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then AC_SUBST([CPPFLAGS],["-I${netcdf_include_path} ${CPPFLAGS}"]) fi AC_ARG_WITH([netcdf-lib], AC_HELP_STRING([--with-netcdf-lib=DIR], [location of netcdf libraries]), [netcdf_lib_path=$withval]) if test [ -n "$netcdf_lib_path" ] ; then AC_SUBST([LIBS],["-L${netcdf_lib_path} ${LIBS}"]) fi #-- UDUNITS include and library path -------------------------------------------# AC_ARG_WITH([udunits-include], AC_HELP_STRING([--with-udunits-include=DIR], [location of udunits header files]), [udunits_include_path=$withval]) if test [ -n "$udunits_include_path" ] ; then AC_SUBST([CPPFLAGS],["-I${udunits_include_path} ${CPPFLAGS}"]) fi AC_ARG_WITH([udunits-lib], AC_HELP_STRING([--with-udunits-lib=DIR], [location of udunits libraries]), [udunits_lib_path=$withval]) if test [ -n "$udunits_lib_path" ] ; then AC_SUBST([LIBS],["-L${udunits_lib_path} ${LIBS}"]) fi #-- Optional include path for udunits.dat (UDUNITS 1) --------------------------# AC_ARG_WITH([udunits-dat], AC_HELP_STRING([--with-udunits-dat=FILE], [location of udunits.dat file]), [udunits_dat_file=$withval]) #-- Optional include path for HDF5 ---------------------------------------------# AC_ARG_WITH([hdf5-lib], AC_HELP_STRING([--with-hdf5-lib=DIR], [location of hdf5 libraries]), [hdf5_lib_path=$withval]) if test [ -n "$hdf5_lib_path" ] ; then AC_SUBST([LIBS],["-L${hdf5_lib_path} ${LIBS}"]) fi #-- Optional local copy of units file(s) (UDUNITS 1 and 2) ---------------------# AC_ARG_ENABLE([units-copy], AC_HELP_STRING([--enable-units-copy@<:@=PATH@:>@], [place a local copy of units data file(s) in the package @<:@no@:>@]), [do_units_copy="${enableval}"], [do_units_copy=no]) #-------------------------------------------------------------------------------# # Find the compiler and compiler options to use # #-------------------------------------------------------------------------------# : ${R_HOME=`R RHOME`} if test -z "${R_HOME}"; then echo "Could not determine R_HOME" exit 1 fi CC=`${R_HOME}/bin/R CMD config CC` CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS` #-- Check for NetCDF and UDUNITS library ---------------------------------------# AC_CHECK_LIB(netcdf, nc_open, [], [ AC_CHECK_LIB(netcdf, nc_create, [have_netcdf_hdf5=TRUE], AC_MSG_ERROR(netcdf library not found), [-lhdf5 -lhdf5_hl -lcurl -lz]) if test "${have_netcdf_hdf5}" = TRUE; then LIBS="${LIBS} -lnetcdf -lhdf5 -lhdf5_hl -lcurl -lz" fi ]) AC_CHECK_LIB(udunits2, utInit, [], [have_udunits=FALSE]) if test "${have_udunits}" = FALSE; then AC_CHECK_LIB(udunits2, utScan, [], [have_udunits_expat=FALSE], [-lexpat]) if test "${have_udunits_expat}" = FALSE; then AC_CHECK_LIB(udunits, main, [], AC_MSG_ERROR(udunits library not found)) else LIBS="${LIBS} -lexpat" fi fi #-- Check for netcdf.h and udunits.h -------------------------------------------# AC_CHECK_HEADERS(netcdf.h, [], AC_MSG_ERROR(netcdf header netcdf.h not found)) AC_CHECK_HEADERS(udunits.h, [], AC_MSG_ERROR(udunits header udunits.h not found)) #-- Make local copy of units file(s) (UDUNITS 1 and 2) if requested ------------# if test "${do_units_copy}" != no ; then if test "${do_units_copy}" = yes ; then do_units_copy="${udunits_dat_file}" fi if test -z "${do_units_copy}" ; then for dir in /usr/share/udunits /usr/local/share/udunits \ /usr/etc/udunits.dat /usr/local/etc/udunits.dat ; do if test -e "${dir}" ; then do_units_copy="${dir}" break fi done if test -z "${do_units_copy}" ; then AC_MSG_ERROR([cannot find units file(s) to copy - use --enable-units-copy=PATH]) fi fi if test -d "${do_units_copy}" ; then mkdir -p inst/udunits 2>/dev/null cp -p "${do_units_copy}"/udunits*.xml inst/udunits/ else mkdir inst 2>/dev/null cp -p "${do_units_copy}" inst/udunits.dat fi fi #-------------------------------------------------------------------------------# # Do substitution # #-------------------------------------------------------------------------------# AC_SUBST(CPPFLAGS) AC_SUBST(LIBS) AC_SUBST(udunits_dat_file) AC_OUTPUT(R/load.R src/Makevars) #-------------------------------------------------------------------------------# RNetCDF/LICENSE.note0000644000175000017500000000656112375264053014737 0ustar sebastiansebastianThis file is intended to clarify ownership, copyright and license. Where possible individual files also carry brief copyright notices. Copyrights ========== All files of this package were created by Pavel Michna and are licensed under the terms of the GNU General Public License (see below). Because large parts of the documentation are taken from the "NetCDF User's Guide for C" and from the udunits(3) manpage, it is appropriate to cite Ucar's copyright notice for the NetCDF library: Copyright 1993-1999 University Corporation for Atmospheric Research/Unidata Portions of this software were developed by the Unidata Program at the University Corporation for Atmospheric Research. Access and use of this software shall impose the following obligations and understandings on the user. The user is granted the right, without any fee or cost, to use, copy, modify, alter, enhance and distribute this software, and any derivative works thereof, and its supporting documentation for any purpose whatsoever, provided that this entire notice appears in all copies of the software, derivative works and supporting documentation. Further, UCAR requests that the user credit UCAR/Unidata in any publications that result from the use of this software or in any product that includes this software. The names UCAR and/or Unidata, however, may not be used in any advertising or publicity to endorse or promote any products or commercial entity unless specific written permission is obtained from UCAR/Unidata. The user also understands that UCAR/Unidata is not obligated to provide the user with any support, consulting, training or assistance of any kind with regard to the use, operation and performance of this software nor to provide the user with any updates, revisions, new versions or "bug fixes." THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE. All other files not falling under Ucar's copyright (these are especially the R and C code files provided here) are copyright (C) 2004-2014 Pavel Michna. License ======= This is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. The file COPYING in the top-level directory is a copy of the 'GNU General Public License'. Pavel Michna RNetCDF/DESCRIPTION0000644000175000017500000000155112400657165014465 0ustar sebastiansebastianPackage: RNetCDF Version: 1.6.3-1 Date: 2014-05-26 Title: R Interface to NetCDF Datasets Author: Pavel Michna Maintainer: Pavel Michna Depends: R (>= 2.4.0) SystemRequirements: netcdf (>= 3.6.0), udunits (>= 1.11.7) or udunits2 (>= 2.1.22) Description: This package provides an interface to Unidata's NetCDF library functions (version 3) and furthermore access to Unidata's UDUNITS calendar conversions. The routines and the documentation follow the NetCDF and UDUNITS C interface, so the corresponding manuals can be consulted for more detailed information. License: GPL (>= 2) URL: http://www.unidata.ucar.edu/packages/netcdf/ http://www.unidata.ucar.edu/packages/udunits/ NeedsCompilation: yes Repository: CRAN Date/Publication: 2014-08-31 19:42:13 Packaged: 2014-08-31 17:41:33 UTC; ripley RNetCDF/configure.win0000755000175000017500000000013612375264053015461 0ustar sebastiansebastianmkdir -p ${R_PACKAGE_DIR}/share cp -r ${UDUNITS2_HOME}/share/udunits ${R_PACKAGE_DIR}/share RNetCDF/INSTALL0000644000175000017500000000361112375264053014010 0ustar sebastiansebastianThis file describes the command line arguments which can be passed during installation of the RNetCDF package and gives some further hints. Software Requirements ===================== NetCDF library version 3.6.0 or greater (64-bit file support). UDUNITS library either version 1 or 2.1 or greater. RNetCDF uses however only the version 1 calendar functions. If the NetCDF library (version 4) is linked against HDF5, the HDF5 library must be included in the search path, optionally with the configure argument "--with-hdf5-lib=DIR". If using Fink on Mac OS X, be sure that the corresponding R version (either i386 or x86_64) is used (R32 or R64). Compiling with R64 against i386 will most likely lead to runtime errors. R CMD INSTALL Options ===================== --with-netcdf-include=DIR location of netcdf header files --with-netcdf-lib=DIR location of netcdf libraries --with-udunits-include=DIR location of udunits header files --with-udunits-lib=DIR location of udunits libraries --with-udunits-dat=FILE location of udunits.dat file --with-hdf5-lib=DIR location of hdf5 libraries (if installed) --enable-units-copy[=PATH] place a local copy of units data file(s) in the package [no] R CMD INSTALL Example ===================== R CMD INSTALL --configure-args="--with-netcdf-include='/sw/include' \ --with-netcdf-lib='/sw/lib'" RNetCDF_1.6.3-1.tar.gz LD_LIBRARY_PATH =============== If a runtime error happens, you might need to set or modify the environment variable LD_LIBRARY_PATH with the directories where the NetCDF and/or UDUNITS and/or HDF5 libraries are located (especially for non-standard installations): export LD_LIBRARY_PATH=/sw/lib:$LD_LIBRARY_PATH R CMD check Example =================== R CMD check --install-args="--configure-args='--with-netcdf-include=/sw/include \ --with-netcdf-lib=/sw/lib'" RNetCDF_1.6.3-1.tar.gz RNetCDF/man/0000755000175000017500000000000012375264053013531 5ustar sebastiansebastianRNetCDF/man/open.nc.Rd0000644000175000017500000000333312375264053015362 0ustar sebastiansebastian\name{open.nc} \alias{open.nc} \title{Open a NetCDF Dataset} \description{Open an existing NetCDF dataset for reading and (optionally) writing.} \usage{ open.nc(con, write=FALSE, share=FALSE, prefill=TRUE, ...) } \arguments{ \item{con}{Filename of the NetCDF dataset to be opened.} \item{write}{If \code{FALSE} (default), the dataset will be opened read-only. If \code{TRUE}, the dataset will be opened read-write.} \item{share}{The buffer scheme. If \code{FALSE} (default), dataset access is buffered and cached for performance. However, if one or more processes may be reading while another process is writing the dataset, set to \code{FALSE}.} \item{prefill}{The prefill mode. If \code{TRUE} (default), newly defined variables are initialised with fill values when they are first accessed. This allows unwritten array elements to be detected when reading, but it also implies duplicate writes if all elements are subsequently written with user-specified data. Enhanced write performance can be obtained by setting \code{prefill=FALSE}.} \item{...}{Arguments passed to or from other methods (not used).} } \details{This function opens an existing NetCDF dataset for access. By default, the dataset is opened read-only. If \code{write=TRUE}, then the dataset can be changed. This includes appending or changing data, adding dimensions, variables, and attributes.} \value{Object of class "\code{NetCDF}" which points to the NetCDF dataset.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a void NetCDF dataset nc <- create.nc("foo.nc") close.nc(nc) ## Open the NetCDF dataset for writing nc <- open.nc("foo.nc", write=TRUE) close.nc(nc) } \keyword{file} RNetCDF/man/var.def.nc.Rd0000644000175000017500000000451012375264053015744 0ustar sebastiansebastian\name{var.def.nc} \alias{var.def.nc} \title{Define a NetCDF Variable} \description{Define a new NetCDF variable.} \usage{var.def.nc(ncfile, varname, vartype, dimensions)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{varname}{Variable name. Must begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore ("\code{_}"). Case is significant.} \item{vartype}{One of the set of predefined NetCDF external data types. The valid NetCDF external data types are \code{NC_BYTE}, \code{NC_CHAR}, \code{NC_SHORT}, \code{NC_INT}, \code{NC_FLOAT}, and \code{NC_DOUBLE}.} \item{dimensions}{Vector of \code{ndims} dimension IDs or their names corresponding to the variable dimensions or \code{NA} if a scalar variable should be created. If the ID (or name) of the unlimited dimension is included, it must be last.} } \details{This function creates a new NetCDF variable. A NetCDF variable has a name, a type, and a shape, which are specified when it is defined. A variable may also have values, which are established later in data mode. Ordinarily, the name, type, and shape are fixed when the variable is first defined. The name may be changed, but the type and shape of a variable cannot be changed. However, a variable defined in terms of the unlimited dimension can grow without bound in that dimension. The fastetst varying dimension has to be first in \code{dimensions}, the slowest varying dimension last (this is the same way as an array is defined in R; i.e., opposite to the CDL conventions). A NetCDF variable in an open NetCDF dataset is referred to by a small integer called a variable ID. Variable IDs are 0, 1, 2,..., in the order in which the variables were defined within a NetCDF dataset. Attributes may be associated with a variable to specify such properties as units.