E."] coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975) ################################################### ### code chunk number 17: ALDII-resp-confint-exp ################################################### exp(coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975)) ################################################### ### code chunk number 18: ALDII-epilepsy ################################################### data("epilepsy", package = "HSAUR3") itp <- interaction(epilepsy$treatment, epilepsy$period) tapply(epilepsy$seizure.rate, itp, mean) tapply(epilepsy$seizure.rate, itp, var) ################################################### ### code chunk number 19: ALDII-plot1 ################################################### layout(matrix(1:2, nrow = 1)) ylim <- range(epilepsy$seizure.rate) placebo <- subset(epilepsy, treatment == "placebo") progabide <- subset(epilepsy, treatment == "Progabide") boxplot(seizure.rate ~ period, data = placebo, ylab = "Number of seizures", xlab = "Period", ylim = ylim, main = "Placebo") boxplot(seizure.rate ~ period, data = progabide, main = "Progabide", ylab = "Number of seizures", xlab = "Period", ylim = ylim) ################################################### ### code chunk number 20: ALDII-plot2 ################################################### layout(matrix(1:2, nrow = 1)) ylim <- range(log(epilepsy$seizure.rate + 1)) boxplot(log(seizure.rate + 1) ~ period, data = placebo, main = "Placebo", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) boxplot(log(seizure.rate + 1) ~ period, data = progabide, main = "Progabide", ylab = "Log number of seizures", xlab = "Period", ylim = ylim) ################################################### ### code chunk number 21: ALDII-epilepsy-gee ################################################### per <- rep(log(2),nrow(epilepsy)) epilepsy$period <- as.numeric(epilepsy$period) names(epilepsy)[names(epilepsy) == "treatment"] <- "trt" fm <- seizure.rate ~ base + age + trt + offset(per) epilepsy_glm <- glm(fm, data = epilepsy, family = "poisson") epilepsy_gee1 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "independence", scale.fix = TRUE, scale.value = 1) epilepsy_gee2 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = TRUE, scale.value = 1) epilepsy_gee3 <- gee(fm, data = epilepsy, family = "poisson", id = subject, corstr = "exchangeable", scale.fix = FALSE, scale.value = 1) ################################################### ### code chunk number 22: ALDII-espilepsy-glm-summary ################################################### summary(epilepsy_glm) ################################################### ### code chunk number 23: ALDII-espilepsy-gee1-summary ################################################### summary(epilepsy_gee1) ################################################### ### code chunk number 24: ALDII-espilepsy-gee2-summary ################################################### summary(epilepsy_gee2) ################################################### ### code chunk number 25: ALDII-espilepsy-gee3-summary ################################################### summary(epilepsy_gee3) ################################################### ### code chunk number 26: ALDII-respiratory-lmer ################################################### library("lme4") resp_lmer <- glmer(status ~ baseline + month + trt + gender + age + centre + (1 | subject), family = binomial(), data = resp) exp(fixef(resp_lmer)) ################################################### ### code chunk number 27: ALDII-resp-lmer-dirty ################################################### su <- summary(resp_lmer) if (!interactive()) { summary <- function(x) { cat("\n...\n") cat("Fixed effects:\n") lme4V <- packageDescription("lme4")$Version if (compareVersion("0.999999-2", lme4V) >= 0) { printCoefmat(su@coefs) } else { printCoefmat(su$coefficients) } cat("\n...\n") } } ################################################### ### code chunk number 28: ALDII-resp-lmer-summary ################################################### summary(resp_lmer) HSAUR3/inst/doc/Ch_recursive_partitioning.Rnw0000644000175000017500000005514114133304452021000 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Recursive Partitioning} %%\VignetteDepends{vcd,lattice,randomForest,partykit} \setcounter{chapter}{8} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ <>= library("vcd") library("lattice") library("randomForest") library("partykit") ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) mai <- par("mai") options(SweaveHooks = list(nullmai = function() { par(mai = rep(0, 4)) }, twomai = function() { par(mai = c(0, mai[2], 0, 0)) }, threemai = function() { par(mai = c(0, mai[2], 0.1, 0)) })) numbers <- c("zero", "one", "two", "three", "four", "five", "six", "seven", "eight", "nine") @ \chapter[Recursive Partitioning]{Recursive Partitioning: Predicting Body Fat, Glaucoma Diagnosis, and Happiness in China \label{RP}} \section{Introduction} \section{Recursive Partitioning} \section{Analysis Using \R{}} \subsection{Predicting Body Fat Content} The \Rcmd{rpart} function from \Rpackage{rpart} can be used to grow a regression tree. The response variable and the covariates are defined by a model formula in the same way as for \Rcmd{lm}, say. By default, a large initial tree is grown, we restrict the number of observations required to establish a potential binary split to at least ten: <>= library("rpart") data("bodyfat", package = "TH.data") bodyfat_rpart <- rpart(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat, control = rpart.control(minsplit = 10)) @ A \Rcmd{print} method for \Rclass{rpart} objects is available; however, a graphical representation \citep[here utilizing functionality offered from package \Rpackage{partykit},][]{PKG:partykit} shown in Figure~\ref{RP-bodyfat-plot} is more convenient. Observations that satisfy the condition shown for each node go to the left and observations that don't are an element of the right branch in each node. %' As expected, higher values for waist and hip circumferences and wider knees correspond to higher values of body fat content. The rightmost terminal node consists of only three rather extreme observations. \begin{figure} \begin{center} <>= library("partykit") plot(as.party(bodyfat_rpart), tp_args = list(id = FALSE)) @ \caption{Initial tree for the body fat data with the distribution of body fat in terminal nodes visualized via boxplots. \label{RP-bodyfat-plot}} \end{center} \end{figure} \index{Cross-validation} To determine if the tree is appropriate or if some of the branches need to be subjected to pruning we can use the \Robject{cptable} element of the \Rclass{rpart} object: <>= print(bodyfat_rpart$cptable) opt <- which.min(bodyfat_rpart$cptable[,"xerror"]) @ The \Robject{xerror} column contains estimates of cross-validated prediction error for different numbers of splits (\Robject{nsplit}). The best tree has \Sexpr{numbers[bodyfat_rpart$cptable[opt, "nsplit"] + 1]} splits. Now we can prune back the large initial tree using <>= cp <- bodyfat_rpart$cptable[opt, "CP"] bodyfat_prune <- prune(bodyfat_rpart, cp = cp) @ The result is shown in Figure~\ref{RP-bodyfat-pruneplot}. Note that the inner nodes three and six have been removed from the tree. Still, the rightmost terminal node might give very unreliable extreme predictions. \begin{figure} \begin{center} <>= plot(as.party(bodyfat_prune), tp_args = list(id = FALSE)) @ \caption{Pruned regression tree for body fat data. \label{RP-bodyfat-pruneplot}} \end{center} \end{figure} Given this model, one can predict the (unknown, in real circumstances) body fat content based on the covariate measurements. Here, using the known values of the response variable, we compare the model predictions with the actually measured body fat as shown in Figure~\ref{RP-bodyfat-predict}. The three observations with large body fat measurements in the rightmost terminal node can be identified easily. \begin{figure} \begin{center} <>= DEXfat_pred <- predict(bodyfat_prune, newdata = bodyfat) xlim <- range(bodyfat$DEXfat) plot(DEXfat_pred ~ DEXfat, data = bodyfat, xlab = "Observed", ylab = "Predicted", ylim = xlim, xlim = xlim) abline(a = 0, b = 1) @ \caption{Observed and predicted DXA measurements. \label{RP-bodyfat-predict}} \end{center} \end{figure} \subsection{Glaucoma Diagnosis} <>= set.seed(290875) @ <>= data("GlaucomaM", package = "TH.data") glaucoma_rpart <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 100)) glaucoma_rpart$cptable opt <- which.min(glaucoma_rpart$cptable[,"xerror"]) cp <- glaucoma_rpart$cptable[opt, "CP"] glaucoma_prune <- prune(glaucoma_rpart, cp = cp) @ \setkeys{Gin}{width = 0.65\textwidth} \begin{figure} \begin{center} <>= plot(as.party(glaucoma_prune), tp_args = list(id = FALSE)) @ \caption{Pruned classification tree of the glaucoma data with class distribution in the leaves. \label{RP:gl}} \end{center} \end{figure} \setkeys{Gin}{width=0.95\textwidth} \index{Classification tree!choice of tree size} \index{Tree size} As we discussed earlier, the choice of the appropriately sized tree is not a trivial problem. For the glaucoma data, the above choice of three leaves is very unstable across multiple runs of cross-validation. As an illustration of this problem we repeat the very same analysis as shown above and record the optimal number of splits as suggested by the cross-validation runs. <>= nsplitopt <- vector(mode = "integer", length = 25) for (i in 1:length(nsplitopt)) { cp <- rpart(Class ~ ., data = GlaucomaM)$cptable nsplitopt[i] <- cp[which.min(cp[,"xerror"]), "nsplit"] } @ \newpage <>= table(nsplitopt) @ Although for \Sexpr{sum(nsplitopt == 1)} runs of cross-validation a simple tree with one split only is suggested, larger trees would have been favored in \Sexpr{sum(nsplitopt > 1)} of the cases. This short analysis shows that we should not trust the tree in Figure~\ref{RP:gl} too much. \index{Bagging} \index{Bootstrap approach!glaucoma diagnosis data} One way out of this dilemma is the aggregation of multiple trees via bagging. In \R{}, the bagging idea can be implemented by three or four lines of code. Case count or weight vectors representing the bootstrap samples can be drawn from the multinominal distribution with parameters $n$ and $p_1 = 1/n, \dots, p_n = 1/n$ via the \Rcmd{rmultinom} function. For each weight vector, one large tree is constructed without pruning and the \Rclass{rpart} objects are stored in a list, here called \Robject{trees}: <>= trees <- vector(mode = "list", length = 25) n <- nrow(GlaucomaM) bootsamples <- rmultinom(length(trees), n, rep(1, n)/n) mod <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 0)) for (i in 1:length(trees)) trees[[i]] <- update(mod, weights = bootsamples[,i]) @ The \Rcmd{update} function re-evaluates the call of \Robject{mod}, however, with the weights being altered, i.e., fits a tree to a bootstrap sample specified by the weights. It is interesting to have a look at the structures of the multiple trees. For example, the variable selected for splitting in the root of the tree is not unique as can be seen by <>= table(sapply(trees, function(x) as.character(x$frame$var[1]))) @ Although \Robject{varg} is selected most of the time, other variables such as \Robject{vari} occur as well -- a further indication that the tree in Figure~\ref{RP:gl} is questionable and that hard decisions are not appropriate for the glaucoma data. In order to make use of the ensemble of trees in the list \Robject{trees} we estimate the conditional probability of suffering from glaucoma given the covariates for each observation in the original data set by <>= classprob <- matrix(0, nrow = n, ncol = length(trees)) for (i in 1:length(trees)) { classprob[,i] <- predict(trees[[i]], newdata = GlaucomaM)[,1] classprob[bootsamples[,i] > 0,i] <- NA } @ Thus, for each observation we get \Sexpr{length(trees)} estimates. However, each observation has been used for growing one of the trees with probability $0.632$ and thus was not used with probability $0.368$. Consequently, the estimate from a tree where an observation was not used for growing is better for judging the quality of the predictions and we label the other estimates with \Robject{NA}. Now, we can average the estimates and we vote for glaucoma when the average of the estimates of the conditional glaucoma probability exceeds $0.5$. The comparison between the observed and the predicted classes does not suffer from overfitting since the predictions are computed from those trees for which