RNetCDF/0000755000176200001440000000000013166521652011446 5ustar liggesusersRNetCDF/COPYING0000644000176200001440000004313112454177460012506 0ustar liggesusers GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. 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/inst/0000755000176200001440000000000013166006011012406 5ustar liggesusersRNetCDF/inst/udunits/0000755000176200001440000000000013166006011014101 5ustar liggesusersRNetCDF/inst/udunits/udunits2.xml0000644000176200001440000000100712461345204016405 0ustar liggesusers udunits2-prefixes.xml udunits2-base.xml udunits2-derived.xml udunits2-accepted.xml udunits2-common.xml RNetCDF/inst/udunits/udunits2-accepted.xml0000644000176200001440000001552412461345204020164 0ustar liggesusers 60 s minute min 60 min hour h hr 24 h day d 3.141592653589793238462643383279 pi π (pi/180) rad arc_degree ° angular_degree degree arcdeg °/60 arc_minute ' ′ angular_minute arcminute arcmin '/60 arc_second " ″ angular_second arcsecond arcsec dm^3 liter L litre l 1000 kg metric_ton t tonne 1.60217733e-19 J electronvolt eV electron_volt 1.6605402e-27 kg unified_atomic_mass_unit u atomic_mass_unit atomicmassunit amu 1.495979e11 m astronomical_unit ua 1852 m nautical_mile nautical_mile/hour international_knot knot_international knot 1e-10 m angstrom ångström Å Å dam^2 are a 100 are hectare 100 fm^2 barn b 1000 hPa bar cm/s^2 gal 3.7e10 Bq curie Ci 2.58e-4 C/kg roentgen R cSv rem RNetCDF/inst/udunits/udunits2-common.xml0000644000176200001440000015110112461345204017674 0ustar liggesusers s sec A amp K °K degree_kelvin degrees_kelvin degree_K degrees_K degreeK degreesK deg_K degs_K degK degsK cd candle mole einstein Hz baud Bd bps degree_Celsius ℃ celsius degree_C degrees_C degreeC degreesC deg_C degs_C degC degsC knot kt kts 6.02214179e23/mol avogadro_constant 0.01 percent % 1e-6 ppm ppmv 1e-9 ppb ppbv 1e-12 ppt pptv 1e-15 ppq ppqv 0.9 arc_degree grade 2 pi rad circle cycle turn revolution rotation arc_degree degree_north degrees_north degree_N degrees_N degreeN degreesN degree_east degrees_east degree_E degrees_E degreeE degreesE degree_true degrees_true degree_T degrees_T degreeT degreesT -1 degree_east degree_west degrees_west degree_W degrees_W degreeW degreesW 2.916667e-2 kg assay_ton 2.834952e-2 kg avoirdupois_ounce 4.5359237e-1 kg avoirdupois_pound pound lb 2e-4 kg carat 6.479891e-5 kg grain gr 5.080235e1 kg long_hundredweight 1.555174e-3 kg pennyweight 4.535924e1 kg short_hundredweight 14.59390 kg slug 3.110348e-2 kg troy_ounce apothecary_ounce 3.732417e-1 kg troy_pound apothecary_pound 20 grain scruple 60 grain apdram 480 grain apounce 5760 grain appound 94 pound bag 2000 pound short_ton ton 2240 pound long_ton 1e-15 m fermi 9.46073e15 m light_year 1e-6 m micron 2.54e-5 m mil 3.085678e16 m parsec 3.514598e-4 m printers_point 2.011684e1 m chain 12 printers_point printers_pica pica nautical_mile nmile (1200/3937) m US_survey_foot US_survey_feet 3 US_survey_feet US_survey_yard 5280 US_survey_feet US_survey_mile US_statute_mile 16.5 US_survey_feet rod pole perch 660 US_survey_feet furlong 6 US_survey_feet fathom 2.54 cm international_inch inch in 12 international_inches international_foot international_feet foot feet ft 3 international_feet international_yard yard yd 5280 international_feet international_mile mile mi inch/72 big_point inch/3 barleycorn 191.835 foot arpentlin rotation/second rotation_per_second rotations_per_second rps cps rotation/minute rpm 1.111111e-7 kg/m denier 