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) close.nc(nc) } \keyword{file} RNetCDF/man/att.rename.nc.Rd0000644000175000017500000000274012375264053016460 0ustar sebastiansebastian\name{att.rename.nc} \alias{att.rename.nc} \title{Rename a NetCDF Attribute} \description{Rename a NetCDF attribute.} \usage{att.rename.nc(ncfile, variable, attribute, newname)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the attribute's variable, or \code{"NC_GLOBAL"} for a global attribute.} \item{attribute}{The current attribute name or ID.} \item{newname}{The new name to be assigned to the specified attribute.} } \details{This function changes the name of an existing attribute in a NetCDF dataset open for writing. An attribute cannot be renamed to have the same name as another attribute of the same variable.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") ## Rename these attributes att.rename.nc(nc, "temperature", "missing_value", "my_missing_value") att.rename.nc(nc, "NC_GLOBAL", "title", "my_title") close.nc(nc) } \keyword{file} RNetCDF/man/create.nc.Rd0000644000175000017500000000350112375264053015661 0ustar sebastiansebastian\name{create.nc} \alias{create.nc} \title{Create a NetCDF Dataset} \description{Create a new NetCDF dataset.} \usage{create.nc(filename, clobber=TRUE, large=FALSE, share=FALSE, prefill=TRUE)} \arguments{ \item{filename}{Filename for the NetCDF dataset to be created.} \item{clobber}{The creation mode. If \code{TRUE} (default), any existing dataset with the same filename will be overwritten. Otherwise set to \code{FALSE}.} \item{large}{The file format. If \code{FALSE} (default), create a NetCDF classic format file, otherwise create a 64-bit offset format file. The 64-bit offset format imposes fewer restrictions on data files larger than 2 GB, but it cannot be read by NetCDF library versions earlier than 3.6.0.} \item{share}{The buffer scheme. If \code{FALSE} (default), dataset access is buffered and cached for performance. However, if one or more processes may be reading while another process is writing the dataset, set to \code{FALSE}.} \item{prefill}{The prefill mode. If \code{TRUE} (default), newly defined variables are initialised with fill values when they are first accessed. This allows unwritten array elements to be detected when reading, but it also implies duplicate writes if all elements are subsequently written with user-specified data. Enhanced write performance can be obtained by setting \code{prefill=FALSE}.} } \details{This function creates a new NetCDF dataset, returning an object of class "\code{NetCDF}" that can be used in R. A creation mode flag specifies whether to overwrite any existing dataset with the same name.} \value{Object of class "\code{NetCDF}" which points to the NetCDF dataset.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a void NetCDF dataset nc <- create.nc("foo.nc") close.nc(nc) } \keyword{file} RNetCDF/man/att.put.nc.Rd0000644000175000017500000000433312375264053016021 0ustar sebastiansebastian\name{att.put.nc} \alias{att.put.nc} \title{Put a NetCDF Attribute} \description{Put an attribute to a NetCDF dataset.} \usage{att.put.nc(ncfile, variable, name, type, value)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the variable to which the attribute will be assigned or \code{"NC_GLOBAL"} for a global attribute.} \item{name}{Attribute name. Must begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore ("\code{_}"). Case is significant. Attribute name conventions are assumed by some NetCDF generic applications, e.g., \code{units} as the name for a string attribute that gives the units for a NetCDF variable.} \item{type}{One of the set of predefined NetCDF external data types. The valid NetCDF external data types are \code{NC_BYTE}, \code{NC_CHAR}, \code{NC_SHORT}, \code{NC_INT}, \code{NC_FLOAT}, and \code{NC_DOUBLE}.} \item{value}{Attribute value. This can be either a single numeric value or a vector of numeric values, or alternatively a character string.} } \details{Names commencing with underscore ("\code{_}") are reserved for use by the NetCDF library. Most generic applications that process NetCDF datasets assume standard attribute conventions and it is strongly recommended that these be followed unless there are good reasons for not doing so.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \note{\code{NC_BYTE} is always interpreted as signed.} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "temperature", "long_name", "NC_CHAR", "air temperature") att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") att.put.nc(nc, "NC_GLOBAL", "history", "NC_CHAR", paste("Created on", date())) close.nc(nc) } \keyword{file} RNetCDF/man/utcal.nc.Rd0000644000175000017500000000335712375264053015537 0ustar sebastiansebastian\name{utcal.nc} \alias{utcal.nc} \title{Convert Temporal Amounts to UTC Referenced Dates} \description{Convert temporal amounts to UTC referenced date and time.} \usage{utcal.nc(unitstring, value, type="n")} \arguments{ \item{unitstring}{A temporal unit with an origin (e.g., ``days since 1900-01-01'').} \item{value}{An amount (quantity) of the given temporal unit.} \item{type}{Character string which determines the output type. Can be either \code{n} for numeric or \code{s} for output in string form.} } \details{Converts the amount, \code{value}, of the temporal unit, \code{unitstring}, into a UTC-referenced date and time. The UDUNITS package uses a mixed Gregorian/Julian calendar system. Dates prior to 1582-10-15 are assumed to use the Julian calendar, which was introduced by Julius Caesar in 46 BCE and is based on a year that is exactly 365.25 days long. Dates on and after 1582-10-15 are assumed to use the Gregorian calendar, which was introduced on that date and is based on a year that is exactly 365.2425 days long. (A year is actually approximately 365.242198781 days long.) Seemingly strange behavior of the UDUNITS package can result if a user-given time interval includes the changeover date.} \value{If the output type is set to numeric, a matrix containing the corresponding date(s) and time(s), with the following columns: year, month, day, hour, minute, second. Otherwise a vector of strings in the form \code{"YYYY-MM-DD hh:mm:ss"}.} \references{\url{http://www.unidata.ucar.edu/packages/udunits/}} \author{Pavel Michna} \examples{ ## Convert units to UTC referenced time utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5)) utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5), type="s") } \keyword{utilities} RNetCDF/man/var.put.nc.Rd0000644000175000017500000001207412375264053016022 0ustar sebastiansebastian\name{var.put.nc} \alias{var.put.nc} \title{Put Data Into a NetCDF Variable} \description{Write the contents of a NetCDF variable.} \usage{var.put.nc(ncfile, variable, data, start=NA, count=NA, na.mode=0, pack=FALSE)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the variable.} \item{data}{The (multidimensional) array containing the data to write.} \item{start}{A vector of indices indicating where to start writing the passed values (beginning at 1). The length of this vector must equal the number of dimensions the variable has. Order is leftmost varying fastest (as got from \code{\link[RNetCDF]{print.nc}}; opposite to the CDL conventions). If set to \code{NA}, writing starts for each dimension at position 1.} \item{count}{A vector of integers indicating the count of values to write along each dimension. Order is leftmost varying fastest (as got from \code{\link[RNetCDF]{print.nc}}; opposite to the CDL conventions). The length of this vector must equal the number of dimensions the variable has. If set to \code{NA}, the dimesions are taken from \code{data}.} \item{na.mode}{Set the mode how missing values (\code{NA}) are handled: 0=accept \code{_FillValue} or \code{missing_value} attribute, 1=accept only \code{_FillValue} attribute, 2=accept only \code{missing_value} attribute.} \item{pack}{Variables are packed if \code{pack=TRUE} and the attributes \code{add_offset} and \code{scale_factor} are defined. Default is \code{FALSE}.} } \details{This function writes values to a NetCDF variable. Type conversion is done by the NetCDF library itself. This means, that double precision values are passed from R to the corresponding C-function, no matter which type the variable has. Only the R type \code{character} is treated separately. When writing values of type \code{NC_CHAR}, it is mandatory that the first element of \code{count} contains the value of this dimension's length (usually \code{max_string_length}), the maximum string length is given by this value. R arrays of type \code{character} need therefore one additional dimension when written to a NetCDF dataset. Values of \code{NA} are supported if the variable's missing value attribute (as defined in \code{na.mode}) is set. They are converted to the corresponding value before written to disk. If \code{na.mode=0} and both attributes are defined, the value of \code{_FillValue} is used. To reduce the storage space required by a NetCDF file, numeric variables can be "packed" into types of lower precision. The packing operation involves subtraction of attribute \code{add_offset} before division by attribute \code{scale_factor}. This packing operation is performed automatically for variables defined with the two attributes \code{add_offset} and \code{scale_factor} if argument \code{pack} is set to \code{TRUE}. If \code{pack} is \code{FALSE}, \code{data} values are assumed to be packed correctly and are written to the variable without alteration. Data in a NetCDF file is conceived as being a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The \code{start} and \code{count} indices that this routine takes indicate where the writing starts along each dimension, and the count of values along each dimension to write. Awkwardness arises mainly from one thing: NetCDF data are written with the last dimension varying fastest, whereas R works opposite. Thus, the order of the dimensions according to the CDL conventions (e.g., time, latitude, longitude) is reversed in the R array (e.g., longitude, latitude, time).} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \note{\code{NC_BYTE} is always interpreted as signed. For best performance, it is recommended that the definition of dimensions, variables and attributes is completed before variables are read or written.} \author{Pavel Michna, Milton Woods} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) dim.def.nc(nc, "max_string_length", 32) ## Create three variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) var.def.nc(nc, "name", "NC_CHAR", c("max_string_length", "station")) ## Put some missing_value attribute for temperature att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) ## Define variable values mytime <- c(1:2) mytemperature <- c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9) myname <- c("alfa", "bravo", "charlie", "delta", "echo") dim(mytemperature) <- c(5,2) ## Put the data with indicated start/count var.put.nc(nc, "time", mytime, 1, length(mytime)) var.put.nc(nc, "temperature", mytemperature, c(1,1), c(5,2)) var.put.nc(nc, "name", myname, c(1,1), c(32,5)) sync.nc(nc) ## Put the data with default start/count var.put.nc(nc, "time", mytime) var.put.nc(nc, "temperature", mytemperature) var.put.nc(nc, "name", myname) close.nc(nc) } \keyword{file} RNetCDF/man/utinvcal.nc.Rd0000644000175000017500000000323312375264053016245 0ustar sebastiansebastian\name{utinvcal.nc} \alias{utinvcal.nc} \title{Convert UTC Referenced Dates Into Temporal Amounts} \description{Convert a UTC referenced date into a temporal amount.} \usage{utinvcal.nc(unitstring, value)} \arguments{ \item{unitstring}{A temporal unit with an origin (e.g., ``days since 1900-01-01'').} \item{value}{A vector or a matrix containing the dates to convert. Each row must contain year, month, day, hour, minute and second.} } \value{A vector containing the amount(s) of the temporal unit(s) that the date(s) correspond(s) to.} \details{Converts a UTC-referenced date and time into the amount, \code{value}, of the temporal unit, \code{unitstring}. The UDUNITS package uses a mixed Gregorian/Julian calendar system. Dates prior to 1582-10-15 are assumed to use the Julian calendar, which was introduced by Julius Caesar in 46 BCE and is based on a year that is exactly 365.25 days long. Dates on and after 1582-10-15 are assumed to use the Gregorian calendar, which was introduced on that date and is based on a year that is exactly 365.2425 days long. (A year is actually approximately 365.242198781 days long.) Seemingly strange behavior of the UDUNITS package can result if a user-given time interval includes the changeover date. If the dates are given in string form, the structure must be exactly \code{"YYYY-MM-DD hh:mm:ss"}.