each single observation was \stress{not} used for growing. <>= avg <- rowMeans(classprob, na.rm = TRUE) predictions <- factor(ifelse(avg > 0.5, "glaucoma", "normal")) predtab <- table(predictions, GlaucomaM$Class) predtab @ Thus, an honest estimate of the probability of a glaucoma prediction when the patient is actually suffering from glaucoma is <>= round(predtab[1,1] / colSums(predtab)[1] * 100) @ per cent. For <>= round(predtab[2,2] / colSums(predtab)[2] * 100) @ percent of normal eyes, the ensemble does not predict glaucomateous damage. \begin{figure} \begin{center} <>= library("lattice") gdata <- data.frame(avg = rep(avg, 2), class = rep(as.numeric(GlaucomaM$Class), 2), obs = c(GlaucomaM[["varg"]], GlaucomaM[["vari"]]), var = factor(c(rep("varg", nrow(GlaucomaM)), rep("vari", nrow(GlaucomaM))))) panelf <- function(x, y) { panel.xyplot(x, y, pch = gdata$class) panel.abline(h = 0.5, lty = 2) } print(xyplot(avg ~ obs | var, data = gdata, panel = panelf, scales = "free", xlab = "", ylab = "Estimated Class Probability Glaucoma")) @ \caption{Estimated class probabilities depending on two important variables. The $0.5$ cut-off for the estimated glaucoma probability is depicted as a horizontal line. Glaucomateous eyes are plotted as circles and normal eyes are triangles. \label{RP:glplot}} \end{center} \end{figure} \index{Random forest} The bagging procedure is a special case of a more general approach called \stress{random forest} \citep{HSAUR:Breiman2001b}. The package \Rpackage{randomForest} \citep{PKG:randomForest} can be used to compute such ensembles via <>= library("randomForest") rf <- randomForest(Class ~ ., data = GlaucomaM) @ and we obtain out-of-bag estimates for the prediction error via <>= table(predict(rf), GlaucomaM$Class) @ \subsection{Trees Revisited} For the body fat data, such a \stress{conditional inference tree} can be computed using the \Rcmd{ctree} function \index{Conditional tree} <>= bodyfat_ctree <- ctree(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat) @ This tree doesn't require a pruning procedure because an internal stop criterion based on formal statistical tests prevents the procedure from overfitting the data. The tree structure is shown in Figure~\ref{RP-bodyfat-ctree-plot}. Although the structure of this tree and the tree depicted in Figure~\ref{RP-bodyfat-pruneplot} are rather different, the corresponding predictions don't vary too much. \begin{figure} \begin{center} <>= plot(bodyfat_ctree, tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of body fat content shown for each terminal leaf. \label{RP-bodyfat-ctree-plot}} \end{center} \end{figure} Very much the same code is needed to grow a tree on the glaucoma data: <>= glaucoma_ctree <- ctree(Class ~ ., data = GlaucomaM) @ and a graphical representation is depicted in Figure~\ref{RP-glaucoma-ctree-plot} showing both the cutpoints and the $p$-values of the associated independence tests for each node. The first split is performed using a cutpoint defined with respect to the volume of the optic nerve above some reference plane, but in the inferior part of the eye only (\Robject{vari}). \begin{figure} \begin{center} <>= plot(glaucoma_ctree, tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of glaucomateous eyes shown for each terminal leaf. \label{RP-glaucoma-ctree-plot}} \end{center} \end{figure} \subsection{Happiness in China} \index{Chinese Health and Family Life Survey} A conditional inference tree is a simple alternative to the proportional odds model for the regression analysis of the happiness variable from the Chinese Health and Family Life Survey. In each node, a linear association test introduced in Section~\ref{CI:Lanza} taking the ordering of the happiness levels into account is applied for selecting variables and split-points. Before we fit the tree with the \Rcmd{ctree} function, we recode the levels of the happiness variable to allow plotting of these symbols with restricted page space: \newpage <>= levels(CHFLS$R_happy) levels(CHFLS$R_happy) <- LETTERS[1:4] CHFLS_ctree <- ctree(R_happy ~ ., data = CHFLS) @ The resulting tree is depicted in Figure~\ref{RP-CHFLS-ctree-plot} and very nicely backs up the results obtained from the proportional odds model in Chapter~\ref{GLM}. The distribution of self-reported happiness is shifted from very unhappy to very happy with increasing values of self-reported health, i.e., women that reported excellent health (mind the $>$ sign in the right label of the root split!) were at least somewhat happy with only a few exceptions. Women with poor or not good health reported being not too happy much more often. There seems to be further differentiation with respect to geography and also income but the differences in the distributions depicted in the terminal leaves are negligible. \begin{figure} \begin{center} <>= plot(CHFLS_ctree, ep_args = list(justmin = 10), tp_args = list(id = FALSE)) @ \caption{Conditional inference tree with the distribution of self-reported happiness shown for each terminal leaf. The levels of happiness have been abbreviated (A: very unhappy, B: not too happy, C: somewhat happy; D: very happy). The \Rcmd{justmin} argument ensures that split descriptions longer than $10$ characters are displayed over two lines. \label{RP-CHFLS-ctree-plot}} \end{center} \end{figure} \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_recursive_partitioning.R0000644000175000017500000002332214133304567020436 0ustar nileshnilesh### R code from vignette source 'Ch_recursive_partitioning.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: RP-setup ################################################### library("vcd") library("lattice") library("randomForest") library("partykit") ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme ltheme$strip.background$col <- "transparent" ## change strip bg lattice.options(default.theme = ltheme) mai <- par("mai") options(SweaveHooks = list(nullmai = function() { par(mai = rep(0, 4)) }, twomai = function() { par(mai = c(0, mai[2], 0, 0)) }, threemai = function() { par(mai = c(0, mai[2], 0.1, 0)) })) numbers <- c("zero", "one", "two", "three", "four", "five", "six", "seven", "eight", "nine") ################################################### ### code chunk number 4: RP-bodyfat-rpart ################################################### library("rpart") data("bodyfat", package = "TH.data") bodyfat_rpart <- rpart(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat, control = rpart.control(minsplit = 10)) ################################################### ### code chunk number 5: RP-bodyfat-plot ################################################### getOption("SweaveHooks")[["nullmai"]]() library("partykit") plot(as.party(bodyfat_rpart), tp_args = list(id = FALSE)) ################################################### ### code chunk number 6: RP-bodyfat-cp ################################################### print(bodyfat_rpart$cptable) opt <- which.min(bodyfat_rpart$cptable[,"xerror"]) ################################################### ### code chunk number 7: RP-bodyfat-prune ################################################### cp <- bodyfat_rpart$cptable[opt, "CP"] bodyfat_prune <- prune(bodyfat_rpart, cp = cp) ################################################### ### code chunk number 8: RP-bodyfat-pruneplot ################################################### getOption("SweaveHooks")[["twomai"]]() plot(as.party(bodyfat_prune), tp_args = list(id = FALSE)) ################################################### ### code chunk number 9: RP-bodyfat-predict ################################################### DEXfat_pred <- predict(bodyfat_prune, newdata = bodyfat) xlim <- range(bodyfat$DEXfat) plot(DEXfat_pred ~ DEXfat, data = bodyfat, xlab = "Observed", ylab = "Predicted", ylim = xlim, xlim = xlim) abline(a = 0, b = 1) ################################################### ### code chunk number 10: RP-seed-again ################################################### set.seed(290875) ################################################### ### code chunk number 11: RP-glaucoma-rpart ################################################### data("GlaucomaM", package = "TH.data") glaucoma_rpart <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 100)) glaucoma_rpart$cptable opt <- which.min(glaucoma_rpart$cptable[,"xerror"]) cp <- glaucoma_rpart$cptable[opt, "CP"] glaucoma_prune <- prune(glaucoma_rpart, cp = cp) ################################################### ### code chunk number 12: RP-glaucoma-plot ################################################### getOption("SweaveHooks")[["nullmai"]]() plot(as.party(glaucoma_prune), tp_args = list(id = FALSE)) ################################################### ### code chunk number 13: RP-glaucoma-cp ################################################### nsplitopt <- vector(mode = "integer", length = 25) for (i in 1:length(nsplitopt)) { cp <- rpart(Class ~ ., data = GlaucomaM)$cptable nsplitopt[i] <- cp[which.min(cp[,"xerror"]), "nsplit"] } ################################################### ### code chunk number 14: RP-glaucoma-cp-print ################################################### table(nsplitopt) ################################################### ### code chunk number 15: RP-glaucoma-bagg ################################################### trees <- vector(mode = "list", length = 25) n <- nrow(GlaucomaM) bootsamples <- rmultinom(length(trees), n, rep(1, n)/n) mod <- rpart(Class ~ ., data = GlaucomaM, control = rpart.control(xval = 0)) for (i in 1:length(trees)) trees[[i]] <- update(mod, weights = bootsamples[,i]) ################################################### ### code chunk number 16: RP-glaucoma-splits ################################################### table(sapply(trees, function(x) as.character(x$frame$var[1]))) ################################################### ### code chunk number 17: RP-glaucoma-baggpred ################################################### classprob <- matrix(0, nrow = n, ncol = length(trees)) for (i in 1:length(trees)) { classprob[,i] <- predict(trees[[i]], newdata = GlaucomaM)[,1] classprob[bootsamples[,i] > 0,i] <- NA } ################################################### ### code chunk number 18: RP-glaucoma-avg ################################################### avg <- rowMeans(classprob, na.rm = TRUE) predictions <- factor(ifelse(avg > 0.5, "glaucoma", "normal")) predtab <- table(predictions, GlaucomaM$Class) predtab ################################################### ### code chunk number 19: RP-glaucoma-sens ################################################### round(predtab[1,1] / colSums(predtab)[1] * 100) ################################################### ### code chunk number 20: RP-glaucoma-spez ################################################### round(predtab[2,2] / colSums(predtab)[2] * 100) ################################################### ### code chunk number 21: RP-glaucoma-baggplot ################################################### library("lattice") gdata <- data.frame(avg = rep(avg, 2), class = rep(as.numeric(GlaucomaM$Class), 2), obs = c(GlaucomaM[["varg"]], GlaucomaM[["vari"]]), var = factor(c(rep("varg", nrow(GlaucomaM)), rep("vari", nrow(GlaucomaM))))) panelf <- function(x, y) { panel.xyplot(x, y, pch = gdata$class) panel.abline(h = 0.5, lty = 2) } print(xyplot(avg ~ obs | var, data = gdata, panel = panelf, scales = "free", xlab = "", ylab = "Estimated Class Probability Glaucoma")) ################################################### ### code chunk number 22: RP-glaucoma-rf ################################################### library("randomForest") rf <- randomForest(Class ~ ., data = GlaucomaM) ################################################### ### code chunk number 23: RP-glaucoma-rf-oob ################################################### table(predict(rf), GlaucomaM$Class) ################################################### ### code chunk number 24: RP-bodyfat-ctree ################################################### bodyfat_ctree <- ctree(DEXfat ~ age + waistcirc + hipcirc + elbowbreadth + kneebreadth, data = bodyfat) ################################################### ### code chunk number 25: RP-bodyfat-ctree-plot ################################################### plot(bodyfat_ctree, tp_args = list(id = FALSE)) ################################################### ### code chunk number 26: RP-glaucoma-ctree ################################################### glaucoma_ctree <- ctree(Class ~ ., data = GlaucomaM) ################################################### ### code chunk number 27: RP-glaucoma-ctree-plot ################################################### plot(glaucoma_ctree, tp_args = list(id = FALSE)) ################################################### ### code chunk number 28: RP-CHFLS-ctree ################################################### levels(CHFLS$R_happy) levels(CHFLS$R_happy) <- LETTERS[1:4] CHFLS_ctree <- ctree(R_happy ~ ., data = CHFLS) ################################################### ### code chunk number 29: RP-CHFLS-ctree-plot ################################################### plot(CHFLS_ctree, ep_args = list(justmin = 10), tp_args = list(id = FALSE)) HSAUR3/inst/NEWS0000644000175000017500000000121014133303116013012 0ustar nileshnilesh 1.0-11 (2021-10-18) o reduce size of tar.gz archive 1.0-11 (2021-04-06) o reduce size of tar.gz archive 1.0-10 (2020-09-21) o remove dependency on alr3 1.0-9 (2018-05-28) o update to mice 3.0.0 1.0-8 (2017-08-18) o remove longtable.sty 1.0-7 (2017-06-21) o use logrank_test instead of surv_test (for coin 1.2-0) 1.0-6 (2017-02-28) o tm is not actually needed 1.0-5 (2015-07-28) o NAMESPACE updates 1.0-4 (2015-03-09) o wgs84 -> WGS84 1.0-3 (2015-01-05) o remove platform-dependent Makefiles 1.0-2 (2014-08-18) o tools::delimMatch o png figures 1.0-1 (2014-06-26) o update URL o fix vignette index entries HSAUR3/cleanup0000755000175000017500000000146714133304614012735 0ustar nileshnilesh#!