1e-6 kg/m tex 5.72135e-11 kg/(Pa.s.m^2) perm_0C perms_0C 5.74525e-11 kg/(Pa.s.m^2) perm_23C perms_23C 5.067075e-10 m^2 circular_mil 9.869233e-13 m^2 darcy 160 rod^2 acre 1.233489e3 m^3 acre_foot acre_feet 2.359737e-3 m^3 board_foot board_feet 3.523907e-2 m^3 bushel bu bushel/4 peck pk 4.546090e-3 m^3 Canadian_liquid_gallon 4.404884e-3 m^3 US_dry_gallon cm^3 cc 1 m^3 stere 2.831685 m^3 register_ton US_dry_gallon/4 US_dry_quart dry_quart US_dry_gallon/8 US_dry_pint dry_pint 3.785412e-3 m^3 US_liquid_gallon liquid_gallon gallon 42 US_liquid_gallon barrel bbl barrel/4 firkin US_liquid_gallon/4 US_liquid_quart liquid_quart quart US_liquid_gallon/8 US_liquid_pint liquid_pint pint pt US_liquid_gallon/16 US_liquid_cup liquid_cup cup US_liquid_gallon/32 US_liquid_gill liquid_gill gill US_liquid_gallon/128 US_fluid_ounce US_liquid_ounce fluid_ounce liquid_ounce oz floz US_fluid_ounce/2 tablespoon Tbl Tbsp tbsp Tblsp tblsp US_fluid_ounce/8 fldr US_fluid_ounce/16 dram dr tablespoon/3 teaspoon tsp 4.546090e-3 m^3 UK_liquid_gallon UK_liquid_gallon/4 UK_liquid_quart UK_liquid_gallon/8 UK_liquid_pint UK_liquid_gallon/16 UK_liquid_cup UK_liquid_gallon/32 UK_liquid_gill UK_liquid_gallon/160 UK_fluid_ounce UK_liquid_ounce lg(re (1e-6 m)^3) BZ 1e-8 s shake 8.616409e4 s sidereal_day 3.590170e3 s sidereal_hour 5.983617e1 s sidereal_minute 0.9972696 s sidereal_second 3.155815e7 s sidereal_year 3.15569259747e7 s tropical_year year yr 29.530589 day lunar_month 365 day common_year 366 day leap_year 365.25 day Julian_year 365.2425 day Gregorian_year 27.321661 day sidereal_month 27.321582 day tropical_month 14 day fortnight 7 day week 0.01 s jiffy 1e9 year eon year/12 month 1e6 m^3/s sverdrup 9.806650 m/s^2 standard_free_fall standard_free_fall gravity gravity 1000 kg/m^3 conventional_water water H2O h2o gravity 999.972 kg/m^3 water_4C waters_4C water_39F waters_39F gravity 999.001 kg/m^3 water_60F waters_60F gravity 13595.10 kg/m^3 mercury_0C mercuries_0C mercury_32F mercuries_32F conventional_mercury conventional_mercuries Hg gravity 13556.8 kg/m^3 mercury_60F mercuries_60F standard_free_fall force 1e-5 N dyne 9.806650e-3 N pond 9.806650 N force_kilogram kilogram_force kilograms_force kgf 2.780139e-1 N force_ounce ounce_force ounces_force ozf 4.4482216152605 N force_pound pound_force pounds_force lbf 1.382550e-1 N poundal gram force gram_force grams_force force_gram gf 2000 force_pound force_ton ton_force tons_force 1000 lbf kip 1.01325e5 Pa standard_atmosphere atmosphere atm 1 kg gravity/cm2 technical_atmosphere at cm H2O cm_H2O cmH2O inch water_39F inch_H2O_39F inches_H2O_39F inch water_60F inch_H2O_60F inches_H2O_60F foot water foot_water feet_water foot_H2O feet_H2O footH2O feetH2O ftH2O fth2o cm Hg cm_Hg cmHg mm mercury_0C millimeter_Hg_0C millimeters_Hg_0C inch mercury_32F inch_Hg_32F inches_Hg_32F inch mercury_60F inch_Hg_60F inches_Hg_60F mm Hg millimeter_Hg millimeters_Hg torr mm_Hg mm_hg mmHg mmhg inch Hg inch_Hg inches_Hg in_Hg inHg 1 pound gravity/in^2 psi kip/in^2 ksi 0.1 N/m^2 barie barye lg(re 20e-6 Pa) B_SPL 1e-1 Pa.s poise 1e-4 m^2/s stokes St 10/(Pa.s) rhe 1e-7 J erg 1.05505585262e3 J IT_Btu IT_Btus Btu Btus 1.05506e8 J EC_therm 4.184000 J thermochemical_calorie 4.1868 J IT_calorie calorie cal 4.184 MJ/kg TNT 4.184e9 J ton_TNT tons_TNT 1.054804e8 J US_therm therm thm watt.hour watthour 1e9 eV bev V.A voltampere VA 9.80950e3 W boiler_horsepower 7.456999e2 W shaft_horsepower horsepower hp 7.35499e2 W metric_horsepower 