} \references{\url{http://www.unidata.ucar.edu/packages/udunits/}} \author{Pavel Michna} \examples{ ## Convert UTC referenced time to other time units utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(1900,1,1,5,25,0)) utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", "1900-01-01 05:25:00") } \keyword{utilities} RNetCDF/man/print.nc.Rd0000644000175000017500000000316512375264053015560 0ustar sebastiansebastian\name{print.nc} \alias{print.nc} \title{Print Summary Information About a NetCDF Dataset} \description{Print summary information about a NetCDF dataset.} \usage{print.nc(x, ...)} \arguments{ \item{x}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{...}{Arguments passed to or from other methods (not used).} } \details{This function prints information about a NetCDF dataset. This includes a list of all dimensions and their length, a list of all variables and their attributes (including their values) and a list of all global attributes (including their values). The output of this function is almost identical with a \code{"ncdump -h"} call. Because arrays in R have their leftmost subscript varying fastest, the fastest varying dimensions are printed first. } \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "temperature", "long_name", "NC_CHAR", "air temperature") att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") att.put.nc(nc, "NC_GLOBAL", "history", "NC_CHAR", paste("Created on", date())) ## Print summary information about the dataset print.nc(nc) close.nc(nc) } \keyword{file} RNetCDF/man/var.rename.nc.Rd0000644000175000017500000000216012375264053016454 0ustar sebastiansebastian\name{var.rename.nc} \alias{var.rename.nc} \title{Rename a NetCDF Variable} \description{Rename a NetCDF variable.} \usage{var.rename.nc(ncfile, variable, newname)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{Either the ID or the name of the variable to be renamed.} \item{newname}{The new variable name.} } \details{This function renames an existing variable in a NetCDF dataset open for writing. A variable cannot be renamed to have the same name as another variable.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Rename these variables var.rename.nc(nc, 0, "mytime") var.rename.nc(nc, "temperature", "mytemperature") close.nc(nc) } \keyword{file} RNetCDF/man/att.delete.nc.Rd0000644000175000017500000000240712375264053016453 0ustar sebastiansebastian\name{att.delete.nc} \alias{att.delete.nc} \title{Delete a NetCDF Attribute} \description{Delete a NetCDF attribute.} \usage{att.delete.nc(ncfile, variable, attribute)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the attribute's variable, or \code{"NC_GLOBAL"} for a global attribute.} \item{attribute}{The name of the attribute to be deleted.} } \details{This function deletes a NetCDF attribute from a NetCDF dataset open for writing.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") ## Delete these attributes att.delete.nc(nc, "temperature", "missing_value") att.delete.nc(nc, "NC_GLOBAL", "title") close.nc(nc) } \keyword{file} RNetCDF/man/att.copy.nc.Rd0000644000175000017500000000434712375264053016170 0ustar sebastiansebastian\name{att.copy.nc} \alias{att.copy.nc} \title{Copy Attribute from One NetCDF to Another} \description{Copy attribute from one NetCDF to another.} \usage{att.copy.nc(ncfile.in, variable.in, attribute, ncfile.out, variable.out)} \arguments{ \item{ncfile.in}{Object of class "\code{NetCDF}" which points to the input NetCDF dataset from which the attribute will be copied (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable.in}{ID or name of the variable in the input NetCDF dataset from which the attribute will be copied, or \code{"NC_GLOBAL"} for a global attribute.} \item{attribute}{Name or ID of the attribute in the input NetCDF dataset to be copied.} \item{ncfile.out}{Object of class "\code{NetCDF}" which points to the output NetCDF dataset to which the attribute will be copied (as returned from \code{\link[RNetCDF]{open.nc}}). It is permissible for the input and output NetCDF object to be the same.} \item{variable.out}{ID or name of the variable in the output NetCDF dataset to which the attribute will be copied, or \code{"NC_GLOBAL"} to copy to a global attribute.} } \details{This function copies an attribute from one open NetCDF dataset to another. It can also be used to copy an attribute from one variable to another within the same NetCDF dataset.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create two new NetCDF datasets and define two dimensions nc.1 <- create.nc("foo_1.nc") nc.2 <- create.nc("foo_2.nc") dim.def.nc(nc.1, "station", 5) dim.def.nc(nc.1, "time", unlim=TRUE) dim.def.nc(nc.2, "station", 5) dim.def.nc(nc.2, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc.1, "time", "NC_INT", "time") var.def.nc(nc.1, "temperature", "NC_DOUBLE", c(0,1)) var.def.nc(nc.2, "time", "NC_INT", "time") var.def.nc(nc.2, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes to the first dataset att.put.nc(nc.1, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc.1, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") ## Copy the attributes to the second dataset att.copy.nc(nc.1, 1, 0, nc.2, 1) att.copy.nc(nc.1, "NC_GLOBAL", "title", nc.2, "NC_GLOBAL") close.nc(nc.1) close.nc(nc.2) } \keyword{file} RNetCDF/man/00RNetCDF.Rd0000644000175000017500000000505412375264053015351 0ustar sebastiansebastian\name{RNetCDF} \alias{RNetCDF} \title{R Interface to NetCDF Datasets} \description{ This package provides an interface to Unidata's NetCDF library functions (version 3) and furthermore access to Unidata's UDUNITS calendar conversions. The routines and the documentation follow the NetCDF and UDUNITS C interface, so the corresponding manuals can be consulted for more detailed information. NetCDF is an abstraction that supports a view of data as a collection of self-describing, portable objects that can be accessed through a simple interface. Array values may be accessed directly, without knowing details of how the data are stored. Auxiliary information about the data, such as what units are used, may be stored with the data. Generic utilities and application programs can access NetCDF datasets and transform, combine, analyze, or display specified fields of the data. The external types supported by the NetCDF interface are: \tabular{ll}{ \code{NC_CHAR} \tab 8-bit characters intended for representing text. \cr \code{NC_BYTE} \tab 8-bit signed or unsigned integers. \cr \code{NC_SHORT} \tab 16-bit signed integers. \cr \code{NC_INT} \tab 32-bit signed integers. \cr \code{NC_FLOAT} \tab 32-bit IEEE floating-point. \cr \code{NC_DOUBLE} \tab 64-bit IEEE floating-point. \cr } These types are called ``external'', because they correspond to the portable external representation for NetCDF data. When a program reads external NetCDF data into an internal variable, the data is converted, if necessary, into the specified internal type. Similarly, if you write internal data into a NetCDF variable, this may cause it to be converted to a different external type, if the external type for the NetCDF variable differs from the internal type. First versions of the R and C code of this package were based on the \code{netCDF} package by Thomas Lumley and the \code{ncdf} package by David Pierce. Milton Woods added some enhancements of the NetCDF library version 3.6. A high-level interface based on this library is the \code{ncvar} package by Juerg Schmidli. It simplifies the handling of datasets which contain lots of metadata. Different metadata conventions are supported including the CF metadata conventions used by the climate modeling and forecasting community. } \references{ \url{http://www.unidata.ucar.edu/packages/netcdf/} \url{http://www.unidata.ucar.edu/packages/udunits/} } \note{The NetCDF and the UDUNITS library must be already installed on the system.} \author{Pavel Michna} \keyword{file} RNetCDF/man/sync.nc.Rd0000644000175000017500000000261212375264053015374 0ustar sebastiansebastian\name{sync.nc} \alias{sync.nc} \title{Synchronize a NetCDF Dataset} \description{Synchronize an open NetCDF dataset to disk.} \usage{sync.nc(ncfile)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} } \details{This function offers a way to synchronize the disk copy of a NetCDF dataset with in-memory buffers. There are two reasons one might want to synchronize after writes: To minimize data loss in case of abnormal termination, or to make data available to other processes for reading immediately after it is written.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Define variable values mytime <- c(1:2) mytemperature <- c(0.0, 1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8, 9.9) ## Put the data var.put.nc(nc, "time", mytime, 1, length(mytime)) var.put.nc(nc, "temperature", mytemperature, c(1,1), c(5,2)) ## Synchronize to disk sync.nc(nc) ## Now the data can be read var.get.nc(nc, 0) var.get.nc(nc, "temperature") close.nc(nc) } \keyword{file} RNetCDF/man/var.inq.nc.Rd0000644000175000017500000000330712375264053016000 0ustar sebastiansebastian\name{var.inq.nc} \alias{var.inq.nc} \title{Inquire About a NetCDF Variable} \description{Inquire about a NetCDF variable.} \usage{var.inq.nc(ncfile, variable)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{Either the ID or the name of the variable to be inquired.} } \details{This function returns information about a NetCDF variable. Information about a variable include its name, its ID, its type, its number of dimensions, a vector of the dimension IDs of this variable and the number of attributes. The valid external NetCDF data types are \code{NC_BYTE}, \code{NC_CHAR}, \code{NC_SHORT}, \code{NC_INT}, \code{NC_FLOAT}, and \code{NC_DOUBLE}.} \value{ A list containing the following components: \item{id}{Variable ID.} \item{name}{Variable name.} \item{type}{External NetCDF data type.} \item{ndims}{Number of dimensions the variable was defined as using.} \item{dimids}{Vector of dimension IDs corresponding to the variable dimensions (\code{NA} for scalar variables). Order is leftmost varying fastest.} \item{natts}{Number of variable attributes assigned to this variable.} } \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Inquire about these variables var.inq.nc(nc, 0) var.inq.nc(nc, "temperature") close.nc(nc) } \keyword{file} RNetCDF/man/utinit.nc.Rd0000644000175000017500000000167312375264053015742 0ustar sebastiansebastian\name{utinit.nc} \alias{utinit.nc} \title{Initialize the UDUNITS Library} \description{Initialize the UDUNITS library.} \usage{utinit.nc(path="")} \arguments{ \item{path}{Path to a units file containing initializing unit definitions.} } \details{This function initializes the UDUNITS library. It is called by \code{.First.lib} when the package is loaded. Normally, the user does not need to call this function. If path is non-NULL and not empty, then it specifies a units file containing initializing unit definitions; otherwise, the environment variable \code{UDUNITS_PATH} is checked and, if it exists and is not empty, then it is assumed to contain the pathname of the units file; otherwise, a compile-time default pathname is used. } \references{\url{http://www.unidata.ucar.edu/packages/udunits/}} \author{Pavel Michna} \examples{ ## NOTE: The user will normally never need to call this function utinit.nc() } \keyword{utilities} RNetCDF/man/file.inq.nc.Rd0000644000175000017500000000323712375264053016131 0ustar sebastiansebastian\name{file.inq.nc} \alias{file.inq.nc} \title{Inquire About a NetCDF Dataset} \description{Inquire about a NetCDF dataset.} \usage{file.inq.nc(ncfile)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} } \details{This function returns values for the number of dimensions, the number of variables, the number of global attributes, and the dimension ID of the dimension defined with unlimited length, if any.} \value{ A list containing the following components: \item{ndims}{Number of dimensions defined for this NetCDF dataset.} \item{nvars}{Number of variables defined for this NetCDF dataset.} \item{ngatts}{Number of global attributes for this NetCDF dataset.} \item{unlimdimid}{ID of the unlimited dimension, if there is one for this NetCDF dataset. Otherwise \code{NA} will be returned.