/bin/sh for f in ./R/*~; do rm -f $f done for f in ./man/*~; do rm -f $f done for f in *~; do rm -f $f done for f in .*~; do rm -f $f done for f in ./tests/*~; do rm -f $f done for f in ./inst/*~; do rm -f $f done for f in ./tests/*.ps; do rm -f $f done for f in ./inst/doc/*~; do rm -f $f done for f in ./inst/doc/*.aux; do rm -f $f done for f in ./inst/doc/*.bbl; do rm -f $f done for f in 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LC0>ؘ^+rNFzzup1ߒjhqZ0[DFXBFu)(xOĚvv@EWr+t>eRR(5oLǾVؖY\'Α2qzX=yY"Au(n c g]˰ l|dϺnM@&z Ǝ0E?mW:dTt&9yU YOKRjuݲ/ZE(HauT:׏]L [e9R:y]1E7oA~?endstream endobj 210 0 obj << /Filter /FlateDecode /Length 150 >> stream xU;1 {'0q_N@ -ׇE٬W.,?慅:c8]J`̤\՘pBf3y0IVL;)H%Q3T3!T*_qӊ[;KY I*) vjKԐuSBC endstream endobj 211 0 obj << /Type /XRef /Length 196 /Filter /FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 212 /ID [] >> stream xcb&F~0 $8J ?HZ }?( <M#Ϡh-AKtDrA) DJ`@$j"͙$KAl=fy l`5z AX%Q09D? b,;z]{ *&DVtʂج" l8mg% endstream endobj startxref 204263 %%EOF HSAUR3/inst/doc/Ch_analysis_of_variance.R0000644000175000017500000002064614133304474020022 0ustar nileshnilesh### R code from vignette source 'Ch_analysis_of_variance.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: ANOVA-setup ################################################### library("wordcloud") ################################################### ### code chunk number 4: ANOVA-weightgain-mean-var ################################################### data("weightgain", package = "HSAUR3") tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), mean) tapply(weightgain$weightgain, list(weightgain$source, weightgain$type), sd) ################################################### ### code chunk number 5: ANOVA-weightgain-plot ################################################### plot.design(weightgain) ################################################### ### code chunk number 6: ANOVA-weightgain-aov ################################################### wg_aov <- aov(weightgain ~ source * type, data = weightgain) ################################################### ### code chunk number 7: ANOVA-weightgain-aov-summary ################################################### summary(wg_aov) ################################################### ### code chunk number 8: ANOVA-weightgain-iplot (eval = FALSE) ################################################### ## interaction.plot(weightgain$type, weightgain$source, ## weightgain$weightgain) ################################################### ### code chunk number 9: ANOVA-weightgain-iplot-nice ################################################### interaction.plot(weightgain$type, weightgain$source, weightgain$weightgain, legend = FALSE) legend(1.5, 95, legend = levels(weightgain$source), title = "weightgain$source", lty = c(2,1), bty = "n") ################################################### ### code chunk number 10: ANOVA-weightgain-coef ################################################### coef(wg_aov) ################################################### ### code chunk number 11: ANOVA-weightgain-contrasts ################################################### options("contrasts") ################################################### ### code chunk number 12: ANOVA-weightgain-coef-sum ################################################### coef(aov(weightgain ~ source + type + source:type, data = weightgain, contrasts = list(source = contr.sum))) ################################################### ### code chunk number 13: ANOVA-foster ################################################### data("foster", package = "HSAUR3") ################################################### ### code chunk number 14: ANOVA-foster-plot ################################################### plot.design(foster) ################################################### ### code chunk number 15: ANOVA-foster-aov-one (eval = FALSE) ################################################### ## summary(aov(weight ~ litgen * motgen, data = foster)) ################################################### ### code chunk number 16: ANOVA-foster-aov-one ################################################### summary(aov(weight ~ litgen * motgen, data = foster)) ################################################### ### code chunk number 17: ANOVA-foster-aov-two (eval = FALSE) ################################################### ## summary(aov(weight ~ motgen * litgen, data = foster)) ################################################### ### code chunk number 18: ANOVA-foster-aov-two ################################################### summary(aov(weight ~ motgen * litgen, data = foster)) ################################################### ### code chunk number 19: ANOVA-weightgain-again (eval = FALSE) ################################################### ## summary(aov(weightgain ~ type * source, data = weightgain)) ################################################### ### code chunk number 20: ANOVA-foster-aov ################################################### foster_aov <- aov(weight ~ litgen * motgen, data = foster) ################################################### ### code chunk number 21: ANOVA-foster-tukeyHSD ################################################### foster_hsd <- TukeyHSD(foster_aov, "motgen") foster_hsd ################################################### ### code chunk number 22: ANOVA-foster-tukeyHSDplot ################################################### plot(foster_hsd) ################################################### ### code chunk number 23: ANOVA-water-manova ################################################### data("water", package = "HSAUR3") summary(manova(cbind(hardness, mortality) ~ location, data = water), test = "Hotelling-Lawley") ################################################### ### code chunk number 24: ANOVA-water-means ################################################### tapply(water$hardness, water$location, mean) tapply(water$mortality, water$location, mean) ################################################### ### code chunk number 25: ANOVA-skulls-data ################################################### data("skulls", package = "HSAUR3") means <- aggregate(skulls[,c("mb", "bh", "bl", "nh")], list(epoch = skulls$epoch), mean) means ################################################### ### code chunk number 26: ANOVA-skulls-fig ################################################### pairs(means[,-1], panel = function(x, y) { textplot(x, y, levels(skulls$epoch), new = FALSE, cex = 0.8) }) ################################################### ### code chunk number 27: ANOVA-skulls-manova ################################################### skulls_manova <- manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls) summary(skulls_manova, test = "Pillai") summary(skulls_manova, test = "Wilks") summary(skulls_manova, test = "Hotelling-Lawley") summary(skulls_manova, test = "Roy") ################################################### ### code chunk number 28: ANOVA-skulls-manova2 ################################################### summary.aov(skulls_manova) ################################################### ### code chunk number 29: ANOVA-skulls-manova3 ################################################### summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c3300BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c1850BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "c200BC"))) summary(manova(cbind(mb, bh, bl, nh) ~ epoch, data = skulls, subset = epoch %in% c("c4000BC", "cAD150"))) HSAUR3/inst/doc/Ch_principal_components_analysis.Rnw0000644000175000017500000004132714133304452022334 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Principal Component Analysis} \setcounter{chapter}{18} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Principal Component Analysis]{Principal Component Analysis: The Olympic Heptathlon \label{PCA}} \section{Introduction} \section{Principal Component Analysis} \section{Analysis Using \R{}} To begin it will help to score all seven events in the same direction, so that `large' values are `good'. We will recode the running events to achieve this; <>=a data("heptathlon", package = "HSAUR3") heptathlon$hurdles <- max(heptathlon$hurdles) - heptathlon$hurdles heptathlon$run200m <- max(heptathlon$run200m) - heptathlon$run200m heptathlon$run800m <- max(heptathlon$run800m) - heptathlon$run800m @ \begin{figure} \begin{center} <>= score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) @ \caption{Scatterplot matrix for the \Robject{heptathlon} data (all countries). \label{PCA-heptathlon-scatter}} \end{center} \end{figure} Figure~\ref{PCA-heptathlon-scatter} shows a scatterplot matrix of the results from all $25$ competitors for the seven events. Most of the scatterplots in the diagram suggest that there is a positive relationship between the results for each pairs of events. The exception are the plots involving the javelin event which give little evidence of any relationship between the result for this event and the results from the other six events; we will suggest possible reasons for this below, but first we will examine the numerical values of the between pairs events correlations by applying the \Rcmd{cor} function <>= w <- options("width") options(width = 65) @ <>= round(cor(heptathlon[,-score]), 2) @ <>= options(width = w$width) @ Examination of these numerical values confirms that most pairs of events are positively correlated, some moderately (for example, high jump and shot) and others relatively highly (for example, high jump and hurdles). And we see that the correlations involving the javelin event are all close to zero. One possible explanation for the latter finding is perhaps that training for the other six events does not help much in the javelin because it is essentially a `technical' event. An alternative explanation is found if we examine the scatterplot matrix in Figure~\ref{PCA-heptathlon-scatter} a little more closely. It is very clear in this diagram that for all events except the javelin there is an outlier, the competitor from Papua New Guinea (PNG), who is much poorer than the other athletes at these six events and who finished last in the competition in terms of points scored. But surprisingly in the scatterplots involving the javelin it is this competitor who again stands out but because she has the third highest value for the event. It might be sensible to look again at both the correlation matrix and the scatterplot matrix after removing the competitor from PNG; the relevant \R{} code is <>= heptathlon <- heptathlon[-grep("PNG", rownames(heptathlon)),] @ Now, we again look at the scatterplot and correlation matrix; \begin{figure} \begin{center} <>= score <- which(colnames(heptathlon) == "score") plot(heptathlon[,-score]) @ \caption{Scatterplot matrix for the \Robject{heptathlon} data after removing observations of the PNG competitor. \label{PCA-heptathlon-scatter2}} \end{center} \end{figure} <>= w <- options("width") options(width = 65) @ <>= round(cor(heptathlon[,-score]), 2) @ <>= options(width = w$width) @ The correlations change quite substantially and the