7.460000e2 W electric_horsepower 7.46043e2 W water_horsepower 7.4570e2 W UK_horsepower 12000 Btu/hr refrigeration_ton ton_of_refrigeration tons_of_refrigeration lg(re 1 W) BW lg(re 1 mW) Bm 1.55e-1 K.m^2/W clo 10 A abampere 7.957747e-1 A gilbert 3.335640e-10 A statampere 10 A biot 1e9 F abfarad 1e-9 H abhenry 1e9 S abmho 1e-9 ohm abohm 1e-8 V abvolt 1.602176487e-19 C e 9.64957e4 C chemical_faraday 9.65219e4 C physical_faraday 9.648531e4 C C12_faraday faraday 1e-9 T gamma 1e-4 T gauss 1e-8 Wb maxwell 7.957747e1 A/m oersted Oe 3.335640e-10 C statcoulomb 1.112650e-12 F statfarad 8.987554e11 H stathenry 1.112650e-12 S statmho 8.987554e11 ohm statohm 2.997925e2 V statvolt 1.256637e-7 Wb unit_pole lg(re 1 V) BV lg(re 0.775 V) Bv lg(re 1e-6 V) BµV K/1.8 °R degree_rankine degrees_rankine degreeR degreesR degree_R degrees_R degR degsR deg_R degs_R °R @ 459.67 °F ℉ fahrenheit degree_fahrenheit degrees_fahrenheit degreeF degreesF degree_F degrees_F degF degsF deg_F degs_F 1.076391e-1 lx footcandle 3.426259 cd/m^2 footlambert (1e4/pi) cd/m^2 lambert 1e4 cd/m^2 stilb sb 1e4 lm/m^2 phot ph 1 cd/m^2 nit nt 4.184000e4 J/m^2 langley cd/(pi m^2) blondel apostilb 100/m kayser gravity geopotential dynamic gp 2056 hours work_year work_year/12 work_month 1e-6 m^2 s^-1 K kg^-1 potential_vorticity_unit PVU 1 count 1 bit 8 octet byte 446.2 micromoles/meter^2 dobson DU mol/6.02214129e23 molecule molec nucleon nuc RNetCDF/inst/udunits/udunits2-base.xml0000644000176200001440000000567412461345204017333 0ustar liggesusers meter m metre kilogram kg second s ampere A kelvin K mole mol candela cd RNetCDF/inst/udunits/udunits.dat0000644000176200001440000004054312461345204016303 0ustar liggesusers# $Id: udunits.dat,v 1.19 2009/09/17 16:23:50 steve Exp $ # # The first column is the unit name. The second column indicates whether or # not the unit name has a plural form (i.e. with an 's' appended). # A 'P' indicates that the unit has a plural form, whereas, a 'S' indicates # that the unit has a singular form only. The remainder of the line is the # definition for the unit. # # '#' is the to-end-of-line comment-character. # # NB: When adding to this table, be *very* careful to distinquish between # the letter 'O' and the numeral zero '0'. For example, the following two # entries don't do what one might otherwise expect: # # mercury_0C mercury_32F # millimeter_Hg_0C mm mercury_OC # # BASE UNITS. These must be first and are identified by a nil definition. # ampere P # electric current count P # dimensionless decimal number candela P # luminous intensity kelvin P # thermodynamic temperature kilogram P # mass meter P # length mole P # amount of substance second P # time radian P # plane angle # # CONSTANTS # percent S 0.01 PI S 3.14159265358979323846 bakersdozen S 13 pair P 2 ten P 10 dozen S 12 score S 20 hundred P 100 thousand P 1.0e3 million P 1.0e6 % S percent pi S PI # # NB: All subsequent definitions must be given in terms of # earlier definitions. Forward referencing is not permitted. # # # The following are non-base units of the fundamental quantities # bit P count # unit of information # # UNITS OF ELECTRIC CURRENT # A S ampere amp P ampere abampere P 10 ampere # exact gilbert P 7.957747e-1 ampere statampere P 3.335640e-10 ampere biot P 10 ampere # # UNITS OF LUMINOUS INTENSITY # cd S candela candle P candela # # UNITS OF THERMODYNAMIC TEMPERATURE # degree_Kelvin P kelvin degree_Celsius S kelvin @ 273.15 degree_Rankine P kelvin/1.8 degree_Fahrenheit