} } \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "temperature", "long_name", "NC_CHAR", "air temperature") att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") att.put.nc(nc, "NC_GLOBAL", "history", "NC_CHAR", paste("Created on", date())) ## Inquire about the dataset file.inq.nc(nc) close.nc(nc) } \keyword{file} RNetCDF/man/var.get.nc.Rd0000644000175000017500000001266012375264053015772 0ustar sebastiansebastian\name{var.get.nc} \alias{var.get.nc} \title{Get a NetCDF Variable} \description{Read the contents of a NetCDF variable.} \usage{var.get.nc(ncfile, variable, start=NA, count=NA, na.mode=0, collapse=TRUE, unpack=FALSE)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the variable.} \item{start}{A vector of indices indicating where to start reading the values (beginning at 1). The length of this vector must equal the number of dimensions the variable has. Order is leftmost varying fastest (as got from \code{\link[RNetCDF]{print.nc}}; opposite to the CDL conventions). If not specified (\code{start=NA}), reading starts at index 1.} \item{count}{A vector of integers indicating the count of values to read along each dimension. Order is leftmost varying fastest (as got from \code{\link[RNetCDF]{print.nc}}; opposite to the CDL conventions). The length of this vector must equal the number of dimensions the variable has. If not specified (\code{count=NA}), the entire variable or all values along the corresponding dimension(s) are read.} \item{na.mode}{Set the mode how missing values (\code{NA}) are handled: 0=accept \code{_FillValue} or \code{missing_value} attribute, 1=accept only \code{_FillValue} attribute, 2=accept only \code{missing_value} attribute, 3=no missing value conversion.} \item{collapse}{\code{TRUE} if degenerated dimensions (length=1) should be omitted.} \item{unpack}{Packed variables are unpacked if \code{unpack=TRUE} and the attributes \code{add_offset} and \code{scale_factor} are defined. Default is \code{FALSE}.} } \details{This function returns the value of a variable. Returned values are always in ordinary R double precision (apart from character variables), no matter what precision they are in the on-disk dataset. Values of \code{NA} are supported; values in the data file that match the variable's missing value attribute (as defined in \code{na.mode}) are automatically converted to \code{NA} before being returned to the user. If \code{na.mode=0} and both attributes are defined, the value of \code{_FillValue} is used. To reduce the storage space required by a NetCDF file, numeric variables are sometimes "packed" into types of lower precision. The original data can be recovered (approximately) by multiplication of the stored values by attribute \code{scale_factor} followed by addition of attribute \code{add_offset}. This unpacking operation is performed automatically for variables with attributes \code{scale_factor} and \code{add_offset} if argument \code{unpack} is set to \code{TRUE}. If \code{unpack} is \code{FALSE}, raw values are read from each variable without alteration. Data in a NetCDF file is conceived as being a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The \code{start} and \code{count} indices that this routine takes indicate where the reading starts along each dimension, and the count of values along each dimension to read. The argument \code{collapse} allows to keep degenerated dimensions (if set to \code{FALSE}). As default, array dimensions with length=1 are omitted (e.g., an array with dimensions [2,1,3,4] in the NetCDF dataset is returned as [2,3,4]). Awkwardness arises mainly from one thing: NetCDF data are written with the last dimension varying fastest, whereas R works opposite. Thus, the order of the dimensions according to the CDL conventions (e.g., time, latitude, longitude) is reversed in the R array (e.g., longitude, latitude, time).} \value{A multidimensional array of type \code{numeric} or \code{character} if the data type is \code{NC_CHAR}. No distinction is made between the different storage types of numeric objects. The dimension order according to the CDL conventions is swapped in the R array, because NetCDF data are written with the last dimension varying fastest, whereas R works opposite. Arrays of type \code{character} lose their first dimension, because strings can be indexed with one dimension in R and the first dimension (usually \code{max_string_length}) is therefore needless.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \note{\code{NC_BYTE} is always interpreted as signed.} \author{Pavel Michna, Milton Woods} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) dim.def.nc(nc, "max_string_length", 32) ## Create three variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) var.def.nc(nc, "name", "NC_CHAR", c("max_string_length", "station")) ## Put some missing_value attribute for temperature att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) ## Define variable values mytime <- c(1:2) mytemperature <- c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9) myname <- c("alfa", "bravo", "charlie", "delta", "echo") ## Put the data var.put.nc(nc, "time", mytime, 1, length(mytime)) var.put.nc(nc, "temperature", mytemperature, c(1,1), c(5,2)) var.put.nc(nc, "name", myname, c(1,1), c(32,5)) sync.nc(nc) ## Get the data (or a subset) var.get.nc(nc, 0) var.get.nc(nc, "temperature") var.get.nc(nc, "temperature", c(NA,2), c(NA,1)) var.get.nc(nc, "name") var.get.nc(nc, "name", c(1,2), c(4,2)) var.get.nc(nc, "name", c(1,2), c(NA,2)) close.nc(nc) } \keyword{file} RNetCDF/man/read.nc.Rd0000644000175000017500000000347412375264053015342 0ustar sebastiansebastian\name{read.nc} \alias{read.nc} \title{Read a NetCDF Dataset} \description{Read all data from a NetCDF dataset.} \usage{ read.nc(ncfile, unpack=TRUE) } \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{unpack}{Unpack "packed" variables if set to \code{TRUE} (default).} } \details{This function reads all variable data from a NetCDF dataset into a single list. The list elements (arrays) have the same names as the variables in the NetCDF dataset. Packed variables can optionally be returned in an unpacked state (see \code{\link{var.get.nc}} for more information). } \value{A list with the list elements containing the variable data of the NetCDF dataset.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) dim.def.nc(nc, "max_string_length", 32) ## Create three variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) var.def.nc(nc, "name", "NC_CHAR", c("max_string_length", "station")) ## Put some missing_value attribute for temperature att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) ## Define variable values mytime <- c(1:2) mytemperature <- c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9) myname <- c("alfa", "bravo", "charlie", "delta", "echo") ## Put the data var.put.nc(nc, "time", mytime, 1, length(mytime)) var.put.nc(nc, "temperature", mytemperature, c(1,1), c(5,2)) var.put.nc(nc, "name", myname, c(1,1), c(32,5)) sync.nc(nc) ## Get the data read.nc(nc) close.nc(nc) } \keyword{file} RNetCDF/man/dim.def.nc.Rd0000644000175000017500000000350412375264053015727 0ustar sebastiansebastian\name{dim.def.nc} \alias{dim.def.nc} \title{Define a NetCDF Dimension} \description{Define a new NetCDF dimension.} \usage{dim.def.nc(ncfile, dimname, dimlength=1, unlim=FALSE)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{dimname}{Dimension name. Must begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore ("\code{_}"). Case is significant.} \item{dimlength}{Length of dimension, that is, number of values for this dimension as an index to variables that use it. This must be a positive integer. If an unlimited dimension is created (\code{unlim=TRUE}), the value of \code{length} is not used.} \item{unlim}{Set to \code{TRUE} if an unlimited dimension should be created, otherwise to \code{FALSE}.} } \details{This function creates a new NetCDF dimension. There is a suggested limit (100) to the number of dimensions. Ordinarily, the name and length of a dimension are fixed when the dimension is first defined. The name may be changed later, but the length of a dimension (other than the unlimited dimension) cannot be changed without copying all the data to a new NetCDF dataset with a redefined dimension length. A NetCDF dimension in an open NetCDF dataset is referred to by a small integer called a dimension ID. In the C interface, dimension IDs are 0, 1, 2, ..., in the order in which the dimensions were defined. At most one unlimited length dimension may be defined for each NetCDF dataset.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) close.nc(nc) } \keyword{file} RNetCDF/man/close.nc.Rd0000644000175000017500000000147612375264053015534 0ustar sebastiansebastian\name{close.nc} \alias{close.nc} \title{Close a NetCDF Dataset} \description{Close an open NetCDF dataset.} \usage{close.nc(con, ...)} \arguments{ \item{con}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{...}{Arguments passed to or from other methods (not used).} } \details{This function closes an open NetCDF dataset. After an open NetCDF dataset is closed, its NetCDF ID may be reassigned to the next NetCDF dataset that is opened or created. Therefore, the passed object (\code{ncfile}) should be deleted by the user after calling this function.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a void NetCDF dataset nc <- create.nc("foo.nc") close.nc(nc) } \keyword{file} RNetCDF/man/dim.inq.nc.Rd0000644000175000017500000000253212375264053015760 0ustar sebastiansebastian\name{dim.inq.nc} \alias{dim.inq.nc} \title{Inquire About a NetCDF Dimension} \description{Inquire about a NetCDF dimension.} \usage{dim.inq.nc(ncfile, dimension)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{dimension}{Either the ID or the name of the dimension to be inquired.} } \details{This function returns information about a NetCDF dimension. Information about a dimension include its name, its ID, its length and a flag if it is the unlimited dimension of this NetCDF dataset, if any. The length of the unlimited dimension, if any, is the number of records written so far.} \value{ A list containing the following components: \item{id}{Dimension ID.} \item{name}{Dimension name.} \item{length}{Length of dimension. For the unlimited dimension, this is the number of records written so far.} \item{unlim}{\code{TRUE} if it is the unlimited dimension, \code{FALSE} otherwise.} } \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Inquire about the dimensions dim.inq.nc(nc, 0) dim.inq.nc(nc, "time") close.nc(nc) } \keyword{file} RNetCDF/man/att.inq.nc.Rd0000644000175000017500000000365512375264053016006 0ustar sebastiansebastian\name{att.inq.nc} \alias{att.inq.nc} \title{Inquire About a NetCDF Attribute} \description{ Inquire about a NetCDF attribute. } \usage{att.inq.nc(ncfile, variable, attribute)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{Either the ID or the name of the attribute's variable or \code{"NC_GLOBAL"} for a global attribute.} \item{attribute}{Either the ID or the name of the attribute to be inquired.} } \details{This function returns information about a NetCDF attribute. Information about an attribute include its ID, its name, its type, and its length. The valid external NetCDF data types are \code{NC_BYTE}, \code{NC_CHAR}, \code{NC_SHORT}, \code{NC_INT}, \code{NC_FLOAT}, and \code{NC_DOUBLE}. In general, attributes are rather accessed by name than by their ID (which is called number) because the attribute number is more volatile than the name, since it can change when other attributes of the same variable are deleted.} \value{ A list containing the following components: \item{id}{Attribute ID.} \item{name}{Attribute name.} \item{type}{External NetCDF data type.} \item{length}{Length of this attribute.} } \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") ## Inquire about these attributes att.inq.nc(nc, "temperature", "missing_value") att.inq.nc(nc, "NC_GLOBAL", "title") close.nc(nc) } \keyword{file} RNetCDF/man/att.get.nc.Rd0000644000175000017500000000330412375264053015765 0ustar sebastiansebastian\name{att.get.nc} \alias{att.get.nc} \title{Get a NetCDF Attribute} \description{Get an attribute from a NetCDF dataset.} \usage{att.get.nc(ncfile, variable, attribute)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{variable}{ID or name of the variable from which the attribute will be read, or \code{"NC_GLOBAL"} for a global attribute.} \item{attribute}{Attribute name or ID.} } \details{This function returns the value of the attribute.} \value{A vector of type \code{character} if the on-disk type is \code{NC_CHAR}, otherwise \code{numeric}. No distinction is made between the different storage types of numeric objects.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \note{\code{NC_BYTE} is always interpreted as signed.} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Create two variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) ## Put some attributes att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) att.put.nc(nc, "temperature", "long_name", "NC_CHAR", "air temperature") att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "Data from Foo") att.put.nc(nc, "NC_GLOBAL", "history", "NC_CHAR", paste("Created on", date())) ## Get these attributes att.get.nc(nc, "temperature", "missing_value") att.get.nc(nc, "temperature", "long_name") att.get.nc(nc, "NC_GLOBAL", "title") att.get.nc(nc, "NC_GLOBAL", "history") close.nc(nc) } \keyword{file} RNetCDF/man/dim.rename.nc.Rd0000644000175000017500000000173312375264053016442 0ustar sebastiansebastian\name{dim.rename.nc} \alias{dim.rename.nc} \title{Rename a NetCDF Dimension} \description{Rename a NetCDF dimension.} \usage{dim.rename.nc(ncfile, dimension, newname)} \arguments{ \item{ncfile}{Object of class "\code{NetCDF}" which points to the NetCDF dataset (as returned from \code{\link[RNetCDF]{open.nc}}).} \item{dimension}{Either the ID or the name of the dimension to be renamed.} \item{newname}{The new dimension name.} } \details{This function renames an existing dimension in a NetCDF dataset open for writing. A dimension cannot be renamed to have the same name as another dimension.} \references{\url{http://www.unidata.ucar.edu/packages/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) ## Rename the dimensions dim.rename.nc(nc, 0, "mystation") dim.rename.nc(nc, "time", "mytime") close.nc(nc) } \keyword{file} RNetCDF/tests/0000755000175000017500000000000012375264053014120 5ustar sebastiansebastianRNetCDF/tests/RNetCDF-test.R0000644000175000017500000002327512375264053016416 0ustar sebastiansebastian#===============================================================================# # # # Name: RNetCDF-test.R # # # # Version: 1.6.3-1 # # # # Purpose: Test functions to the NetCDF interface for R. # # # # Author: Pavel Michna (michna@giub.unibe.ch) # # Milton Woods (m.woods@bom.gov.au) # # # # Copyright: (C) 2010-2014 Pavel Michna # # # #===============================================================================# # # # This program is free software; you can redistribute it and/or modify # # it under the terms of the GNU General Public License as published by # # the Free Software Foundation; either version 2 of the License, or # # (at your option) any later version. # # # # This program is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details. # # # # You should have received a copy of the GNU General Public License # # along with this program; if not, write to the Free Software # # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # # # #===============================================================================# # Implementation and Revisions # #-------------------------------------------------------------------------------# # Author Date Description # # ------ ---- ----------- # # pm 29/12/10 First implementation # # mw 18/07/12 Test packed variables # # # #===============================================================================# #===============================================================================# # Load library # #===============================================================================# library(RNetCDF) #===============================================================================# # Run tests # #===============================================================================# #-------------------------------------------------------------------------------# # NetCDF library functions # #-------------------------------------------------------------------------------# #--Initialize ------------------------------------------------------------------# cat("Starting NetCDF tests...\n") nccount <- 0 ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("foo.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) dim.def.nc(nc, "max_string_length", 32) ## Create three variables, one as coordinate variable var.def.nc(nc, "time", "NC_INT", "time") var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1)) var.def.nc(nc, "packvar", "NC_BYTE", c("station")) var.def.nc(nc, "name", "NC_CHAR", c("max_string_length", "station")) ## Put some missing_value attribute for temperature att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9) ## Define the packing used by packvar att.put.nc(nc, "packvar", "scale_factor", "NC_DOUBLE", 10) att.put.nc(nc, "packvar", "add_offset", "NC_DOUBLE", -5) ## Define variable values mytime <- c(1:2) mytemperature <- c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9) mypackvar <- seq_len(5)*10-5 myname <- c("alfa", "bravo", "charlie", "delta", "echo") ## Put the data var.put.nc(nc, "time", mytime, 1, length(mytime)) var.put.nc(nc, "temperature", mytemperature, c(1,1), c(5,2)) var.put.nc(nc, "packvar", mypackvar, pack=TRUE) var.put.nc(nc, "name", myname, c(1,1), c(32,5)) sync.nc(nc) #-- Test 1 (read) --------------------------------------------------------------# cat("Test 1 ... ") x <- c(1, 2) y <- var.get.nc(nc, 0) if(sum(y %in% x) == 2) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 2 (read) --------------------------------------------------------------# cat("Test 2 ... ") x <- matrix(data=c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9), ncol=2) y <- var.get.nc(nc, "temperature") if(sum(y %in% x) == 10) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 3 (read) --------------------------------------------------------------# cat("Test 3 ... ") x <- c(6.6, 7.7, NA, NA, 9.9) y <- var.get.nc(nc, "temperature", c(NA,2), c(NA,1)) if(sum(y %in% x) == 5) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 4 (read) --------------------------------------------------------------# cat("Test 4 ... ") x <- c("alfa", "bravo", "charlie", "delta", "echo" ) y <- var.get.nc(nc, "name") if(sum(y %in% x) == 5) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 5 (read) --------------------------------------------------------------# cat("Test 5 ... ") x <- c("brav", "char") y <- var.get.nc(nc, "name", c(1,2), c(4,2)) if(sum(y %in% x) == 2) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 6 (read) --------------------------------------------------------------# cat("Test 6 ... ") x <- c("bravo", "charlie") y <- var.get.nc(nc, "name", c(1,2), c(NA,2)) if(sum(y %in% x) == 2) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Test 7 (read unpacked) -----------------------------------------------------# cat("Test 7 ... ") y <- var.get.nc(nc, "packvar", unpack=TRUE) if(isTRUE(all.equal(mypackvar, as.vector(y)))) { cat("OK\n") nccount <- nccount + 1 } else cat("failed\n") #-- Close file -----------------------------------------------------------------# close.nc(nc) #-------------------------------------------------------------------------------# # UDUNITS calendar functions # #-------------------------------------------------------------------------------# #--Initialize ------------------------------------------------------------------# cat("Starting UDUNITS tests...\n") utcount <- 0 #-- Test 1 (utcal.nc() - numeric values) ---------------------------------------# cat("Test 1 ... ") x <- matrix(data=c(1899, 1900, 1900, 1900, 1900, 1900, 12, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1, 1, 23, 0, 1, 2, 3, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ncol=6) y <- utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5)) if(sum(y == x) == 36) { cat("OK\n") utcount <- utcount + 1 } else cat("failed\n") #-- Test 2 (utcal.nc() - string values) ----------------------------------------# cat("Test 2 ... ") x <- c("1899-12-31 23:00:00", "1900-01-01 00:00:00", "1900-01-01 01:00:00", "1900-01-01 02:00:00", "1900-01-01 03:00:00", "1900-01-01 04:00:00") y <- utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5), type="s") if(sum(y == x) == 6) { cat("OK\n") utcount <- utcount + 1 } else cat("failed\n") #-- Test 3 (utinvcal.nc() - numeric values) ------------------------------------# cat("Test 3 ... ") x <- 6.416667 y <- utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(1900,1,1,5,25,0)) if(round(x, 6) == round(y, 6)) { cat("OK\n") utcount <- utcount + 1 } else cat("failed\n") #-- Test 4 (utinvcal.nc() - string values) -------------------------------------# cat("Test 4 ... ") x <- 6.416667 y <- utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", "1900-01-01 05:25:00") if(round(x, 6) == round(y, 6)) { cat("OK\n") utcount <- utcount + 1 } else cat("failed\n") #-------------------------------------------------------------------------------# # Overall summary # #-------------------------------------------------------------------------------# cat("Totally ", nccount+utcount, "/ 11 tests passed. ") if(nccount != 7) stop("Some NetCDF tests failed.", call.=FALSE) if(utcount != 4) stop("Some UDUNITS tests failed.", call.=FALSE) cat("Package seems to work properly.\n") #===============================================================================# #===============================================================================# # SCRATCH # #===============================================================================# RNetCDF/src/0000755000175000017500000000000012375264053013545 5ustar sebastiansebastianRNetCDF/src/Makevars.in0000644000175000017500000000005412375264053015645 0ustar sebastiansebastianPKG_CPPFLAGS = @CPPFLAGS@ PKG_LIBS = @LIBS@ RNetCDF/src/Makevars.win0000644000175000017500000000021712375264053016035 0ustar sebastiansebastianPKG_CPPFLAGS=-I$(NETCDF)/libsrc -I$(UDUNITS2_HOME)/include PKG_LIBS=-L$(NETCDF)/libsrc -lnetcdf -L$(UDUNITS2_HOME)$(R_ARCH) -ludunits2 -lexpat RNetCDF/src/RNetCDF.c0000644000175000017500000022174312400657115015101 0ustar sebastiansebastian/*=============================================================================*\ * * * Name: RNetCDF.c * * * * Version: 1.6.3-1 * * * * Purpose: NetCDF interface for R. * * * * Author: Pavel Michna (michna@giub.unibe.ch) * * Milton Woods (m.woods@bom.gov.au) * * * * Copyright: (C) 2004-2014 Pavel Michna * * * *=============================================================================* * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * *=============================================================================* * Implementation and Revisions * *-----------------------------------------------------------------------------* * Author Date Description * * ------ ---- ----------- * * pm 12/06/04 First implementation * * pm 09/07/04 Support scalar variables * * pm 21/07/04 Changed error handling * * pm 03/01/05 Corrected minor bugs * * pm 25/07/06 Changed SET_STRING_ELT to SET_VECTOR_ELT * * mw 14/04/08 Changed nc_redef and nc_enddef usage * * to avoid unnecessary data movement within a file * * mw 14/04/08 Added new modes (large, prefill, share) to * * functions nc_open and nc_create * * pm 24/11/10 Restored nc_redef and nc_enddef usage and added * * enddef option for having the same effect * * pm 01/12/10 Removed argument SEXP enddef, checking for NC_DEFINE * * pm 03/12/10 Minor bug corrections at possible memory leaks * * pm 15/12/10 Minor bug corrections * * pm 25/12/10 Added UDUNITS-2 message override handling (R_ut_init) * * pm 04/01/11 Corrected string handling in R_nc_get_vara_text * * pm 05/01/11 Removed extra zeroing after Calloc * * pm 26/05/14 Corrected memory leak issue (lines 1338 and 1593) * * * \*=============================================================================*/ /*=============================================================================*\ * Includes * \*=============================================================================*/ #include #include #include #include #include #include /*=============================================================================*\ * NetCDF library functions * \*=============================================================================*/ /*-----------------------------------------------------------------------------*\ * R_nc_copy_att() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_copy_att (SEXP ncid_in, SEXP varid_in, SEXP globflag_in, SEXP attname, SEXP ncid_out, SEXP varid_out, SEXP globflag_out) { int ncvarid_in, ncvarid_out, status, errstatus; int enddef = 0; /* Keep for possible future use as argument */ char ncattname[NC_MAX_NAME]; SEXP retlist, retlistnames; /*-- Create output object and initialize return values --------------------*/ PROTECT(retlist = allocVector(VECSXP, 2)); SET_VECTOR_ELT(retlist, 0, allocVector(REALSXP, 1)); SET_VECTOR_ELT(retlist, 1, allocVector(STRSXP, 1)); PROTECT(retlistnames = allocVector(STRSXP, 2)); SET_STRING_ELT(retlistnames, 0, mkChar("status")); SET_STRING_ELT(retlistnames, 1, mkChar("errmsg")); setAttrib(retlist, R_NamesSymbol, retlistnames); strcpy(ncattname, CHAR(STRING_ELT(attname, 