new scatterplot matrix in Figure~\ref{PCA-heptathlon-scatter2} does not point us to any further extreme observations. In the remainder of this chapter we analyze the \Robject{heptathlon} data with the observations of the competitor from Papua New Guinea removed. <>= w <- options("digits") options(digits = 4) @ Because the results for the seven heptathlon events are on different scales we shall extract the principal components from the correlation matrix. A principal component analysis of the data can be applied using the \Rcmd{prcomp} function with the \Rcmd{scale} argument set to \Robject{TRUE} to ensure the analysis is carried out on the correlation matrix. The result is a list containing the coefficients defining each component (sometimes referred to as \stress{loadings}), \index{Loadings} the principal component scores, etc. The required code is (omitting the \Robject{score} variable) <>= heptathlon_pca <- prcomp(heptathlon[, -score], scale = TRUE) print(heptathlon_pca) @ The \Rcmd{summary} method can be used for further inspection of the details: <>= summary(heptathlon_pca) @ <>= options(digits = w$digits) @ The linear combination for the first principal component is <>= a1 <- heptathlon_pca$rotation[,1] a1 @ We see that the hurdles and long jump competitions receive the highest weight but the javelin result is less important. For computing the first principal component, the data need to be rescaled appropriately. The center and the scaling used by \Rcmd{prcomp} internally can be extracted from the \Robject{heptathlon\_pca} via <>= center <- heptathlon_pca$center scale <- heptathlon_pca$scale @ Now, we can apply the \Rcmd{scale} function to the data and multiply with the loadings matrix in order to compute the first principal component score for each competitor <>= hm <- as.matrix(heptathlon[,-score]) drop(scale(hm, center = center, scale = scale) %*% heptathlon_pca$rotation[,1]) @ or, more conveniently, by extracting the first from all precomputed principal components <>= predict(heptathlon_pca)[,1] @ \begin{figure} \begin{center} <>= plot(heptathlon_pca) @ \caption{Barplot of the variances explained by the principal components (with observations for PNG removed). \label{PCA-heptathlon-pca-plot}} \end{center} \end{figure} <>= sdev <- heptathlon_pca$sdev prop12 <- round(sum(sdev[1:2]^2)/sum(sdev^2)*100, 0) @ The first two components account for $\Sexpr{prop12}\%$ of the variance. A barplot of each component's variance (see %%' Figure~\ref{PCA-heptathlon-pca-plot}) shows how the first two components dominate. A plot of the data in the space of the first two principal components, with the points labeled by the name of the corresponding competitor, can be produced as shown with Figure~\ref{PCA-heptathlon-biplot}. In addition, the first two loadings for the events are given in a second coordinate system, also illustrating the special role of the javelin event. This graphical representation is known as \stress{biplot} \citep{HSAUR:Gabriel1971}. \index{Biplot} A biplot is a graphical representation of the information in an $n \times p$ data matrix. The `bi' is a reflection that the technique produces a diagram that gives variance and covariance information about the variables and information about generalized distances between individuals. The coordinates used to produce the biplot can all be obtained directly from the principal components analysis of the covariance matrix of the data and so the plots can be viewed as an alternative representation of the results of such an analysis. Full details of the technical details of the biplot are given in \cite{HSAUR:Gabriel1981} and in \cite{HSAUR:GowerHand1996}. Here we simply construct the biplot for the heptathlon data (without PNG); the result is shown in Figure~\ref{PCA-heptathlon-biplot}. The plot clearly shows that the winner of the gold medal, Jackie Joyner-Kersee, accumulates the majority of her points from the three events long jump, hurdles, and 200m. \begin{figure} \begin{center} <>= biplot(heptathlon_pca, col = c("gray", "black")) @ <>= tmp <- heptathlon[, -score] rownames(tmp) <- abbreviate(gsub(" \\(.*", "", rownames(tmp))) biplot(prcomp(tmp, scale = TRUE), col = c("black", "lightgray"), xlim = c(-0.5, 0.7)) @ \caption{Biplot of the (scaled) first two principal components (with observations for PNG removed). \label{PCA-heptathlon-biplot}} \end{center} \end{figure} The correlation between the score given to each athlete by the standard scoring system used for the heptathlon and the first principal component score can be found from <>= cor(heptathlon$score, heptathlon_pca$x[,1]) @ This implies that the first principal component is in good agreement with the score assigned to the athletes by official Olympic rules; a scatterplot of the official score and the first principal component is given in Figure~\ref{PCA-heptathlonscore}. \begin{figure} \begin{center} <>= plot(heptathlon$score, heptathlon_pca$x[,1]) @ \caption{Scatterplot of the score assigned to each athlete in 1988 and the first principal component. \label{PCA-heptathlonscore}} \end{center} \end{figure} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_conditional_inference.Rnw0000644000175000017500000003731214133304452020523 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Conditional Inference} %%\VignetteDepends{coin} \setcounter{chapter}{3} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Conditional Inference]{Conditional Inference: Guessing Lengths, Suicides, Gastrointestinal Damage, and Newborn Infants \label{CI}} <>= data("roomwidth", package = "HSAUR3") nobs <- table(roomwidth$unit) ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - length(unique(x))) library("coin") @ \section{Introduction} \section{Conditional Test Procedures} \section{Analysis Using \R{}} \subsection{Estimating the Width of a Room Revised} The unconditional analysis of the room width estimated by two groups of students in \Sexpr{ch("SI")} led to the conclusion that the estimates in meters are slightly larger than the estimates in feet. Here, we reanalyze these data in a conditional framework. First, we convert meters into feet and store the vector of observations in a variable \Robject{y}: <>= data("roomwidth", package = "HSAUR3") convert <- ifelse(roomwidth$unit == "feet", 1, 3.28) feet <- roomwidth$unit == "feet" meter <- !feet y <- roomwidth$width * convert @ The test statistic is simply the difference in means <>= T <- mean(y[feet]) - mean(y[meter]) T @ In order to approximate the conditional distribution of the test statistic $T$ we compute $9999$ test statistics for shuffled $y$ values. A permutation of the $y$ vector can be obtained from the \Rcmd{sample} function. <>= meandiffs <- double(9999) for (i in 1:length(meandiffs)) { sy <- sample(y) meandiffs[i] <- mean(sy[feet]) - mean(sy[meter]) } @ \begin{figure} \begin{center} <>= hist(meandiffs) abline(v = T, lty = 2) abline(v = -T, lty = 2) @ \caption{An approximation for the conditional distribution of the difference of mean \Robject{roomwidth} estimates in the feet and meters group under the null hypothesis. The vertical lines show the negative and positive absolute value of the test statistic $T$ obtained from the original data. \label{CI:perm}} \end{center} \end{figure} The distribution of the test statistic $T$ under the null hypothesis of independence of room width estimates and groups is depicted in Figure~\ref{CI:perm}. Now, the value of the test statistic $T$ for the original unshuffled data can be compared with the distribution of $T$ under the null hypothesis (the vertical lines in Figure~\ref{CI:perm}). The $p$-value, i.e., the proportion of test statistics $T$ larger than \Sexpr{-round(T, 3)} or smaller than \Sexpr{round(T, 3)}, is <>= greater <- abs(meandiffs) > abs(T) mean(greater) @ with a confidence interval of <>= binom.test(sum(greater), length(greater))$conf.int @ Note that the approximated conditional $p$-value is roughly the same as the $p$-value reported by the $t$-test in \Sexpr{ch("SI")}. \renewcommand{\nextcaption}{\R{} output of the exact permutation test applied to the \Robject{roomwidth} data. \label{CI-roomwidth-p-fig}} \SchunkLabel <>= library("coin") independence_test(y ~ unit, data = roomwidth, distribution = exact()) @ \SchunkRaw \renewcommand{\nextcaption}{\R{} output of the exact conditional Wilcoxon rank sum test applied to the \Robject{roomwidth} data. \label{CI-roomwidth-w-fig}} \SchunkLabel <>= wilcox_test(y ~ unit, data = roomwidth, distribution = exact()) @ \SchunkRaw \subsection{Crowds and Threatened Suicide} \renewcommand{\nextcaption}{\R{} output of Fisher's exact test for the %' \Robject{suicides} data. \label{CI-suicides-fig}} \SchunkLabel <>= data("suicides", package = "HSAUR3") fisher.test(suicides) @ \SchunkRaw <>= ftp <- round(fisher.test(suicides)$p.value, 3) ctp <- round(chisq.test(suicides)$p.value, 3) @ \subsection{Gastrointestinal Damage} \label{CI:Lanza} Here we are interested in the comparison of two groups of patients, where one group received a placebo and the other one Misoprostol. In the trials shown here, the response variable is measured on an ordered scale -- see Table~\ref{CI:scores}. Data from four clinical studies are available and thus the observations are naturally grouped together. From the \Rclass{data.frame} \Robject{Lanza} we can construct a three-way table as follows: <>= data("Lanza", package = "HSAUR3") xtabs(~ treatment + classification + study, data = Lanza) @ <>= options(width = 65) @ For the first study, the null hypothesis of independence of treatment and gastrointestinal damage, i.e., of no treatment effect of Misoprostol, is tested by <>= library("coin") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "I") @ and, by default, the conditional distribution is approximated by the corresponding limiting distribution. The $p$-value indicates a strong treatment effect. For the second study, the asymptotic $p$-value is a little bit larger: <>= cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II") @ and we make sure that the implied decision is correct by calculating a confidence interval for the exact $p$-value: <>= p <- cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "II", distribution = approximate(B = 19999)) pvalue(p) @ The third and fourth study indicate a strong treatment effect as well: <>= cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "III") cmh_test(classification ~ treatment, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30)), subset = Lanza$study == "IV") @ At the end, a separate analysis for each study is unsatisfactory. Because the design of the four studies is the same, we can use \Robject{study} as a block variable and perform a global linear-association test investigating the treatment effect of Misoprostol in all four studies. The block variable can be incorporated into the \Rclass{formula} by the \texttt{|} symbol. <>= cmh_test(classification ~ treatment | study, data = Lanza, scores = list(classification = c(0, 1, 6, 17, 30))) @ Based on this result, a strong treatment effect can be established. \subsection{Teratogenesis} \index{Teratogenesis} In this example, the medical doctor (MD) and the research assistant (RA) assessed the number of anomalies ($0, 1, 2$ or $3$) for each of $395$ babies: <>= anomalies <- c(235, 23, 3, 0, 41, 35, 8, 0, 20, 11, 11, 1, 2, 1, 3, 1) anomalies <- as.table(matrix(anomalies, ncol = 4, dimnames = list(MD = 0:3, RA = 0:3))) anomalies @ We are interested in testing whether the number of anomalies assessed by the medical doctor differs structurally from the number reported by the research assistant. Because we compare \stress{paired} observations, i.e., one pair of measurements for each newborn, a test of marginal homogeneity (a generalization of McNemar's test, \Sexpr{ch("SI")}) needs to be applied: %%' %\newpage <>= mh_test(anomalies) @ The $p$-value indicates a deviation from the null hypothesis. However, the levels of the response are not treated as ordered. Similar to the analysis of the gastrointestinal damage data above, we can take this information into account by the definition of an appropriate score. Here, the number of anomalies is a natural choice: <>= mh_test(anomalies, scores = list(response = c(0, 1, 2, 3))) @ In our case, one can conclude that the assessment of the number of anomalies differs between the medical doctor and the research assistant. %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_cluster_analysis.Rnw0000644000175000017500000004355014133304452017567 