P degree_Rankine @ 459.67 #C S degree_Celsius # `C' means `coulomb' Celsius S degree_Celsius celsius S degree_Celsius degree_centigrade S degree_Celsius # approx. was just `centigrade' degC S degree_Celsius degreeC S degree_Celsius degree_C S degree_Celsius degree_c S degree_Celsius deg_C S degree_Celsius deg_c S degree_Celsius degK S kelvin degreeK S kelvin degree_K S kelvin degree_k S kelvin deg_K S kelvin deg_k S kelvin K S kelvin Kelvin P kelvin degF S degree_Fahrenheit degreeF S degree_Fahrenheit degree_F S degree_Fahrenheit degree_f S degree_Fahrenheit deg_F S degree_Fahrenheit deg_f S degree_Fahrenheit F S degree_Fahrenheit Fahrenheit P degree_Fahrenheit fahrenheit P degree_Fahrenheit degR S degree_Rankine degreeR S degree_Rankine degree_R S degree_Rankine degree_r S degree_Rankine deg_R S degree_Rankine deg_r S degree_Rankine #R S degree_Rankine # `R' means `roentgen' Rankine P degree_Rankine rankine P degree_Rankine # # UNITS OF MASS # assay_ton P 2.916667e-2 kilogram # was 2.916667e2 (typo!) avoirdupois_ounce P 2.834952e-2 kilogram avoirdupois_pound P 4.5359237e-1 kilogram # exact carat P 2e-4 kilogram grain P 6.479891e-5 kilogram # exact gram P 1e-3 kilogram # exact g S gram kg S kilogram long_hundredweight P 5.080235e1 kilogram metric_ton P 1e3 kilogram # exact pennyweight P 1.555174e-3 kilogram short_hundredweight P 4.535924e1 kilogram slug P 14.59390 kilogram troy_ounce P 3.110348e-2 kilogram troy_pound P 3.732417e-1 kilogram atomic_mass_unit P 1.66054e-27 kilogram # was 1.66044e-27 tonne P metric_ton apothecary_ounce P troy_ounce apothecary_pound P troy_pound pound P avoirdupois_pound metricton P metric_ton gr S grain scruple P 20 grain apdram P 60 grain apounce P 480 grain appound P 5760 grain atomicmassunit P atomic_mass_unit amu P atomic_mass_unit t S tonne lb P pound bag P 94 pound short_ton P 2000 pound long_ton P 2240 pound ton P short_ton shortton P short_ton longton P long_ton # # UNITS OF LENGTH # angstrom P decinanometer astronomical_unit P 1.495979e11 meter fermi P 1e-15 meter # exact m S meter metre P meter light_year P 9.46073e15 meter # was ASTM's 9.46055e15 meter micron P 1e-6 meter # exact mil P 2.54e-5 meter # exact nautical_mile P 1.852000e3 meter # exact parsec P 3.085678e16 meter printers_point P 3.514598e-4 meter # God help us! There's an international foot and a US survey foot and # they're not the same! # US Survey foot stuff: US_survey_foot S (1200/3937) meter # exact US_survey_feet S US_survey_foot # alias US_survey_yard P 3 US_survey_feet # exact US_survey_mile P 5280 US_survey_feet # exact US_statute_mile P US_survey_mile # alias rod P 16.5 US_survey_feet # exact pole P rod # alias perch S rod # alias perches S perch # alias furlong P 660 US_survey_feet # exact fathom P 6 US_survey_feet # exact # International foot stuff: international_inch S 2.54 cm # exact international_inches S international_inch # alias international_foot S 12 international_inches # exact international_feet S international_foot # alias international_yard P 3 international_feet # exact international_mile P 5280 international_feet # exact # Alias unspecified units to the international units: inch S international_inch # alias foot S international_foot # alias yard P international_yard # alias mile P international_mile # alias # The following should hold regardless: inches S inch # alias in S inches # alias feet S foot # alias ft S feet # alias yd S yard # alias mi S mile # alias chain P 2.011684e1 