0))); status = -1; errstatus = 0; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Check if handling global attributes ----------------------------------*/ if(INTEGER(globflag_in)[0] == 1) ncvarid_in = NC_GLOBAL; else ncvarid_in = INTEGER(varid_in)[0]; if(INTEGER(globflag_out)[0] == 1) ncvarid_out = NC_GLOBAL; else ncvarid_out = INTEGER(varid_out)[0]; /*-- Enter define mode ----------------------------------------------------*/ status = nc_redef(INTEGER(ncid_out)[0]); if((status != NC_NOERR) && (status != NC_EINDEFINE)) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); REAL(VECTOR_ELT(retlist, 0))[0] = status; UNPROTECT(2); return(retlist); } /*-- Copy the attribute ---------------------------------------------------*/ status = nc_copy_att(INTEGER(ncid_in)[0], ncvarid_in, ncattname, INTEGER(ncid_out)[0], ncvarid_out); if(status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); errstatus = status; } /*-- Leave define mode ----------------------------------------------------*/ if(enddef != 0) { status = nc_enddef(INTEGER(ncid_out)[0]); if(status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); errstatus = status; } } /*-- Returning the list ---------------------------------------------------*/ REAL(VECTOR_ELT(retlist, 0))[0] = (double)errstatus; UNPROTECT(2); return(retlist); } /*-----------------------------------------------------------------------------*\ * R_nc_delete_att() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_delete_att (SEXP ncid, SEXP varid, SEXP globflag, SEXP attname) { int ncvarid, status, errstatus; int enddef = 0; /* Keep for possible future use as argument */ char ncattname[NC_MAX_NAME]; SEXP retlist, retlistnames; /*-- Create output object and initialize return values --------------------*/ PROTECT(retlist = allocVector(VECSXP, 2)); SET_VECTOR_ELT(retlist, 0, allocVector(REALSXP, 1)); SET_VECTOR_ELT(retlist, 1, allocVector(STRSXP, 1)); PROTECT(retlistnames = allocVector(STRSXP, 2)); SET_STRING_ELT(retlistnames, 0, mkChar("status")); SET_STRING_ELT(retlistnames, 1, mkChar("errmsg")); setAttrib(retlist, R_NamesSymbol, retlistnames); strcpy(ncattname, CHAR(STRING_ELT(attname, 0))); status = -1; errstatus = 0; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Check if it is a global attribute ------------------------------------*/ if(INTEGER(globflag)[0] == 1) ncvarid = NC_GLOBAL; else ncvarid = INTEGER(varid)[0]; /*-- Enter define mode ----------------------------------------------------*/ status = nc_redef(INTEGER(ncid)[0]); if((status != NC_NOERR) && (status != NC_EINDEFINE)) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); REAL(VECTOR_ELT(retlist, 0))[0] = status; UNPROTECT(2); return(retlist); } /*-- Delete the attribute -------------------------------------------------*/ status = nc_del_att(INTEGER(ncid)[0], ncvarid, ncattname); if(status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); errstatus = status; } /*-- Leave define mode ----------------------------------------------------*/ if(enddef != 0) { status = nc_enddef(INTEGER(ncid)[0]); if(status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); errstatus = status; } } /*-- Returning the list ---------------------------------------------------*/ REAL(VECTOR_ELT(retlist, 0))[0] = (double)errstatus; UNPROTECT(2); return(retlist); } /*-----------------------------------------------------------------------------*\ * R_nc_get_att() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_get_att (SEXP ncid, SEXP varid, SEXP name, SEXP numflag, SEXP globflag) { int ncvarid, i, status; char ncattname[NC_MAX_NAME], *cvalue; double *dvalue; size_t attlen; SEXP retlist, retlistnames; /*-- Create output object and initialize return values --------------------*/ PROTECT(retlist = allocVector(VECSXP, 3)); SET_VECTOR_ELT(retlist, 0, allocVector(REALSXP, 1)); SET_VECTOR_ELT(retlist, 1, allocVector(STRSXP, 1)); PROTECT(retlistnames = allocVector(STRSXP, 3)); SET_STRING_ELT(retlistnames, 0, mkChar("status")); SET_STRING_ELT(retlistnames, 1, mkChar("errmsg")); SET_STRING_ELT(retlistnames, 2, mkChar("value")); setAttrib(retlist, R_NamesSymbol, retlistnames); strcpy(ncattname, CHAR(STRING_ELT(name, 0))); status = -1; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Check if it is a global attribute ------------------------------------*/ if(INTEGER(globflag)[0] == 1) ncvarid = NC_GLOBAL; else ncvarid = INTEGER(varid)[0]; /*-- Get the attribute's length -------------------------------------------*/ status = nc_inq_attlen(INTEGER(ncid)[0], ncvarid, ncattname, &attlen); if(status != NC_NOERR) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); REAL(VECTOR_ELT(retlist, 1))[0] = status; UNPROTECT(2); return(retlist); } /*-- Get the attribute ----------------------------------------------------*/ if(INTEGER(numflag)[0] == 1) { dvalue = Calloc((int)attlen, double); status = nc_get_att_double(INTEGER(ncid)[0], ncvarid, ncattname, dvalue); if(status != NC_NOERR) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); REAL(VECTOR_ELT(retlist, 1))[0] = status; UNPROTECT(2); Free(dvalue); return(retlist); } SET_VECTOR_ELT(retlist, 2, allocVector(REALSXP, (int)attlen)); for(i=0; i 0) { for(i=0; i 0) { for(i=0; i 0) { for(i=0; i 0) { for(i=0; i Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. RNetCDF/R/0000755000175000017500000000000012375264053013157 5ustar sebastiansebastianRNetCDF/R/load.R.in0000644000175000017500000000051612375264053014630 0ustar sebastiansebastian".onLoad" <- function(lib, pkg) { datfile <- system.file("udunits.dat", package=pkg) if(nzchar(datfile)) Sys.setenv("UDUNITS_PATH"=datfile) xmlfile <- system.file("udunits", "udunits2.xml", package=pkg) if(nzchar(xmlfile)) Sys.setenv("UDUNITS2_XML_PATH"=xmlfile) utinit.nc("@udunits_dat_file@") } RNetCDF/R/windows/0000755000175000017500000000000012375264053014651 5ustar sebastiansebastianRNetCDF/R/windows/load.R0000644000175000017500000000023412375264053015712 0ustar sebastiansebastian".onLoad" <- function(libname, pkgname) { Sys.setenv(UDUNITS2_XML_PATH = file.path(libname, pkgname, "share/udunits/udunits2.xml")) utinit.nc("") } RNetCDF/R/RNetCDF.R0000644000175000017500000013064212375264053014475 0ustar sebastiansebastian#===============================================================================# # # # Name: RNetCDF.R # # # # Version: 1.6.3-1 # # # # Purpose: NetCDF interface for R. # # # # Author: Pavel Michna (michna@giub.unibe.ch) # # Milton Woods (m.woods@bom.gov.au) # # # # Copyright: (C) 2004-2014 Pavel Michna # # # #===============================================================================# # # # This program is free software; you can redistribute it and/or modify # # it under the terms of the GNU General Public License as published by # # the Free Software Foundation; either version 2 of the License, or # # (at your option) any later version. # # # # This program is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details. # # # # You should have received a copy of the GNU General Public License # # along with this program; if not, write to the Free Software # # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # # # #===============================================================================# # Implementation and Revisions # #-------------------------------------------------------------------------------# # Author Date Description # # ------ ---- ----------- # # pm 12/06/04 First implementation # # pm 09/07/04 Support scalar variables # # pm 21/07/04 Changed error handling # # pm 28/07/04 Minor modifications # # pm 12/09/04 New na.mode=3 and collapse=TRUE/FALSE in var.get.nc() # # pm 24/07/06 Handling dates in string form (udunits) # # mw 14/04/08 Added new modes (large, prefill, share) # # to nc_open and nc_create # # pm 24/11/10 Added new option enddef to att and dim/var definitions # # pm 01/12/10 Removed option enddef, checking in C code for mode # # pm 14/02/12 Corrected bug in att.delete.nc # # pm 02/06/12 Added function read.nc() # # pm 16/07/12 Added packing/unpacking of data (code from mw) # # mw 21/08/14 Allow reading of character vector or scalar # # # #===============================================================================# #===============================================================================# # NetCDF library functions # #===============================================================================# #-------------------------------------------------------------------------------# # att.copy.nc() # #-------------------------------------------------------------------------------# att.copy.nc <- function(ncfile.in, variable.in, attribute, ncfile.out, variable.out) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile.in ) == "NetCDF") stopifnot(class(ncfile.out) == "NetCDF") stopifnot(is.character(attribute) || is.numeric(attribute) ) stopifnot(is.character(variable.in) || is.numeric(variable.in) ) stopifnot(is.character(variable.out) || is.numeric(variable.out)) #-- Get the varids as integer if necessary, handle global attributes -------# varid.in <- NULL varid.out <- NULL globflag.in <- 0 globflag.out <- 0 if(is.character(variable.in) && variable.in != "NC_GLOBAL") varid.in <- try(var.inq.nc(ncfile.in, variable.in)$id) else varid.in <- variable.in if(is.character(variable.in) && variable.in == "NC_GLOBAL") { globflag.in <- 1 varid.in <- -1 } if(is.character(variable.out) && variable.out != "NC_GLOBAL") varid.out <- try(var.inq.nc(ncfile.out, variable.out)$id) else varid.out <- variable.out if(is.character(variable.out) && variable.out == "NC_GLOBAL") { globflag.out <- 1 varid.out <- -1 } if(class(varid.in) == "try-error" || class(varid.out) == "try-error") return(invisible(NULL)) if(is.null(varid.in) || is.null(varid.out)) return(invisible(NULL)) #-- Get the attribute name if necessary ------------------------------------# if(is.character(attribute)) attname <- attribute else attname <- try(att.inq.nc(ncfile.in, variable.in, attribute)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_copy_att", as.integer(ncfile.in), as.integer(varid.in), as.integer(globflag.in), as.character(attname), as.integer(ncfile.out), as.integer(varid.out), as.integer(globflag.out), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # att.delete.nc() # #-------------------------------------------------------------------------------# att.delete.nc <- function(ncfile, variable, attribute) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable) ) stopifnot(is.character(attribute) || is.numeric(attribute)) #-- Get the varid as integer if necessary, handle global attributes --------# varid <- NULL globflag <- 0 if(is.character(variable) && variable != "NC_GLOBAL") varid <- try(var.inq.nc(ncfile, variable)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- Get the attribute name if necessary ------------------------------------# if(is.character(attribute)) attname <- attribute else attname <- try(att.inq.nc(ncfile, variable, attribute)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_delete_att", as.integer(ncfile), as.integer(varid), as.integer(globflag), as.character(attname), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # att.get.nc() # #-------------------------------------------------------------------------------# att.get.nc <- function(ncfile, variable, attribute) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable) ) stopifnot(is.character(attribute) || is.numeric(attribute)) #-- Get the varid as integer if necessary, handle global attributes --------# varid <- NULL globflag <- 0 if(is.character(variable) && variable != "NC_GLOBAL") varid <- try(var.inq.nc(ncfile, variable)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- Inquire the attribute to get its name and storage mode -----------------# attinfo <- try(att.inq.nc(ncfile, variable, attribute)) if(class(attinfo) == "try-error" || is.null(attinfo)) return(invisible(NULL)) ifelse(is.character(attribute), attname <- attribute, attname <- attinfo$name) ifelse(attinfo$type == "NC_CHAR", numflag <- 0, numflag <- 1); #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_get_att", as.integer(ncfile), as.integer(varid), as.character(attname), as.integer(numflag), as.integer(globflag), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { nc$status <- NULL nc$errmsg <- NULL return(nc$value) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # att.inq.nc() # #-------------------------------------------------------------------------------# att.inq.nc <- function(ncfile, variable, attribute) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable) ) stopifnot(is.character(attribute) || is.numeric(attribute)) #-- Look if handle attribute by name or ID ---------------------------------# attid <- -1 attname <- "" ifelse(is.character(attribute), nameflag <- 1, nameflag <- 0) ifelse(is.character(attribute), attname <- attribute, attid <- attribute) #-- Get the varid as integer if necessary, handle global attributes --------# varid <- NULL globflag <- 0 if(is.character(variable) && variable != "NC_GLOBAL") varid <- try(var.inq.nc(ncfile, variable)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_inq_att", as.integer(ncfile), as.integer(varid), as.character(attname), as.integer(attid), as.integer(nameflag), as.integer(globflag), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { nc$status <- NULL nc$errmsg <- NULL return(nc) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # att.put.nc() # #-------------------------------------------------------------------------------# att.put.nc <- function(ncfile, variable, name, type, value) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) stopifnot(is.character(name)) stopifnot(is.character(type)) stopifnot(is.character(value) || is.numeric(value)) #-- Get the varids as integer if necessary, handle global attributes -------# varid <- NULL globflag <- 0 if(is.character(variable) && variable != "NC_GLOBAL") varid <- try(var.inq.nc(ncfile, variable)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- Determine if attribute is numeric or character -------------------------# ifelse(is.numeric(value), numflag <- 1, numflag <- 0) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_put_att", as.integer(ncfile), as.integer(varid), as.character(name), as.character(type), as.integer(length(value)), as.integer(numflag), as.integer(globflag), value, PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # att.rename.nc() # #-------------------------------------------------------------------------------# att.rename.nc <- function(ncfile, variable, attribute, newname) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable) ) stopifnot(is.character(attribute) || is.numeric(attribute)) stopifnot(is.character(newname)) #-- Get the varid as integer if necessary, handle global attributes --------# varid <- NULL globflag <- 0 if(is.character(variable) && variable != "NC_GLOBAL") varid <- try(var.inq.nc(ncfile, variable)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- Get the attribute name if necessary ------------------------------------# if(is.character(attribute)) attname <- attribute else attname <- try(att.inq.nc(ncfile, variable, attribute)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_rename_att", as.integer(ncfile), as.integer(varid), as.integer(globflag), as.character(attname), as.character(newname), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # close.nc() # #-------------------------------------------------------------------------------# close.nc <- function(con, ...) { #-- Check args -------------------------------------------------------------# stopifnot(class(con) == "NetCDF") #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_close", as.integer(con), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # create.nc() # #-------------------------------------------------------------------------------# create.nc <- function(filename, clobber=TRUE, large=FALSE, share=FALSE, prefill=TRUE) { #-- Convert logical values to integers -------------------------------------# iclobber <- ifelse(clobber == TRUE, 1, 0) ## Overwrite existing file (y/n) ilarge <- ifelse(large == TRUE, 1, 0) ishare <- ifelse(share == TRUE, 1, 0) iprefill <- ifelse(prefill == TRUE, 1, 0) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_create", as.character(filename), as.integer(iclobber), as.integer(ilarge), as.integer(ishare), as.integer(iprefill), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { ncfile <- nc$ncid attr(ncfile, "class") <- "NetCDF" return(ncfile) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # dim.def.nc() # #-------------------------------------------------------------------------------# dim.def.nc <- function(ncfile, dimname, dimlength=1, unlim=FALSE) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(dimname)) stopifnot(is.numeric(dimlength)) stopifnot(is.logical(unlim)) #-- Handle UNLIMITED -------------------------------------------------------# unlimflag <- ifelse(unlim == TRUE, 1, 0) ncdimlength <- ifelse(unlim == TRUE, 0, dimlength) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_def_dim", as.integer(ncfile), as.character(dimname), as.integer(ncdimlength), as.integer(unlimflag), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # dim.inq.nc() # #-------------------------------------------------------------------------------# dim.inq.nc <- function(ncfile, dimension) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(dimension) || is.numeric(dimension)) #-- Look if handle dimension by name or ID ---------------------------------# dimid <- -1 dimname <- "" ifelse(is.character(dimension), nameflag <- 1, nameflag <- 0) ifelse(is.character(dimension), dimname <- dimension, dimid <- dimension) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_inq_dim", as.integer(ncfile), as.integer(dimid), as.character(dimname), as.integer(nameflag), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { nc$status <- NULL nc$errmsg <- NULL nc$unlim <- ifelse(nc$unlim == 1, TRUE, FALSE) return(nc) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # dim.rename.nc() # #-------------------------------------------------------------------------------# dim.rename.nc <- function(ncfile, dimension, newname) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(dimension) || is.numeric(dimension)) stopifnot(is.character(newname)) #-- Look if handle dimension by name or ID ---------------------------------# dimid <- -1 dimname <- "" ifelse(is.character(dimension), nameflag <- 1, nameflag <- 0) ifelse(is.character(dimension), dimname <- dimension, dimid <- dimension) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_rename_dim", as.integer(ncfile), as.integer(dimid), as.character(dimname), as.integer(nameflag), as.character(newname), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # file.inq.nc() # #-------------------------------------------------------------------------------# file.inq.nc <- function(ncfile) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_inq_file", as.integer(ncfile), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { nc$status <- NULL nc$errmsg <- NULL if(nc$unlimdimid == -1) nc$unlimdimid <- NA return(nc) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # open.nc() # #-------------------------------------------------------------------------------# open.nc <- function(con, write=FALSE, share=FALSE, prefill=TRUE, ...) { #-- Check args -------------------------------------------------------------# stopifnot(is.character(con)) stopifnot(is.logical(write)) stopifnot(is.logical(share)) stopifnot(is.logical(prefill)) #-- Open read only (y/n) ---------------------------------------------------# iwrite <- ifelse(write == TRUE, 1, 0) ishare <- ifelse(share == TRUE, 1, 0) iprefill <- ifelse(prefill == TRUE, 1, 0) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_open", as.character(con), as.integer(iwrite), as.integer(ishare), as.integer(iprefill), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { ncfile <- nc$ncid attr(ncfile, "class") <- "NetCDF" return(ncfile) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # print.nc() # #-------------------------------------------------------------------------------# print.nc <- function(x, ...) { #-- Check args -------------------------------------------------------------# stopifnot(class(x) == "NetCDF") #-- Inquire about the file -------------------------------------------------# fileinfo <- try(file.inq.nc(x)) if(class(fileinfo) == "try-error" || is.null(fileinfo)) return(invisible(NULL)) #-- Inquire about all dimensions -------------------------------------------# if(fileinfo$ndims != 0) { cat("dimensions:\n") for(i in 0:(fileinfo$ndims-1)) { diminfo <- dim.inq.nc(x, i) if(diminfo$unlim == FALSE) cat(" ", diminfo$name, " = ", diminfo$length, " ;\n", sep="") else cat(" ", diminfo$name, " = UNLIMITED ; // (", diminfo$length, " currently)\n", sep="") } } #-- Inquire about all variables --------------------------------------------# if(fileinfo$nvars != 0) { cat("variables:\n") for(i in 0:(fileinfo$nvars-1)) { varinfo <- var.inq.nc(x, i) vartype <- substring(tolower(varinfo$type), 4) cat(" ", vartype, " ", varinfo$name, sep="") if(varinfo$ndims > 0) { cat("(") for(j in 1:(varinfo$ndims-1)) if(j > 0 && varinfo$ndims > 1) cat(dim.inq.nc(x, varinfo$dimids[j])$name, ", ", sep="") cat(dim.inq.nc(x, varinfo$dimids[varinfo$ndims])$name, sep="") cat(")") } cat(" ;\n") #-- Inquire about variable attributes ------------------------------# if(varinfo$natts != 0) { for(j in 0:(varinfo$natts-1)) { attinfo <- att.inq.nc(x, i, j) cat(rep(" ", 16), varinfo$name, ":", attinfo$name, sep="") if(attinfo$type == "NC_CHAR") cat(" = \"", att.get.nc(x, i, j), "\" ;\n", sep="") else cat( " = ", att.get.nc(x, i, j), " ;\n", sep="") } } } } #-- Inquire about gobal attributes------------------------------------------# if(fileinfo$ngatts != 0) { cat("\n// global attributes:\n") i <- "NC_GLOBAL" for(j in 0:(fileinfo$ngatts-1)) { attinfo <- att.inq.nc(x, i, j) cat(rep(" ", 16), ":", attinfo$name, sep="") if(attinfo$type == "NC_CHAR") cat(" = \"", att.get.nc(x, i, j), "\" ;\n", sep="") else cat( " = ", att.get.nc(x, i, j), " ;\n", sep="") } } } #-------------------------------------------------------------------------------# # sync.nc() # #-------------------------------------------------------------------------------# sync.nc <- function(ncfile) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_sync", as.integer(ncfile), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.def.nc() # #-------------------------------------------------------------------------------# var.def.nc <- function(ncfile, varname, vartype, dimensions) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(varname)) stopifnot(is.character(vartype)) if(any(is.na(dimensions)) && length(dimensions) != 1) stop("NAs not allowed in dimensions unless defining a scalar variable", call.=FALSE) if(!any(is.na(dimensions))) stopifnot(mode(dimensions) == "character" || mode(dimensions) == "numeric") #-- Determine dimids from dimname if necessary, handle scalar variables ----# dimids <- vector() if(any(is.na(dimensions))) { dimids <- -1 ndims <- 0 } else { if(mode(dimensions) == "numeric") dimids <- dimensions else for(i in seq_along(dimensions)) try(dimids[i] <- dim.inq.nc(ncfile, dimensions[i])$id, silent=TRUE) if(length(dimids) != length(dimensions)) stop("Could not determine all dimension ids", call.=FALSE) dimids <- dimids[length(dimids):1] ## R to C convention ndims <- length(dimids) } #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_def_var", as.integer(ncfile), as.character(varname), as.character(vartype), as.integer(ndims), as.integer(dimids), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.get.nc() # #-------------------------------------------------------------------------------# var.get.nc <- function(ncfile, variable, start=NA, count=NA, na.mode=0, collapse=TRUE, unpack=FALSE) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) stopifnot(is.numeric(start) || is.logical(start)) stopifnot(is.numeric(count) || is.logical(count)) stopifnot(is.logical(collapse)) stopifnot(is.logical(unpack)) if(!any(na.mode == c(0,1,2,3))) stop("Wrong na.mode", call.=FALSE) #-- Inquire the variable ---------------------------------------------------# varinfo <- try(var.inq.nc(ncfile, variable)) if(class(varinfo) == "try-error" || is.null(varinfo)) return(invisible(NULL)) #-- Get the varid as integer if necessary ----------------------------------# ifelse(is.character(variable), varid <- varinfo$id, varid <- variable) #-- Get the variable dimensions if start and count contain NAs -------------# if(varinfo$ndims > 0) { r.start <- vector() r.count <- vector() for(i in 1:varinfo$ndims) { r.start[i] <- 1 r.count[i] <- dim.inq.nc(ncfile, varinfo$dimids[i])$length } if(any(is.na(start)) && length(start) == 1) start <- rep(NA, varinfo$ndims) if(any(is.na(count)) && length(count) == 1) count <- rep(NA, varinfo$ndims) start[is.na(start)] <- r.start[is.na(start)] count[is.na(count)] <- r.count[is.na(count)] } #-- Handle scalar variables ------------------------------------------------# if(varinfo$ndims == 0) { start[1] <- 1 count[1] <- 1 } #-- Allocate memory for variable and get number of dimensions --------------# varsize <- vector() varsize[1] <- prod(count) varsize[2] <- count[1] ## Needed for character data ndims <- varinfo$ndims #-- Switch from R to C convention ------------------------------------------# if(varinfo$ndims > 0) { c.start <- start[length(start):1] - 1 c.count <- count[length(count):1] } else { c.start <- 0 c.count <- 1 } #-- Check for correct number of dimensions in start and count --------------# if(varinfo$ndims > 0) if(length(c.start) != ndims || length(c.count) != ndims) stop("Length of start/count is not ndims", call.