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Cluster Analysis} %%\VignetteDepends{scatterplot3d,mclust,mvtnorm,lattice} \setcounter{chapter}{20} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ %% lower png resolution for vignettes \SweaveOpts{resolution = 100} <>= library("mclust") library("mvtnorm") mai <- par("mai") options(SweaveHooks = list(rmai = function() { par(mai = mai * c(1,1,1,2))})) data("pottery", package = "HSAUR3") @ \chapter[Cluster Analysis]{Cluster Analysis: Classifying Romano-British Pottery and Exoplanets \label{CA}} \section{Introduction} \section{Cluster Analysis} \section{Analysis Using \R{}} \subsection{Classifying Romano-British Pottery} We start our analysis with computing the dissimilarity matrix containing the Euclidean distance of the chemical measurements on all $\Sexpr{nrow(pottery)}$ pots. The resulting $\Sexpr{nrow(pottery)} \times \Sexpr{nrow(pottery)}$ matrix can be inspected by an \stress{image plot}, here obtained from \index{Image plot} function \Rcmd{levelplot} available in package \Rpackage{lattice} \citep{PKG:lattice, HSAUR:Sarkar2008}. Such a plot associates each cell of the dissimilarity matrix with a color or a gray value. We choose a very dark grey for cells with distance zero (i.e., the diagonal elements of the dissimilarity matrix) and pale values for cells with greater Euclidean distance. Figure~\ref{CA-pottery-distplot} leads to the impression that there are at least three distinct groups with small inter-cluster differences (the dark rectangles) whereas much larger distances can be observed for all other cells. \begin{figure} \begin{center} <>= pottery_dist <- dist(pottery[, colnames(pottery) != "kiln"]) library("lattice") levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number") @ <>= trellis.par.set(standard.theme(color = FALSE)) plot(levelplot(as.matrix(pottery_dist), xlab = "Pot Number", ylab = "Pot Number")) @ \caption{Image plot of the dissimilarity matrix of the \Robject{pottery} data. \label{CA-pottery-distplot}} \end{center} \end{figure} We now construct three series of partitions using single, complete, and average linkage hierarchical clustering as introduced in Subsections~\ref{CA:HC} and \ref{CA:diss}. The function \Rcmd{hclust} performs all three procedures based on the dissimilarity matrix of the data; its \Rcmd{method} argument is used to specify how the distance between two clusters is assessed. The corresponding \Rcmd{plot} method draws a dendrogram; the code and results are given in Figure~\ref{CA-pottery-hclust}. Again, all three dendrograms lead to the impression that three clusters fit the data best (although this judgement is very informal). \begin{figure} \begin{center} <>= pottery_single <- hclust(pottery_dist, method = "single") pottery_complete <- hclust(pottery_dist, method = "complete") pottery_average <- hclust(pottery_dist, method = "average") layout(matrix(1:3, ncol = 3)) plot(pottery_single, main = "Single Linkage", sub = "", xlab = "") plot(pottery_complete, main = "Complete Linkage", sub = "", xlab = "") plot(pottery_average, main = "Average Linkage", sub = "", xlab = "") @ \caption{Hierarchical clustering of \Robject{pottery} data and resulting dendrograms. \label{CA-pottery-hclust}} \end{center} \end{figure} From the \Robject{pottery\_average} object representing the average linkage hierarchical clustering, we derive the three-cluster solution by cutting the dendrogram at a height of four (which, based on the right display in Figure~\ref{CA-pottery-hclust} leads to a partition of the data into three groups). Our interest is now a comparison with the kiln sites at which the pottery was found. <>= pottery_cluster <- cutree(pottery_average, h = 4) xtabs(~ pottery_cluster + kiln, data = pottery) @ The contingency table shows that cluster 1 contains all pots found at kiln site number one, cluster 2 contains all pots from kiln sites number two and three, and cluster three collects the ten pots from kiln sites four and five. In fact, the five kiln sites are from three different regions defined by one, two and three, and four and five, so the clusters actually correspond to pots from three different regions. \subsection{Classifying Exoplanets} \begin{figure} \begin{center} <>= data("planets", package = "HSAUR3") library("scatterplot3d") scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, pch = 16, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, scale.y = 0.7, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") @ \caption{3D scatterplot of the logarithms of the three variables available for each of the exoplanets. \label{CA-planets-scatter}} \end{center} \end{figure} \begin{figure} \begin{center} <>= rge <- apply(planets, 2, max) - apply(planets, 2, min) planet.dat <- sweep(planets, 2, rge, FUN = "/") n <- nrow(planet.dat) wss <- rep(0, 10) wss[1] <- (n - 1) * sum(apply(planet.dat, 2, var)) for (i in 2:10) wss[i] <- sum(kmeans(planet.dat, centers = i)$withinss) plot(1:10, wss, type = "b", xlab = "Number of groups", ylab = "Within groups sum of squares") @ \caption{Within-cluster sum of squares for different numbers of clusters for the exoplanet data. \label{CA-planets-ss}} \end{center} \end{figure} Sadly Figure~\ref{CA-planets-ss} gives no completely convincing verdict on the number of groups we should consider, but using a little imagination `little elbows' can be spotted at the three and five group solutions. %%' We can find the number of planets in each group using <>= planet_kmeans3 <- kmeans(planet.dat, centers = 3) table(planet_kmeans3$cluster) @ The centers of the clusters for the untransformed data can be computed using a small convenience function <>= ccent <- function(cl) { f <- function(i) colMeans(planets[cl == i,]) x <- sapply(sort(unique(cl)), f) colnames(x) <- sort(unique(cl)) return(x) } @ which, applied to the three-cluster solution obtained by $k$-means gets <>= ccent(planet_kmeans3$cluster) @ @ for the three-cluster solution and, for the five cluster solution using <>= planet_kmeans5 <- kmeans(planet.dat, centers = 5) table(planet_kmeans5$cluster) ccent(planet_kmeans5$cluster) @ \subsection{Model-based Clustering in \R{}} We now proceed to apply model-based clustering to the \Robject{planets} data. \R{} functions for model-based clustering are available in package \Rpackage{mclust} \citep{PKG:mclust,HSAUR:FraleyRaftery2002}. Here we use the \Rcmd{Mclust} function since this selects both the most appropriate model for the data \stress{and} the optimal number of groups based on the values of the BIC computed over several models and a range of values for number of groups. The necessary code is: <>= library("mclust") planet_mclust <- Mclust(planet.dat) @ and we first examine a plot of BIC values using the \R{} code that is displayed on top of Figure~\ref{CA-mclust1}. In this diagram the different plotting symbols refer to different model assumptions about the shape of clusters: \begin{description} \item[EII] spherical, equal volume, \item[VII] spherical, unequal volume, \item[EEI] diagonal, equal volume and shape, \item[VEI] diagonal, varying volume, equal shape, \item[EVI] diagonal, equal volume, varying shape, \item[VVI] diagonal, varying volume and shape, \item[EEE] ellipsoidal, equal volume, shape, and orientation, \item[EEV] ellipsoidal, equal volume and equal shape, \item[VEV] ellipsoidal, equal shape, \item[VVV] ellipsoidal, varying volume, shape, and orientation \end{description} \begin{figure} \begin{center} <>= plot(planet_mclust, planet.dat, what = "BIC", col = "black", ylab = "-BIC", ylim = c(0, 350)) @ \caption{Plot of BIC values for a variety of models and a range of number of clusters. \label{CA-mclust1}} \end{center} \end{figure} The BIC selects model VVI (diagonal varying volume and varying shape) with three clusters as the best solution as can be seen from the \Rcmd{print} output: <>= print(planet_mclust) @ This solution can be shown graphically as a scatterplot matrix. The plot is shown in Figure~\ref{CA-planets-mclust-scatter}. Figure~\ref{CA-planets-mclust-scatterclust} depicts the clustering solution in the three-dimensional space. \begin{figure} \begin{center} <>= clPairs(planet.dat, classification = planet_mclust$classification, symbols = 1:3, col = "black") @ \caption{Scatterplot matrix of planets data showing a three-cluster solution from \Rcmd{Mclust}. \label{CA-planets-mclust-scatter}} \end{center} \end{figure} \begin{figure} \begin{center} <>= scatterplot3d(log(planets$mass), log(planets$period), log(planets$eccen + ifelse(planets$eccen == 0, 0.001, 0)), type = "h", angle = 55, scale.y = 0.7, pch = planet_mclust$classification, y.ticklabs = seq(0, 10, by = 2), y.margin.add = 0.1, xlab = "log(mass)", ylab = "log(period)", zlab = "log(eccen)") @ \caption{3D scatterplot of planets data showing a three-cluster solution from \Rcmd{Mclust}. \label{CA-planets-mclust-scatterclust}} \end{center} \end{figure} The number of planets in each cluster and the mean vectors of the three clusters for the untransformed data can now be inspected by using <>= table(planet_mclust$classification) ccent(planet_mclust$classification) @ Cluster 1 consists of planets about the same size as Jupiter with very short periods and eccentricities (similar to the first cluster of the $k$-means solution). Cluster 2 consists of slightly larger planets with moderate periods and large eccentricities, and cluster 3 contains the very large planets with very large periods. These two clusters do not match those found by the $k$-means approach. \bibliographystyle{LaTeXBibTeX/refstyle} \bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_survival_analysis.pdf0000644000175000017500000034724414133304614017773 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 4422 /Filter /FlateDecode /N 97 /First 809 >> stream x[[s۸~[ĕ;cٹձ㵝ILld1+ޤH7ٴBs?`!XԆil 3F3lYb%°(W/—DH4PP0!Pb&,K CTbEL0bBF L+J0-a*dD̴0'K,!YA%JaPŬNbYQoMBL²84xE?kLJE,$c{EhI`peX`> K L`(LW m&h xQ$] `Ũؙ(J #EB4 e532,MqڟC{I`(H +@XfY8d;H#R@i2Kd@bYB"-; c&Bbu4v2 (F bQ1AYǘ^L4K1 3c A` dc ěAaJ(/jI 񃴘^L)vlsb-8Mp)h?ϯ/8;udNHuN 6]\2.I^ܥˬ(~Be:-|7-Rlo"(@?aת};=MYqͮ1r^z?GXg9/w/ng):z^]b5[f_ :D=ܟfwk,X~N }Ud,+ *[\=~&EFO?UoIa"SvңXg wb%.HQ՞,yACAN _neAtC_zZ UaPqo3 LV" $^\˜ڊ$-ļo@Ks Db~.=+W>}&+@x-nsZ7@FaEnu%$prVnRjCZkĶy(팁/nVhOȊ bPi5 Ik v ~.&EIDNYMѪ.U仯N_{0>Y~ANd9+"t#p$\@:TQi쨚cvQ\C/z?ZU vCP#}n`X!n?ZAX G'fBKX\n.J1=j5#?aكR_75]/A^_s~<"_9O_%_U^)/-r,>r>"emRѸKs[|SIV֚7i@fx يˑ$?)қdr4 AkĔ{T|tLZ [,Vz$m:$MmFQ4hM&kmjnqasaYN.]e=<;8g=L=;{tC;hd6qc#xᬕ 7†CIN9ė3que;ϸ+j@R}oхbX~؜8xklͲ*"[&CAKA˶ćTP"T//'wz2"*ZS662|ڙ8 4jT;}*Geb)GrZz]+ѯ~tGZ¹a\옄H1VF!1'{zzL};JE\"*\r\oPکȫs zF+![n-??--?onp@y4>}3M_:]@`6pזq<,|i頖wm^sנmܝ/:3"W2+w_t][R=WŔ8vUBjh##xOߌ*uתHbbkbӠd㪾f9%3N=]~T^n#݂Y2^Нhd7A\Ya @J<!<)w᩽ހ*nZʗm>$}+MچHW|k|m|;դPa}+伳=),U{|D\?,KOaf,᱆>m?m5_UMoLMB*>iY"E |KZ8P2j|>G{(oozEtStjs=zvUk'۬{HYL$^Rw40*LM'0G?f7緫|qzu|pQOpSct햟 նmغ6j6p:`\r\}߁3*oϲ瞽7ڛ㘸£MZeeGqfk2M6Is:;\t>Njf`j5-6cl5S~qCTڋro46f?}hKۤ [&yZLK.t]sWr0۴V8ִK)eEFұqت_Q+YƜL:E$5 %Pǡ2ahY$'e"p#u-?P"i~P^x=6e4`l]w[ EC A^¢BЊ#`Q=ʂ [k*ˆ42(>|q?Nw)h*rW%HA\Y5IqF1~>d".J>\zVT2M=b.r >bۜ!͇W1Zm$^7bGLmd 8؎u:KپJ!$uBx*r^/ӧ؏[>~~i=I>E/?oeX>SPf ]cGF:2&/C;\3'Z#j| i(Y,-U"l%jz=ӉKU&M[gT?9Z}Z'qk]GS;f)~~>jZ(jT]MU!1Qn{Z-'u =ԩV̾w>4ЉЛNDh2%Z56$'-dWGUmteAVv%'w!or8aY'8j߿i=Zv8~6޷r'``a챞,5_M>|cLS˖ugDD?ڶjo~ .FiPl]㺍~x aT+^K$ Bi e@l;$M$*p/˨8H^lBaV QF(̊*Y&#gVb!:^æ|tǟ>Mcq΀ڰ;e!GVC5 ƓQ@6sC#U4D^ҍsG==$̃]ڛ#a& MPkNz$[U^e QGiέH@ZӜ$ABx*,еII &4Yp"M̚>a)̉ 1, |*A )0(~tִ:=%2M²[#0ɤ/& @`aa2[['vڞh4tzz $4a;f~"њ)њ-.| 10DX\w}kDYYG(O$F `|w I5eZ3vRƈİU^ԫ#m |5^# '?~S J(eNξ13} .jj-hw B؉> stream GPL Ghostscript 9.50 2021-10-18T16:49:48+02:00 2021-10-18T16:49:48+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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Ké3fm9ofhYSqi73Ϙ/ 0_բ0ˢDû|v17"_Po@|[EN tvLM>_0R+h ;\Bh"F22 !YQ* RY+C"#.:IBœtjޱ_:yDS+1m7wvZWҾ#LIFnLG,i%y 2KPAm@#b*e$wtD}l "q+zcc&vIجD 0oN;#Qڷ^ӉlC^6I eA}  `m$%$"[ҕĂ9 n77qL2FmJlky5,kLòH2;a>"ka`g2{ S'ϔ$ 3nk!VDme ]1M`$Jjm{`¶S1+# nER7}NE|mow:"dwީͣny^*Yg>6[r%2JZzsXO^qgF};j/6ÞZG䧔f-atx,-1dw'wsa~ۺl^;n&ɱ 2B4I|[480rP7Ĥhg7k>CЙ{3:I+vyU ld@OeRXהAEasyɞW nӦC 'w:w_@FD"(5ph|ajSNbO?rActEHs%[ #~ W'I 3׾ݰedKmјh= f@: ^'w()(HB:}GpE鶫7^m'51m#cÂ%]5dTulV%mvrL <oDy_؂qws4Xzl:0fw[O6/zFW4 ŨE3tǽgry߫dBzmM[ ad!)Rڬq׼"!U,&JS5c+cC*[>tqu!rv, ZYks,C &-e&{xֺ6~/;"dK"(~ NA3kЁ粮j:ac"d(|ٙ)IKG#oJĒ5cG[88Nceq7_Xendstream endobj 71 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:42+02:00 2021-10-18T16:49:42+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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}?