meter printers_pica P 12 printers_point # exact astronomicalunit P astronomical_unit au S astronomical_unit nmile P nautical_mile nmi S nautical_mile pica P printers_pica big_point P inch/72 # exact barleycorn P inch/3 arpentlin P 191.835 foot # # UNITS OF AMOUNT OF SUBSTANCE # mol S mole # # UNITS OF TIME # day P 8.64e4 second # exact hour P 3.6e3 second # exact minute P 60 second # exact s S second sec P second shake P 1e-8 second # exact sidereal_day P 8.616409e4 second sidereal_hour P 3.590170e3 second sidereal_minute P 5.983617e1 second sidereal_second P 0.9972696 second sidereal_year P 3.155815e7 second # Interval between 2 successive passages of sun through vernal equinox # (365.242198781 days -- see # http://www.ast.cam.ac.uk/pubinfo/leaflets/, # http://aa.usno.navy.mil/AA/ # and http://adswww.colorado.edu/adswww/astro_coord.html): tropical_year P 3.15569259747e7 second lunar_month P 29.530589 day common_year P 365 day # exact: 3.153600e7 seconds leap_year P 366 day # exact Julian_year P 365.25 day # exact Gregorian_year P 365.2425 day # exact sidereal_month P 27.321661 day tropical_month P 27.321582 day d S day min P minute hr P hour h S hour fortnight P 14 day # exact week P 7 day # exact jiffy S 0.01 second # believe it or not! jiffies S jiffy # assumed plural spelling year P tropical_year yr P year a S year # "anno" eon P 1e9 year # fuzzy month P year/12 # on average # # UNITS OF PLANE ANGLE # #rad P radian # `rad' means `1e-2 gray' circle P 2 pi radian angular_degree P (pi/180) radian turn P circle degree P angular_degree degree_north S angular_degree degree_east S angular_degree degree_true S angular_degree arcdeg P angular_degree angular_minute P angular_degree/60 angular_second P angular_minute/60 grade P 0.9 angular_degree # exact degrees_north S degree_north degreeN S degree_north degree_N S degree_north degreesN S degree_north degrees_N S degree_north degrees_east S degree_east degreeE S degree_east degree_E S degree_east degreesE S degree_east degrees_E S degree_east degree_west S -1 degree_east degrees_west S degree_west degreeW S degree_west degree_W S degree_west degreesW S degree_west degrees_W S degree_west degrees_true S degree_true degreeT S degree_true degree_T S degree_true degreesT S degree_true degrees_T S degree_true arcminute P angular_minute arcsecond P angular_second arcmin P arcminute arcsec P arcsecond # # The following are derived units with special names. They are useful for # defining other derived units. # steradian P radian2 hertz S 1/second newton P kilogram.meter/second2 coulomb P ampere.second lumen P candela steradian becquerel P 1/second # SI unit of activity of a # # radionuclide standard_free_fall S 9.806650 meter/second2 # exact pascal P newton/meter2 joule P newton.meter Hz S hertz sr S steradian force S standard_free_fall gravity S standard_free_fall free_fall S standard_free_fall lux S lumen/meter2 sphere P 4 pi steradian luxes S lux watt P joule/second gray P joule/kilogram # absorbed dose. derived unit sievert P joule/kilogram # dose equivalent. derived unit conventional_mercury S gravity 13595.10 kg/m3 mercury_0C S gravity 13595.1 kg/m3 # was 13595.065 mercury_60F S gravity 13556.8 kg/m3 # was 13556.806 conventional_water S gravity 1000 kg/m3 # exact water_4C S gravity 999.972 kg/m3 # was 999.97226 water_60F S gravity 999.001 kg/m3 # was 999.00072 volt P watt/ampere mercury_32F S mercury_0C water_39F S water_4C # actually 39.2 F mercury S conventional_mercury # was mercury_32F water S conventional_water # was water_4C farad P coulomb/volt ohm P volt/ampere siemens S ampere/volt weber P volt.second Hg S mercury hg S mercury H2O S water h2o S water tesla P weber/meter2 henry P weber/ampere # # The following are compound units: units whose definitions consist # of two or more base units. They may now be defined in terms of the # preceding units. # # # ACCELERATION # gal P 1e-2 meter/second2 # exact # # Area # are P 1e2 m2 # exact barn P 1e-28 m2 # exact circular_mil P 5.067075e-10 m2 darcy P 9.869233e-13 m2 # permeability of porous solids hectare P 1e4 m2 # exact acre P 160 rod2 # exact b S barn # # ELECTRICITY AND MAGNETISM # abfarad P 1e9 farad # exact abhenry P 1e-9 henry # exact abmho P 1e9 siemens # exact abohm P 1e-9 ohm # exact abvolt P 1e-8 volt # exact C S coulomb e S 1.60217733-19 coulomb # was 1.6021917e-19 chemical_faraday P 9.64957e4 coulomb physical_faraday P 9.65219e4 coulomb C12_faraday P 9.648531e4 coulomb gamma P 1e-9 tesla # exact gauss S 1e-4 tesla # exact H S henry maxwell P 1e-8 weber # exact oersted P 7.957747e1 ampere/meter S S siemens statcoulomb P 3.335640e-10 coulomb statfarad P 1.112650e-12 farad stathenry P 8.987554e11 henry statmho P 1.112650e-12 siemens statohm P 8.987554e11 ohm statvolt P 2.997925e2 volt T S tesla unit_pole P 1.256637e-7 weber V S volt Wb S weber mho P siemens Oe S oersted faraday P C12_faraday # charge of 1 mole of # # electrons # # ENERGY (INCLUDES WORK) # electronvolt P 1.602177e-19 joule erg P 1e-7 joule # exact IT_Btu P 1.05505585262e3 joule # exact, was 1.055056e3 EC_therm P 1.05506e8 joule # exact thermochemical_calorie P 4.184000 joule # exact IT_calorie P 4.1868 joule # exact J S joule ton_TNT S 4.184e9 joule US_therm P 1.054804e8 joule # exact watthour P watt hour therm P US_therm Wh S watthour Btu P IT_Btu calorie P IT_calorie electron_volt P electronvolt thm S therm cal S calorie eV S electronvolt bev S gigaelectron_volt # # FORCE # dyne P 1e-5 newton # exact pond P 9.806650e-3 newton # exact, was 1.806650e-3 (typo) force_kilogram S 9.806650 newton # exact force_ounce S 2.780139e-1 newton force_pound S 4.4482216152605 newton# exact poundal P 1.382550e-1 newton N S newton gf S gram force force_gram P 1e-3 force_kilogram force_ton P 2000 force_pound # exact lbf S force_pound ounce_force S force_ounce kilogram_force S force_kilogram pound_force S force_pound ozf S force_ounce kgf S force_kilogram kip P 1000 lbf ton_force S force_ton gram_force S force_gram # # HEAT # clo P 1.55e-1 kelvin.meter2/watt # # LIGHT # lm S lumen lx S lux footcandle P 1.076391e-1 lux footlambert P 3.426259 candela/meter2 lambert P (1e4/PI) candela/meter2 # exact stilb P 1e4 candela/meter2 # exact phot P 1e4 lumen/meter2 # exact nit P 1 candela/meter2 # exact langley P 4.184000e4 joule/meter2 # exact blondel P candela/(pi meter2) apostilb P blondel nt S nit ph S phot sb S stilb # # MASS PER UNIT LENGTH # denier P 1.111111e-7 kilogram/meter tex P 1e-6 kilogram/meter # exact # # MASS PER UNIT TIME (INCLUDES FLOW) # perm_0C S 5.72135e-11 kg/(pascal second meter2) perm_23C S 5.74525e-11 kg/(pascal second meter2) # # POWER # voltampere P volt ampere VA S volt ampere boiler_horsepower P 9.80950e3 watt shaft_horsepower P 7.456999e2 watt metric_horsepower P 7.35499e2 watt electric_horsepower P 7.460000e2 watt # exact W S watt water_horsepower P 7.46043e2 watt UK_horsepower P 7.4570e2 watt refrigeration_ton P 12000 Btu/hour horsepower P