=FALSE) #-- C function calls -------------------------------------------------------# if(varinfo$type != "NC_CHAR") nc <- .Call("R_nc_get_vara_double", as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(varsize), PACKAGE="RNetCDF") else nc <- .Call("R_nc_get_vara_text", as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(varsize), PACKAGE="RNetCDF") #-- Adjust data ------------------------------------------------------------# if(nc$status == 0) { #-- Set dimensions, collapse degenerate dimensions ---------------------# if (collapse) { keep.dim <- (count > 1) } else { keep.dim <- rep(TRUE,ndims) } if ( varinfo$type == "NC_CHAR" && ndims > 0 ) { # First dimension of character array becomes string length keep.dim[1] <- FALSE } count.dim <- count[keep.dim] #-- Convert missing value to NA if defined in NetCDF file --------------# tolerance <- 1*10^-5 ## Allow rounding error na.flag <- 0 missval.flag <- 0 fillval.flag <- 0 fillval <- try(att.inq.nc(ncfile, varinfo$name, "_FillValue" ), silent=TRUE) missval <- try(att.inq.nc(ncfile, varinfo$name, "missing_value"), silent=TRUE) if(!(class(fillval) == "try-error")) if(!is.null(fillval)) fillval.flag <- 1 if(!(class(missval) == "try-error")) if(!is.null(missval)) missval.flag <- 1 if(na.mode == 0 && missval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "missing_value") na.flag <- 1 } if(na.mode == 0 && fillval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "_FillValue") na.flag <- 1 } if(na.mode == 1 && fillval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "_FillValue") na.flag <- 1 } if(na.mode == 2 && missval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "missing_value") na.flag <- 1 } if(na.flag == 1 && na.mode != 3 && varinfo$type != "NC_CHAR") nc$data[abs(nc$data-na.value) < tolerance] <- NA #-- Unpack variables if requested (missing values are preserved) -------# if(unpack) { offset <- try(att.inq.nc(ncfile, varinfo$name, "add_offset"), silent=TRUE) scale <- try(att.inq.nc(ncfile, varinfo$name, "scale_factor"), silent=TRUE) if((!inherits(offset, "try-error")) && (!inherits(scale, "try-error"))) { add_offset <- att.get.nc(ncfile, varinfo$name, "add_offset") scale_factor <- att.get.nc(ncfile, varinfo$name, "scale_factor") nc$data <- nc$data*scale_factor+add_offset } } #-- Return object if no error ----------------------------------------------# ifelse(length(count.dim) == 0, dim(nc$data) <- (1), dim(nc$data) <- count.dim) return(nc$data) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.inq.nc() # #-------------------------------------------------------------------------------# var.inq.nc <- function(ncfile, variable) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) #-- Look if handle variable by name or ID ----------------------------------# varid <- -1 varname <- "" ifelse(is.character(variable), nameflag <- 1, nameflag <- 0) ifelse(is.character(variable), varname <- variable, varid <- variable) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_inq_var", as.integer(ncfile), as.integer(varid), as.character(varname), as.integer(nameflag), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(nc$status == 0) { nc$status <- NULL nc$errmsg <- NULL if(nc$ndims > 0) nc$dimids <- nc$dimids[(nc$ndims):1] ## C to R convention else nc$dimids <- NA return(nc) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.put.nc() # #-------------------------------------------------------------------------------# var.put.nc <- function(ncfile, variable, data, start=NA, count=NA, na.mode=0, pack=FALSE) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) stopifnot(is.numeric(data) || is.character(data) || is.logical(data)) stopifnot(is.numeric(start) || is.logical(start)) stopifnot(is.numeric(count) || is.logical(count)) stopifnot(is.logical(pack)) if(!any(na.mode == c(0,1,2))) stop("Wrong na.mode", call.=FALSE) #-- Inquire the variable ---------------------------------------------------# varinfo <- try(var.inq.nc(ncfile, variable)) if(class(varinfo) == "try-error" || is.null(varinfo)) return(invisible(NULL)) ndims <- varinfo$ndims #-- Get the varid as integer if necessary ----------------------------------# ifelse(is.character(variable), varid <- varinfo$id, varid <- variable) #-- Get correct mode (numeric/character) if data contain only NAs ----------# if(is.logical(data)) { if(varinfo$type == "NC_CHAR") mode(data) <- "character" else mode(data) <- "numeric" } #-- Get the data dimensions if start and count contain NAs -----------------# if(varinfo$ndims == 0) { start[1] <- 1 count[1] <- 1 } if(any(is.na(start)) && length(start) > 1) stop("start contains NAs and length(start) not 1", call.=FALSE) if(any(is.na(count)) && length(count) > 1) stop("count contains NAs and length(count) not 1", call.=FALSE) if(any(is.na(start)) && varinfo$ndims > 0) start <- rep(1, ndims) if(any(is.na(count)) && varinfo$ndims > 0) { if(is.null(dim(data))) count <- length(data) else count <- dim(data) if(varinfo$type == "NC_CHAR") count <- c(max(nchar(data)), count) } #-- Switch from R to C convention ------------------------------------------# if(varinfo$ndims > 0) { c.start <- start[length(start):1] - 1 c.count <- count[length(count):1] } else { c.start <- 0 c.count <- 1 if(length(data) > 1) stop("Edge+start exceeds dimension bound", call.=FALSE) } #-- Check for correct number of dimensions in start and count --------------# if(varinfo$ndims > 0) if(length(c.start) != ndims || length(c.count) != ndims) stop("Length of start/count is not ndims", call.=FALSE) #-- Check if length of data and count match (numeric data) -----------------# if(is.numeric(data) && length(data) != prod(c.count)) stop("Mismatch in count and length(data)", call.=FALSE) #-- Checks and definitions for character data ------------------------------# if(is.character(data) && varinfo$ndims > 0) { lastdim <- varinfo$dimids[1] ## R to C convention maxstrlen <- dim.inq.nc(ncfile, lastdim)$length if(length(data) != prod(c.count[1:(ndims-1)])) ## already C convention stop("Mismatch in count and length(data)", call.=FALSE) if(max(nchar(data)) > maxstrlen) stop("max(nchar(data)) exceeding variable limits", call.=FALSE) } if(is.character(data)) { varsize <- vector() varsize[1] <- prod(count) varsize[2] <- count[1] } #-- Pack variables if requested (missing values are preserved) -------------# if(pack) { offset <- try(att.inq.nc(ncfile, varinfo$name, "add_offset"), silent=TRUE) scale <- try(att.inq.nc(ncfile, varinfo$name, "scale_factor"), silent=TRUE) if((!inherits(offset, "try-error")) && (!inherits(scale, "try-error"))) { add_offset <- att.get.nc(ncfile, varinfo$name, "add_offset") scale_factor <- att.get.nc(ncfile, varinfo$name, "scale_factor") data <- (data-add_offset)*(1/scale_factor) } } #-- Convert missing value to NA if defined in NetCDF file ------------------# if(is.numeric(data)) { if(any(is.na(data))) { na.flag <- 0 missval.flag <- 0 fillval.flag <- 0 fillval <- try(att.inq.nc(ncfile, varinfo$name, "_FillValue" ), silent=TRUE) missval <- try(att.inq.nc(ncfile, varinfo$name, "missing_value"), silent=TRUE) if(!(class(fillval) == "try-error")) if(!is.null(fillval)) fillval.flag <- 1 if(!(class(missval) == "try-error")) if(!is.null(missval)) missval.flag <- 1 if(na.mode == 0 && missval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "missing_value") na.flag <- 1 } if(na.mode == 0 && fillval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "_FillValue") na.flag <- 1 } if(na.mode == 1 && fillval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "_FillValue") na.flag <- 1 } if(na.mode == 2 && missval.flag == 1) { na.value <- att.get.nc(ncfile, varinfo$name, "missing_value") na.flag <- 1 } if(na.flag == 1) data[is.na(data)] <- na.value else stop("Found NAs but no missing value attribute", call.=FALSE) } } #-- C function calls -------------------------------------------------------# if(is.numeric(data)) nc <- .Call("R_nc_put_vara_double", as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.double(data), PACKAGE="RNetCDF") else nc <- .Call("R_nc_put_vara_text", as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.character(data), as.integer(varsize), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.rename.nc() # #-------------------------------------------------------------------------------# var.rename.nc <- function(ncfile, variable, newname) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) stopifnot(is.character(newname)) #-- Look if handle variable by name or ID ----------------------------------# varid <- -1 varname <- "" ifelse(is.character(variable), nameflag <- 1, nameflag <- 0) ifelse(is.character(variable), varname <- variable, varid <- variable) #-- C function call --------------------------------------------------------# nc <- .Call("R_nc_rename_var", as.integer(ncfile), as.integer(varid), as.character(varname), as.integer(nameflag), as.character(newname), PACKAGE="RNetCDF") if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # read.nc() # #-------------------------------------------------------------------------------# read.nc <- function(ncfile, unpack=TRUE) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.logical(unpack)) #-- Initialise storage -----------------------------------------------------# nvars <- file.inq.nc(ncfile)$nvars varnames <- character(nvars) retlist <- vector("list", nvars) #-- Read data from each variable -------------------------------------------# for(i in seq_len(nvars)) { retlist[[i]] <- var.get.nc(ncfile, i-1, unpack=unpack) varnames[i] <- var.inq.nc(ncfile, i-1)$name } #-- Set names of list elements ---------------------------------------------# names(retlist) <- varnames return(retlist) } #===============================================================================# # Udunits library functions # #===============================================================================# #-------------------------------------------------------------------------------# # utcal.nc() # #-------------------------------------------------------------------------------# utcal.nc <- function(unitstring, value, type="n") { #-- Check args -------------------------------------------------------------# stopifnot(is.character(unitstring)) stopifnot(is.numeric(value) && !any(is.na(value))) stopifnot(type == "n" || type =="s") count <- length(value) #-- C function call --------------------------------------------------------# ut <- .Call("R_ut_calendar", as.character(unitstring), as.integer(count), as.double(value), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(ut$status == 0) { if(type == "n") { colnames(ut$value) <- c("year", "month", "day", "hour", "minute", "second") return(ut$value) } else { x <- apply(ut$value, 1, function(x){paste(x[1],"-", sprintf("%02g",x[2]),"-",sprintf("%02g",x[3])," ", sprintf("%02g",x[4]),":",sprintf("%02g",x[5]),":", sprintf("%02g",x[6]),sep="")}) return(x) } } else stop(ut$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # utinit.nc() # #-------------------------------------------------------------------------------# utinit.nc <- function(path="") { ut <- .Call("R_ut_init", as.character(path), PACKAGE="RNetCDF") if(ut$status != 0) stop(ut$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # utinvcal.nc() # #-------------------------------------------------------------------------------# utinvcal.nc <- function(unitstring, value) { #-- Check args -------------------------------------------------------------# stopifnot(is.character(unitstring)) if(is.character(value)) { stopifnot(any(nchar(value) == 19)) value <- cbind(substr(value,1,4), substr(value,6,7), substr(value,9,10), substr(value,12,13), substr(value,15,16), substr(value,18,19)) value <- matrix(as.numeric(value),ncol=6) } stopifnot(is.numeric(value) && !any(is.na(value))) count <- length(value) if(is.vector(value) && count %% 6 != 0) stop("length(value) not divisible by 6", call.=FALSE) if(is.matrix(value) && ncol(value) != 6) stop("ncol(value) not 6", call.=FALSE) #-- C function call --------------------------------------------------------# ut <- .Call("R_ut_inv_calendar", as.character(unitstring), as.integer(count), as.double(value), PACKAGE="RNetCDF") #-- Return object if no error ----------------------------------------------# if(ut$status == 0) return(ut$value) else stop(ut$errmsg, call.=FALSE) } #===============================================================================# #===============================================================================# # SCRATCH # #===============================================================================#