({`%3(5(HAatDr})_">HV%"/H6Q "@,D2b r6H%8\ WLւɏ Rx)D궁ݠ"/}NH A[7d_XL#8 endstream endobj startxref 276618 %%EOF HSAUR3/inst/doc/Ch_bayesian_inference.Rnw0000644000175000017500000007256114133304452020020 0ustar nileshnilesh \documentclass{chapman} %%% copy Sweave.sty definitions %%% keeps `sweave' from adding `\usepackage{Sweave}': DO NOT REMOVE %\usepackage{Sweave} \RequirePackage[T1]{fontenc} \RequirePackage{graphicx,ae,fancyvrb} \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} \usepackage{relsize} \DefineVerbatimEnvironment{Sinput}{Verbatim}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} \DefineVerbatimEnvironment{Scode}{Verbatim}{} \newenvironment{Schunk}{}{} %%% environment for raw output \newcommand{\SchunkRaw}{\renewenvironment{Schunk}{}{} \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, fontshape=it, fontsize=\small} \rawSinput } %%% environment for labeled output \newcommand{\nextcaption}{} \newcommand{\SchunkLabel}{ \renewenvironment{Schunk}{\begin{figure}[ht] }{\caption{\nextcaption} \end{figure} } \DefineVerbatimEnvironment{Sinput}{Verbatim}{frame = topline} \DefineVerbatimEnvironment{Soutput}{Verbatim}{frame = bottomline, samepage = true, fontfamily=courier, fontshape=it, fontsize=\relsize{-1}} } %%% S code with line numbers \DefineVerbatimEnvironment{Sinput} {Verbatim} { %% numbers=left } \newcommand{\numberSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{numbers=left} } \newcommand{\rawSinput}{ \DefineVerbatimEnvironment{Sinput}{Verbatim}{} } %%% R / System symbols \newcommand{\R}{\textsf{R}} \newcommand{\rR}{{R}} \renewcommand{\S}{\textsf{S}} \newcommand{\SPLUS}{\textsf{S-PLUS}} \newcommand{\rSPLUS}{{S-PLUS}} \newcommand{\SPSS}{\textsf{SPSS}} \newcommand{\EXCEL}{\textsf{Excel}} \newcommand{\ACCESS}{\textsf{Access}} \newcommand{\SQL}{\textsf{SQL}} %%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Robject}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\Rclass}[1]{\hbox{\rm\textit{#1}}} %%\newcommand{\Rcmd}[1]{\hbox{\rm\texttt{#1}}} \newcommand{\Rpackage}[1]{\index{#1 package@{\fontseries{b}\selectfont #1} package} {\fontseries{b}\selectfont #1}} \newcommand{\rpackage}[1]{{\fontseries{b}\selectfont #1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\index{#1 class@\textit{#1} class}\textit{#1}} \newcommand{\Rcmd}[1]{\index{#1 function@\texttt{#1} function}\texttt{#1}} \newcommand{\Roperator}[1]{\texttt{#1}} \newcommand{\Rarg}[1]{\texttt{#1}} \newcommand{\Rlevel}[1]{\texttt{#1}} %%% other symbols \newcommand{\file}[1]{\hbox{\rm\texttt{#1}}} %%\newcommand{\stress}[1]{\index{#1}\textit{#1}} \newcommand{\stress}[1]{\textit{#1}} \newcommand{\booktitle}[1]{\textit{#1}} %%' %%% Math symbols \usepackage{amstext} \usepackage{amsmath} \newcommand{\E}{\mathsf{E}} \newcommand{\Var}{\mathsf{Var}} \newcommand{\Cov}{\mathsf{Cov}} \newcommand{\Cor}{\mathsf{Cor}} \newcommand{\x}{\mathbf{x}} \newcommand{\y}{\mathbf{y}} \renewcommand{\a}{\mathbf{a}} \newcommand{\W}{\mathbf{W}} \newcommand{\C}{\mathbf{C}} \renewcommand{\H}{\mathbf{H}} \newcommand{\X}{\mathbf{X}} \newcommand{\B}{\mathbf{B}} \newcommand{\V}{\mathbf{V}} \newcommand{\I}{\mathbf{I}} \newcommand{\D}{\mathbf{D}} \newcommand{\bS}{\mathbf{S}} \newcommand{\N}{\mathcal{N}} \renewcommand{\L}{L} \renewcommand{\P}{\mathsf{P}} \newcommand{\K}{\mathbf{K}} \newcommand{\m}{\mathbf{m}} \newcommand{\argmin}{\operatorname{argmin}\displaylimits} \newcommand{\argmax}{\operatorname{argmax}\displaylimits} \newcommand{\bx}{\mathbf{x}} \newcommand{\bbeta}{\mathbf{\beta}} %%% links \usepackage{hyperref} \hypersetup{% pdftitle = {A Handbook of Statistical Analyses Using R (3rd Edition)}, pdfsubject = {Book}, pdfauthor = {Torsten Hothorn and Brian S. Everitt}, colorlinks = {black}, linkcolor = {black}, citecolor = {black}, urlcolor = {black}, hyperindex = {true}, linktocpage = {true}, } %%% captions & tables %% : conflics with figure definition in chapman.cls %%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption} %% \usepackage{longtable} \usepackage[figuresright]{rotating} %%% R symbol in chapter 1 \usepackage{wrapfig} %%% Bibliography \usepackage[round,comma]{natbib} \renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}} \citeindexfalse %%% texi2dvi complains that \newblock is undefined, hm... \def\newblock{\hskip .11em plus .33em minus .07em} %%% Example sections \newcounter{exercise}[chapter] \setcounter{exercise}{0} \newcommand{\exercise}{\stepcounter{exercise} \item{Ex.~\arabic{chapter}.\arabic{exercise} }} %% URLs \newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}} %%% for manual corrections %\renewcommand{\baselinestretch}{2} %%% plot sizes \setkeys{Gin}{width=0.95\textwidth} %%% color \usepackage{color} %%% hyphenations \hyphenation{drop-out} \hyphenation{mar-gi-nal} %%% new bidirectional quotes need \usepackage[utf8]{inputenc} %\usepackage{setspace} \definecolor{sidebox_todo}{rgb}{1,1,0.2} \newcommand{\todo}[1]{ \hspace{0pt}% \marginpar{% \fcolorbox{black}{sidebox_todo}{% \parbox{\marginparwidth} { \raggedright\sffamily\footnotesize{TODO: #1}% } }% } } \begin{document} %% Title page \title{A Handbook of Statistical Analyses Using \R{} --- 3rd Edition} \author{Torsten Hothorn and Brian S. Everitt} \maketitle %%\VignetteIndexEntry{Chapter Bayesian Inference} %%\VignetteDepends{rmeta,coin} \setcounter{chapter}{17} \SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE} <>= rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) @ \pagestyle{headings} <>= book <- FALSE @ \chapter[Bayesian Inference]{Incorporating Prior Knowledge via Bayesian Inference: Smoking and Lung Cancer \label{BI}} \section{Introduction} \index{Smoking and lung cancer|(} At the beginning of the 20th century, the death toll due to lung cancer was on the rise and the search for possible causes began. For lung cancer in pit workers, animal experiments showed that the so-called `Schneeberg lung disease' was induced by radiation. But this could not explain the increasing incidence of lung cancer in the general population. The identification of possible risk factors was a challenge for epidemiology and statistics, both disciplines being still in their infancy in the 1920s and 1930s. The first modern controlled epidemiological study on the effect of smoking on lung cancer was performed by Franz Hermann M\"uller as part of his dissertation at the University of Cologne in 1939. The results were published a year later \citep{HSAUR:Mueller1940}. M\"uller sent out questionnaires to the relatives of people who had recently died of lung cancer, asking about the smoking behavior and its intensity of the deceased relative. He also sent the questionnaire to healthy controls to obtain information about the smoking behavior in a control group, although it is not clear how this control group was defined. The number of lung cancer patients and healthy controls in five different groups (nonsmokers to extreme smokers) are given in Table~\ref{BI-Smoking_Mueller1940-tab}. <>= data("Smoking_Mueller1940", package = "HSAUR3") toLatex(HSAURtable(Smoking_Mueller1940), caption = paste("Smoking and lung cancer case-control study by M\\\"uller (1940).", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-15 (moderate), 16-25 (heavy), 26-35 (very heavy),", "and more than 35 (extreme)."), label = "BI-Smoking_Mueller1940-tab") @ Four years later Erich Sch\"oninger also wrote his dissertation on the association between smoking and lung cancer and, together with his supervisor Eberhard Schairer at the University of Jena, published his results on a case-control study \citep{HSAUR:SchairerSchoeninger1944} where he assessed the smoking behavior of lung cancer patients, patients diagnosed with other forms of cancer, and also a healthy control group. The data are given in Table~\ref{BI-Smoking_SchairerSchoeniger1944-tab}. <>= x <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) toLatex(HSAURtable(x, xname = "Smoking_SchairerSchoeniger1944"), caption = paste("Smoking and lung cancer case-control study by Schairer and Sch\\\"oniger (1944). Cancer other than lung cancer omitted.", "The smoking intensities were defined by the number of", "cigarettes smoked daily:", "1-5 (moderate), 6-10 (medium), 11-20 (heavy),", "and more than 20 (very heavy)."), label = "BI-Smoking_SchairerSchoeniger1944-tab") @ Shortly after the war, a Dutch epidemiologist reported on a case-control study performed in Amsterdam \citep{HSAUR:Wassink1945} and found similar results as the two German studies; see Table~\ref{BI-Smoking_Wassink1945-tab}. <>= data("Smoking_Wassink1945", package = "HSAUR3") toLatex(HSAURtable(Smoking_Wassink1945), caption = paste("Smoking and lung cancer case-control study by Wassink (1945).", "Smoking categories correspond to the categories used by M\\\"uller (1940)."), label = "BI-Smoking_Wassink1945-tab") @ In 1950 perhaps the most important, but not the first, case-control study showing an increasing risk of developing lung cancer with the amount of tobacco smoked, was published in Great Britain by Richard Doll and Austin Bradford Hill \citep{HSAUR:DollHill1950}. We restrict discussion here to data obtained for males and the data shown in Table~\ref{BI-Smoking_DollHill1950-tab} corresponds to the most recent amount of tobacco consumed regularly by smokers before disease onset \citep[Table~V in][]{HSAUR:DollHill1950}. <>= data("Smoking_DollHill1950", package = "HSAUR3") x <- as.table(Smoking_DollHill1950[,,"Male", drop = FALSE]) toLatex(HSAURtable(x, xname = "Smoking_DollHill1950"), caption = paste("Smoking and lung cancer case-control study (only males) by Doll and Hill (1950).", "The labels for the smoking categories give the number of cigarettes smoked every day."), label = "BI-Smoking_DollHill1950-tab") @ Although the design of the studies by \cite{HSAUR:Mueller1940} and \cite{HSAUR:SchairerSchoeninger1944}, especially the selection of their control groups, can be criticized \citep[see][for a detailed discussion]{HSAUR:Morabia2013} and the study by \cite{HSAUR:DollHill1950} was larger than the older studies and more detailed information on the smoking behavior was obtained by direct patient interviews, the information provided by the earlier studies was not taken into account by \cite{HSAUR:DollHill1950}. They cite \cite{HSAUR:Mueller1940} in their introduction, but did not compare their findings with his results. It is remarkable to see that both \cite{HSAUR:SchairerSchoeninger1944} and \cite{HSAUR:Wassink1945} extensively made use of the report by \cite{HSAUR:Mueller1940} and go as far as analyzing the merged data \citep[Grafiek I, E, and F, in][]{HSAUR:Wassink1945}. In an informal way, these authors wanted to use the already available information, in today's terms called `prior knowledge', to make a stronger case with the new data. Formal statistical methods to incorporate prior knowledge into data analysis as part of the `Bayesian' way of doing statistical analyses were developed in the second half of the last century, and we will focus on them in the present chapter. \index{Smoking and lung cancer|)} \section{Bayesian Inference} \section{Analysis Using \R{}} \subsection{One-by-one Analysis} For the analysis of the four different case-control studies on smoking and lung cancer, we will (retrospectively, of course) update our knowledge with every new study. We begin with a re-analysis of the data described by \cite{HSAUR:Mueller1940}. Using an approximate permutation test introduced in Chapter~\ref{CI} for the hypothesis of independence of the amount of tobacco smoked and group membership (lung cancer or healthy control), we get <>= library("coin") set.seed(29) independence_test(Smoking_Mueller1940, teststat = "quad", distribution = approximate(100000)) @ and there is clearly a strong association between the number of cigarettes smoked and incidence of lung cancer. Because the amount of tobacco smoked is an ordered categorical variable, it is more appropriate to take this information into account, for example by means of a linear association test (see Chapter~\ref{CI}). Nonsmokers receive a score of zero, and for the remaining groups we choose the mid-point of the intervals of daily cigarettes smoked that were used by \cite{HSAUR:Mueller1940} to define his groups: <>= ssc <- c(0, 1 + 14 / 2, 16 + 9 / 2, 26 + 9 / 2, 40) independence_test(Smoking_Mueller1940, teststat = "quad", scores = list(Smoking = ssc), distribution = approximate(100000)) @ The result shows that the data are in favor of an ordered alternative. The $p$-values obtained from approximate permutation tests are attractive because no distributional assumptions are required, but