shaft_horsepower ton_of_refrigeration P refrigeration_ton hp S horsepower # # PRESSURE OR STRESS # bar P 1e5 pascal # exact standard_atmosphere P 1.01325e5 pascal # exact technical_atmosphere P 1 kg gravity/cm2 # exact inch_H2O_39F S inch water_39F inch_H2O_60F S inch water_60F inch_Hg_32F S inch mercury_32F inch_Hg_60F S inch mercury_60F millimeter_Hg_0C S mm mercury_0C footH2O S foot water cmHg S cm Hg cmH2O S cm water Pa S pascal inch_Hg S inch Hg inch_hg S inch Hg inHg S inch Hg in_Hg S inch Hg in_hg S inch Hg millimeter_Hg S mm Hg mmHg S mm Hg mm_Hg S mm Hg mm_hg S mm Hg torr P mm Hg foot_H2O S foot water ftH2O S foot water psi S 1 pound gravity/in2 ksi S kip/in2 barie P 0.1 newton/meter2 at S technical_atmosphere atmosphere P standard_atmosphere atm P standard_atmosphere barye P barie # # RADIATION UNITS # Bq S becquerel curie P 3.7e10 becquerel # exact rem P 1e-2 sievert # dose equivalent. exact rad P 1e-2 gray # absorbed dose. exact roentgen P 2.58e-4 coulomb/kg # exact Sv S sievert Gy S gray Ci S curie R S roentgen rd S rad # # VELOCITY (INCLUDES SPEED) # c S 2.997925e+8 meter/sec knot P nautical_mile/hour knot_international S knot international_knot S knot kt P knot # # VISCOSITY # poise S 1e-1 pascal second # absolute viscosity. # # exact stokes S 1e-4 meter2/second # exact rhe S 10/(pascal second) # exact St S stokes # # VOLUME (INCLUDES CAPACITY) # acre_foot S 1.233489e3 m3 # but `acre foot' is 1233.4867714897 meters^3. Odd. board_foot S 2.359737e-3 m3 bushel P 3.523907e-2 m3 UK_liquid_gallon P 4.546090e-3 m3 # exact. was 4.546092e-3 Canadian_liquid_gallon P 4.546090e-3 m3 # exact US_dry_gallon P 4.404884e-3 m3 US_liquid_gallon P 3.785412e-3 m3 cc S cm3 liter P 1e-3 m3 # exact. However, from 1901 to # # 1964, 1 liter = 1.000028 dm3 stere P 1 m3 # exact register_ton P 2.831685 m3 # was 3.831685 (typo!) US_dry_quart P US_dry_gallon/4 US_dry_pint P US_dry_gallon/8 US_liquid_quart P US_liquid_gallon/4 US_liquid_pint P US_liquid_gallon/8 US_liquid_cup P US_liquid_gallon/16 US_liquid_gill P US_liquid_gallon/32 US_fluid_ounce P US_liquid_gallon/128 US_liquid_ounce P US_fluid_ounce UK_liquid_quart P UK_liquid_gallon/4 UK_liquid_pint P UK_liquid_gallon/8 UK_liquid_cup P UK_liquid_gallon/16 UK_liquid_gill P UK_liquid_gallon/32 UK_fluid_ounce P UK_liquid_gallon/160 UK_liquid_ounce P UK_fluid_ounce liquid_gallon P US_liquid_gallon fluid_ounce P US_fluid_ounce #liquid_gallon P UK_liquid_gallon #fluid_ounce P UK_fluid_ounce dry_quart P US_dry_quart dry_pint P US_dry_pint liquid_quart P liquid_gallon/4 liquid_pint P liquid_gallon/8 gallon P liquid_gallon barrel P 42 US_liquid_gallon # petroleum industry definition quart P liquid_quart pint P liquid_pint cup P liquid_gallon/16 gill P liquid_gallon/32 tablespoon P US_fluid_ounce/2 teaspoon P tablespoon/3 peck P bushel/4 oz P fluid_ounce floz S fluid_ounce acre_feet S acre_foot board_feet S board_foot Tbl P tablespoon Tbsp S tablespoon tbsp S tablespoon Tblsp S tablespoon tblsp S tablespoon litre P liter L S liter l S liter tsp S teaspoon pk S peck bu S bushel fldr S floz/8 dram P floz/16 bbl S barrel firkin P barrel/4 # exact but barrel is vague pt S pint dr S dram # # COMPUTERS AND COMMUNICATION # baud S 1/second # exact bps S bit/second cps S hertz Bd S baud # # MISC # kayser P 1e2/meter # exact rps S hertz rpm S hertz/60 geopotential S gravity work_year P 2056 hours work_month P work_year/12 gp S geopotential dynamic S geopotential