it is hard to derive estimates and confidence intervals for interpretable parameters from such tests. We will therefore now switch to logistic regression models as described in Chapter~\ref{GLM} to model the odds of lung cancer in the different smoking groups. Before we start, let us define a small function for computing odds (for intercept parameters) and odds ratios (for difference parameters) and corresponding confidence intervals from a logistic regression model: <>= eci <- function(model) cbind("Odds (Ratio)" = exp(coef(model)), exp(confint(model))) @ We model the probability of developing lung cancer given the smoking behavior. Because our data was obtained from case-control studies where the groups (lung cancer patients and healthy controls) were defined first and only after that we observed data on the smoking behavior (in a so-called \stress{choice-based sampling}), this may seem the wrong model to start with. However, the marginal distribution of the two groups only changes the intercept in such a logistic model and the effects of smoking can still be interpreted in the way we require \citep[see][for example]{HSAUR:Tutz2012}. The formula for specifying a logistic regression model can be set up such that the response is a matrix with two columns for each smoking group consisting of the number of lung cancer deaths and the number of healthy controls. Although smoking is an ordered factor, we first fit the model with treatment contrasts, i.e., we can interpret the $\exp$ of the regression coefficients as odds ratios between each smoking group and nonsmokers: <>= smoking <- ordered(rownames(Smoking_Mueller1940), levels = rownames(Smoking_Mueller1940)) contrasts(smoking) <- "contr.treatment" eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) @ We see that all but one of the odds ratios increase with the amount of tobacco smoked with a maximum of almost $30$ for extreme smokers (more than $35$ cigarettes per day). The likelihood confidence intervals are rather wide due to the limited sample size, but also the lower limit increases with smoking. An alternative model formulation can help to compare each smoking group with the preceding group, the so-called split-coding \citep[for this and other codings see][]{HSAUR:Tutz2012}: <>= K <- diag(nlevels(smoking) - 1) K[lower.tri(K)] <- 1 contrasts(smoking) <- rbind(0, K) eci(glm(Smoking_Mueller1940 ~ smoking, family = binomial())) @ The two largest differences are between moderate smokers and nonsmokers (\Robject{smoking1}) and between very heavy and heavy smokers (\Robject{smoking3}). The latter group difference seems, at least judged by the confidence interval, to be larger than expected under a model with no effect of smoking. For the analysis of the three remaining studies, we first perform permutation tests for the independence of smoking and the two groups (lung cancer and healthy controls) in males: <>= xSS44 <- as.table(Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")]) ap <- approximate(100000) pvalue(independence_test(xSS44, teststat = "quad", distribution = ap)) pvalue(independence_test(Smoking_Wassink1945, teststat = "quad", distribution = ap)) xDH50 <- as.table(Smoking_DollHill1950[,, "Male"]) pvalue(independence_test(xDH50, teststat = "quad", distribution = ap)) @ All $p$-values indicate that the data are not well-described by the independence model. \subsection{Joint Bayesian Analysis} For a Bayesian analysis, we first merge the data from all four studies into one data frame. In doing so, we also merge the smoking groups in a way that we only have three groups left: nonsmokers, moderate smokers, and heavy smokers. These groups are chosen in a way that the number of daily cigarettes is comparable. We first merge the heavy, very heavy, and extreme smokers from \cite{HSAUR:Mueller1940} <>= (M <- rbind(Smoking_Mueller1940[1:2,], colSums(Smoking_Mueller1940[3:5,]))) @ and proceed with the lung cancer patients and healthy controls from \cite{HSAUR:SchairerSchoeninger1944} in the same way <>= SS <- Smoking_SchairerSchoeniger1944[, c("Lung cancer", "Healthy control")] (SS <- rbind(SS[1,], colSums(SS[2:3,]), colSums(SS[4:5,]))) @ and finally perform the same exercise for the \cite{HSAUR:Wassink1945} and \cite{HSAUR:DollHill1950} data <>= (W <- rbind(Smoking_Wassink1945[1:2,], colSums(Smoking_Wassink1945[3:4,]))) DH <- Smoking_DollHill1950[,, "Male"] (DH <- rbind(DH[1,], colSums(DH[2:3,]), colSums(DH[4:6,]))) @ The three new groups are now called nonsmokers, moderate smokers, and heavy smokers, and we set up a data frame that contains the number of people in each of the possible groups for all studies: <>= smk <- c("Nonsmoker", "Moderate smoker", "Heavy smoker") x <- expand.grid(Smoking = ordered(smk, levels = smk), Diagnosis = factor(c("Lung cancer", "Control")), Study = c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945", "DollHill1950")) x$weights <- c(as.vector(M), as.vector(SS), as.vector(W), as.vector(DH)) @ Before we fit logistic regression models using the data organized in such a way, we define the contrasts for the smoking ordered factor and expand the data in a way that each row corresponds to one person. This is necessary because the \Rcmd{weights} argument to the \Rcmd{glm} function must not be used to define case weights: <>= contrasts(x$Smoking) <- "contr.treatment" x <- x[rep(1:nrow(x), x$weights),] @ We now compute one logistic regression model for each study for later comparisons: <>= models <- lapply(levels(x$Study), function(s) glm(Diagnosis ~ Smoking, data = x, family = binomial(), subset = Study == s)) names(models) <- levels(x$Study) @ In 1939, M\"uller was hardly in the position to come up with a reasonable prior for the odds ratios between moderate or heavy smokers and nonsmokers. So we also use a noninformative prior and just perform the maximum likelihood analysis: <>= eci(models[["Mueller1940"]]) @ Four years later, the maximum likelihood results obtained for the \cite{HSAUR:SchairerSchoeninger1944} data <>= eci(models[["SchairerSchoeniger1944"]]) @ could have been improved by using a normal prior for the difference in log odds whose distribution is the distribution of the maximum likelihood estimator obtained for M\"uller's data. At least approximately, we can compute posterior $90\%$ credibility intervals and the posterior mode from the Schairer and Sch\"oniger data by analyzing both data sets simultaneously. We should, however, keep in mind that the odds of developing lung cancer for nonsmokers is not really interesting for our analysis and that the four studies may very well differ with respect to this intercept parameter. Consequently, we don't want to specify a prior for the intercept. One way to implement such a strategy is to exclude the intercept term from the joint model while allowing a separate intercept for each of the studies: <>= mM40_SS44 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944")) eci(mM40_SS44) @ We observe two important differences between the maximum likelihood and Bayesian results for the Schairer and Sch\"oniger data: In the Bayesian analysis, the estimated odds ratio for moderate smokers is closer to the smaller value obtained from M\"uller's data and, more important, the credibility intervals are much narrower and, one has to say, more realistic now. An odds ratio as large as $40$ is hardly something one would expect to see in practice. If Wassink had been aware of Bayesian statistics, he could have used the posterior distribution of the parameters from our model \Robject{mM40\_SS44} as a prior distribution for analyzing his data. The maximum likelihood results for his data <>= eci(models[["Wassink1945"]]) @ would have changed to <>= mM40_SS44_W45 <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial(), subset = Study %in% c("Mueller1940", "SchairerSchoeniger1944", "Wassink1945")) eci(mM40_SS44_W45) @ The rather small odds ratios obtained from the model fitted to the Wassink data only are now closer to the estimates obtained from the two previous studies and the variability, as given by the credibility intervals, is much smaller. Now, finally, the model for the Doll and Hill data reports rather large odds ratios with wide confidence intervals: <>= eci(models[["DollHill1950"]]) @ With a (now rather strong) prior defined by the three earlier studies, we get from the joint model for all four studies <>= m_all <- glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial()) eci(m_all) @ <>= r <- eci(m_all) xM <- round(r["SmokingModerate smoker", 2:3], 1) xH <- round(r["SmokingHeavy smoker", 2:3], 1) @ In 1950, the joint evidence based on such an analysis with an odds ratio between $\Sexpr{xM[1]}$ and $\Sexpr{xM[2]}$ for moderate smokers and between $\Sexpr{xH[1]}$ and $\Sexpr{xH[2]}$ for heavy smokers compared to nonsmokers, would have made a much stronger case than any of the single studies alone. It is interesting to see that with this strong prior for the Doll and Hill study, we also get relatively large odds ratios when comparing heavy to moderate smokers (see row labeled \Rcmd{Smoking2}): <>= K <- diag(nlevels(x$Smoking) - 1) K[lower.tri(K)] <- 1 contrasts(x$Smoking) <- rbind(0, K) eci(glm(Diagnosis ~ 0 + Study + Smoking, data = x, family = binomial())) @ \subsection{A Comparison with Meta Analysis} One may ask how the Bayesian approach of progressively updating the estimates considered here differs from a classical meta analysis described in Chapter~\ref{MA}. We first reshape the data into a form suitable for such an analysis <>= y <- xtabs(~ Study + Smoking + Diagnosis, data = x) ntrtM <- margin.table(y, 1:2)[,"Moderate smoker"] nctrl <- margin.table(y, 1:2)[,"Nonsmoker"] ptrtM <- y[,"Moderate smoker","Lung cancer"] pctrl <- y[,"Nonsmoker","Lung cancer"] ntrtH <- margin.table(y, 1:2)[,"Heavy smoker"] ptrtH <- y[,"Heavy smoker","Lung cancer"] @ and then compute joint odds ratios and confidence intervals for moderate and heavy smokers compared to nonsmokers: <>= library("rmeta") meta.MH(ntrt = ntrtM, nctrl = nctrl, ptrt = ptrtM, pctrl = pctrl) meta.MH(ntrt = ntrtH, nctrl = nctrl, ptrt = ptrtH, pctrl = pctrl) @ For moderate smokers, the effect is a little weaker compared with the results reported on earlier and for heavy smokers, the meta analysis identifies a stronger effect for heavy smokers. Nevertheless, the differences between the two rather different approaches are negligible and the conclusions would have been the same. \section{Summary of Findings} We have seen that, using a Bayesian approach to incorporate prior knowledge into a model, the odds of developing lung cancer increase with increased amounts of smoking. Of course, our analysis here is very simplistic, because we ignored that also pipe and cigar smokers were present in the data, we merged the data based on a very rough assessment of the number of cigarettes smoked per day, ignored whether or not the smokers inhaled the smoke into their lungs, or if nonsmokers were subject to passive-smoking, as we call it today. Most importantly, we must not misinterpret findings from case-control studies as casual and, in fact, none of the authors cited here did so. The debate on whether smoking, and which kind of smoking, actually \stress{causes} lung cancer was initiated by the publications cited in this chapter and many famous statisticians took part in the debate, for example, Sir Ronald Fisher \citep{HSAUR:Fisher1959}, took the view that the inference of causation was premature. In retrospect this was one issue (perhaps the only one) where Fisher was mistaken. \section{Final Comments} There remain a few hard-line opponents of Bayesian inference (just a few) who reject the method because of the use of subjective prior distributions which, these opponents feel, have no place in scientific investigations. And there are Bayesians who think that the only defense of using non-Bayesian methods is incompetence. But for an increasing number of statisticians Bayesian inference is very attractive, because we can use the posterior distribution of the parameters to draw conclusions from the data. Although this requires the specification of a prior distribution, we have seen in this chapter that, using data from previous experiments, priors can be defined in a reasonable way. It is not absolutely necessary to rely on rather complex numerical procedures to`estimate' a posterior distribution. When we are willing to cut some corners, we can implement simple Bayesian approaches using standard software. We should also keep in mind that the prior can be interpreted as a penalty on the parameters, and many penalization approaches therefore have an (often implicit) connection to the Bayesian way of doing statistics. Of course, just picking the prior that `works best' is dangerous and almost surely inappropriate. \section*{Exercises} \begin{description} \exercise Produce a forest plot as introduced in Chapter~\ref{MA} for the four smoking studies analyzed here. \exercise Produce a modified forest plot where one can see how the evidence for smoking being related to lung cancer evolved between 1940 and 1950. \exercise Use the \Rpackage{INLA} add-on package to perform a similar analysis by using the coefficients and their standard errors estimated from our initial logistic regression model \texttt{m[["Mueller1940"]]} as parameters of a normal prior for a logistic regression applied to the Schairer and Sch\"oniger data. Compare the resulting credibility intervals for the two odds-ratios with the approximate results obtained in this chapter. \end{description} %%\bibliographystyle{LaTeXBibTeX/refstyle} %%\bibliography{LaTeXBibTeX/HSAUR} \end{document} HSAUR3/inst/doc/Ch_survival_analysis.R0000644000175000017500000001372014133304604017407 0ustar nileshnilesh### R code from vignette source 'Ch_survival_analysis.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: SA-setup ################################################### x <- library("survival") x <- library("coin") x <- library("partykit") ################################################### ### code chunk number 4: SA-glioma-KM ################################################### data("glioma", package = "coin") library("survival") layout(matrix(1:2, ncol = 2)) g3 <- subset(glioma, histology == "Grade3") plot(survfit(Surv(time, event) ~ group, data = g3), main = "Grade III Glioma", lty = c(2, 1), ylab = "Probability", xlab = "Survival Time in Month", legend.text = c("Control", "Treated"), legend.bty = "n") g4 <- subset(glioma, histology == "GBM") plot(survfit(Surv(time, event) ~ group, data = g4), main = "Grade IV Glioma", ylab = "Probability", lty = c(2, 1), xlab = "Survival Time in Month", xlim = c(0, max(glioma$time) * 1.05)) ################################################### ### code chunk number 5: SA-glioma-logrank ################################################### survdiff(Surv(time, event) ~ group, data = g3) ################################################### ### code chunk number 6: SA-glioma-exact ################################################### library("coin") logrank_test(Surv(time, event) ~ group, data = g3, distribution = "exact") ################################################### ### code chunk number 7: SA-glioma-g4 ################################################### logrank_test(Surv(time, event) ~ group, data = g4, distribution = "exact") ################################################### ### code chunk number 8: SA-glioma-hist ################################################### logrank_test(Surv(time, event) ~ group | histology, data = glioma, distribution = approximate(B = 10000)) ################################################### ### code chunk number 9: SA-GBSG2-plot ################################################### data("GBSG2", package = "TH.data") plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2), lty = 1:2, mark.time = FALSE, ylab = "Probability", xlab = "Survival Time in Days") legend(250, 0.2, legend = c("yes", "no"), lty = c(2, 1), title = "Hormonal Therapy", bty = "n") ################################################### ### code chunk number 10: SA-GBSG2-coxph ################################################### GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2) ################################################### ### code chunk number 11: SA-GBSG2-coxph-ci ################################################### ci <- confint(GBSG2_coxph) exp(cbind(coef(GBSG2_coxph), ci))["horThyes",] ################################################### ### code chunk number 12: GBSG2-coxph-summary ################################################### summary(GBSG2_coxph) ################################################### ### code chunk number 13: SA-GBSG2-zph ################################################### GBSG2_zph <- cox.zph(GBSG2_coxph) GBSG2_zph ################################################### ### code chunk number 14: SA-GBSG2-zph-plot ################################################### plot(GBSG2_zph, var = "age") ################################################### ### code chunk number 15: SA-GBSG2-Martingal ################################################### layout(matrix(1:3, ncol = 3)) res <- residuals(GBSG2_coxph) plot(res ~ age, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "Martingale Residuals") abline(h = 0, lty = 3) plot(res ~ pnodes, data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) plot(res ~ log(progrec), data = GBSG2, ylim = c(-2.5, 1.5), pch = ".", ylab = "") abline(h = 0, lty = 3) ################################################### ### code chunk number 16: SA-GBSG2-ctree ################################################### GBSG2_ctree <- ctree(Surv(time, cens) ~ ., data = GBSG2) ################################################### ### code chunk number 17: SA-GBSG2-ctree-plot ################################################### plot(GBSG2_ctree) HSAUR3/inst/doc/Ch_simultaneous_inference.R0000644000175000017500000001514114133304601020373 0ustar nileshnilesh### R code from vignette source 'Ch_simultaneous_inference.Rnw' ################################################### ### code chunk number 1: setup ################################################### rm(list = ls()) s <- search()[-1] s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads"), s)] if (length(s) > 0) sapply(s, detach, character.only = TRUE) if (!file.exists("tables")) dir.create("tables") if (!file.exists("figures")) dir.create("figures") set.seed(290875) options(prompt = "R> ", continue = "+ ", width = 63, # digits = 4, show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") * c(1, 1.05, 1, 1)), bigleftpar = function() par(mai = par("mai") * c(1, 1.7, 1, 1)))) HSAURpkg <- require("HSAUR3") if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3")) rm(HSAURpkg) ### hm, R-2.4.0 --vanilla seems to need this a <- Sys.setlocale("LC_ALL", "C") ### book <- TRUE refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA", "MDS", "CA"), 1:18) ch <- function(x) { ch <- refs[which(refs[,1] == x),] if (book) { return(paste("Chapter~\\\\ref{", ch[1], "}", sep = "")) } else { return(paste("Chapter~", ch[2], sep = "")) } } if (file.exists("deparse.R")) source("deparse.R") setHook(packageEvent("lattice", "attach"), function(...) { lattice.options(default.theme = function() standard.theme("pdf", color = FALSE)) }) ################################################### ### code chunk number 2: singlebook ################################################### book <- FALSE ################################################### ### code chunk number 3: SIMC-setup ################################################### library("multcomp") library("coin") library("sandwich") library("lme4") ################################################### ### code chunk number 4: SIMC-alpha-data-figure ################################################### n <- table(alpha$alength) levels(alpha$alength) <- abbreviate(levels(alpha$alength), 4) plot(elevel ~ alength, data = alpha, varwidth = TRUE, ylab = "Expression Level", xlab = "NACP-REP1 Allele Length") axis(3, at = 1:3, labels = paste("n = ", n)) ################################################### ### code chunk number 5: SIMC-alpha-aov-tukey ################################################### library("multcomp") amod <- aov(elevel ~ alength, data = alpha) amod_glht <- glht(amod, linfct = mcp(alength = "Tukey")) ################################################### ### code chunk number 6: SIMC-alpha-aov-tukey-K ################################################### amod_glht$linfct ################################################### ### code chunk number 7: SIMC-alpha-aov-coefvcov ################################################### coef(amod_glht) vcov(amod_glht) ################################################### ### code chunk number 8: SIMC-alpha-aov-results ################################################### confint(amod_glht) summary(amod_glht) ################################################### ### code chunk number 9: SIMC-aov-tukey-sandwich ################################################### amod_glht_sw <- glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich) summary(amod_glht_sw) ################################################### ### code chunk number 10: SIMC-alpha-confint-plot ################################################### par(mai = par("mai") * c(1, 2.1, 1, 0.5)) layout(matrix(1:2, ncol = 2)) ci1 <- confint(glht(amod, linfct = mcp(alength = "Tukey"))) ci2 <- confint(glht(amod, linfct = mcp(alength = "Tukey"), vcov = sandwich)) ox <- expression(paste("Tukey (ordinary ", bold(S)[n], ")")) sx <- expression(paste("Tukey (sandwich ", bold(S)[n], ")")) plot(ci1, xlim = c(-0.6, 2.6), main = ox, xlab = "Difference", ylim = c(0.5, 3.5)) plot(ci2, xlim = c(-0.6, 2.6), main = sx, xlab = "Difference", ylim = c(0.5, 3.5)) ################################################### ### code chunk number 11: SIMC-trees-setup ################################################### trees513 <- subset(trees513, !species %in% c("fir", "ash/maple/elm/lime", "softwood (other)")) trees513$species <- trees513$species[,drop = TRUE] levels(trees513$species)[nlevels(trees513$species)] <- "hardwood" ################################################### ### code chunk number 12: SIMC-trees-lmer ################################################### mmod <- glmer(damage ~ species - 1 + (1 | lattice / plot), data = trees513, family = binomial()) K <- diag(length(fixef(mmod))) K ################################################### ### code chunk number 13: SIMC-trees-K ################################################### colnames(K) <- rownames(K) <- paste(gsub("species", "", names(fixef(mmod))), " (", table(trees513$species), ")", sep = "") K ################################################### ### code chunk number 14: SIMC-trees-ci ################################################### ci <- confint(glht(mmod, linfct = K)) ci$confint <- 1 - binomial()$linkinv(ci$confint) ci$confint[,2:3] <- ci$confint[,3:2] ################################################### ### code chunk number 15: SIMC-trees-plot ################################################### getOption("SweaveHooks")[["bigleftpar"]]() plot(ci, xlab = "Probability of Damage Caused by Browsing", xlim = c(0, 0.5), main = "", ylim = c(0.5, 5.5)) ################################################### ### code chunk number 16: SIMC-clouds-confband ################################################### confband <- function(subset, main) { mod <- lm(rainfall ~ sne, data = clouds, subset = subset) sne_grid <- seq(from = 1.5, to = 4.5, by = 0.25) K <- cbind(1, sne_grid) sne_ci <- confint(glht(mod, linfct = K)) plot(rainfall ~ sne, data = clouds, subset = subset, xlab = "S-Ne criterion", main = main, xlim = range(clouds$sne), ylim = range(clouds$rainfall)) abline(mod) lines(sne_grid, sne_ci$confint[,2], lty = 2) lines(sne_grid, sne_ci$confint[,3], lty = 2) } ################################################### ### code chunk number 17: SIMC-clouds-lmplot ################################################### layout(matrix(1:2, ncol = 2)) confband(clouds$seeding == "no", main = "No seeding") confband(clouds$seeding == "yes", main = "Seeding") HSAUR3/inst/doc/Ch_principal_components_analysis.pdf0000644000175000017500000055450214133304612022341 0ustar nileshnilesh%PDF-1.5 % 1 0 obj << /Type /ObjStm /Length 3701 /Filter /FlateDecode /N 80 /First 652 >> stream x[Ys8~_M* 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T\R:= m^4Y&aRx ҤJea:=~?Qq;=k&%RBsB}FCӁD" P>PU z%wėbJ08Z [vBgj No$84'K$8U '8\2T8y6l Ҽ :VF I6:guw[/Pv_H} ǔlFi$nդ1t8׍B!OC,"L_ *>}wF_N~m/>-h zkQkwAq׈An&Ev=*i'{BENqϺ^$8Dmt[:\eiM-KNOɸop; ewpE6 e5, E]`m⻵dLk5V(i_umIאg/OCbF *A K - XPW :"Ero`7jjU/8۰&J$3y)v;;( SpX[((~F8QaC`\iC)>6 f#jgγQpymendstream endobj 82 0 obj << /Subtype /XML /Type /Metadata /Length 1645 >> stream GPL Ghostscript 9.50 2021-10-18T16:49:46+02:00 2021-10-18T16:49:46+02:00 LaTeX with hyperref A Handbook of Statistical Analyses Using R (3rd Edition)Torsten Hothorn and Brian S. 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