RNetCDF/inst/udunits/udunits2-prefixes.xml0000644000176200001440000000440612461345204020236 0ustar liggesusers 1e24 yotta Y 1e21 zetta Z 1e18 exa E 1e15 peta P 1e12 tera T 1e9 giga G 1e6 mega M 1e3 kilo k 100 hecto h 10 deka da .1 deci d .01 centi c 1e-3 milli m 1e-6 micro µ μ u 1e-9 nano n 1e-12 pico p 1e-15 femto f 1e-18 atto a 1e-21 zepto z 1e-24 yocto y RNetCDF/inst/udunits/udunits2-derived.xml0000644000176200001440000000751512461345204020037 0ustar liggesusers radian rad rad^2 steradian sr 1/s hertz Hz 1e-3 kg gram g m.kg/s^2 newton N N/m^2 pascal Pa N.m joule J J/s watt W s.A coulomb C W/A volt V C/V farad F V/A ohm Ω Ω A/V siemens S V.s weber Wb Wb/m^2 tesla T Wb/A henry H K @ 273.15 degree_Celsius degrees_Celsius °C cd.sr lumen lm lm/m^2 lux lx mol/s katal kat 1/s becquerel Bq J/kg gray Gy J/kg sievert Sv RNetCDF/configure.ac0000644000176200001440000001025413162431020013717 0ustar liggesusers#-------------------------------------------------------------------------------# # Initialize # #-------------------------------------------------------------------------------# AC_INIT([RNetCDF], [1.9-1]) #-------------------------------------------------------------------------------# # 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` R_CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS` CPPFLAGS="$CPPFLAGS $R_CPPFLAGS" #-------------------------------------------------------------------------------# # Find NetCDF library and header files # #-------------------------------------------------------------------------------# AC_ARG_WITH([nc-config], AS_HELP_STRING([--without-nc-config], [do not use nc-config to get netcdf configuration]), [], [with_nc_config=yes]) AS_IF([test "x$with_nc_config" != xno], [AC_CHECK_PROG(have_nc_config, nc-config, yes, no, [], [])] ) AS_IF([test "x$have_nc_config" == xyes], [ # Find libraries and cflags used to build netcdf: AC_MSG_CHECKING(netcdf linker flags) NETCDF_LIBS=`nc-config --libs` AC_MSG_RESULT($NETCDF_LIBS) LDFLAGS="$NETCDF_LIBS $LDFLAGS" AC_MSG_CHECKING(netcdf pre-processor and compiler flags) NETCDF_CFLAGS=`nc-config --cflags` AC_MSG_RESULT($NETCDF_CFLAGS) CPPFLAGS="$NETCDF_CFLAGS $CPPFLAGS" ], [ # Check that netcdf header files can be compiled: AC_CHECK_HEADERS(netcdf.h, [], AC_MSG_ERROR("netcdf.h was not compiled - defining CPPFLAGS may help")) # Add netcdf library to LIBS if it can be linked (and is not already being linked): AC_SEARCH_LIBS(nc_open, netcdf, [], AC_MSG_ERROR("netcdf library was not linked - defining LDFLAGS may help")) ] ) #-------------------------------------------------------------------------------# # Find UDUNITS library and header files # #-------------------------------------------------------------------------------# # If the expat library is available, prepend it to LIBS # so that udunits2 can be linked if it is installed. # If udunits2 contains its own expat functions, # these will be used in preference to the external library. AC_SEARCH_LIBS(XML_StopParser, expat) # Identify available version of udunits library (1 or 2), # and prepend the library to LIBS if it is not already linked. # Also check for udunits.h in places that depend on the udunits version, # and define macro HAVE_UDUNITS_H or HAVE_UDUNITS2_UDUNITS_H accordingly. udunits=0 AC_SEARCH_LIBS(utFree, udunits2, [ AC_CHECK_HEADERS(udunits2/udunits.h udunits.h, [udunits=2; break]) ], [ AC_SEARCH_LIBS(utScan, udunits, [ AC_CHECK_HEADERS(udunits.h, [udunits=1; break]) ] ) ] ) # Define variables UDUNITS_LIB, UDUNITS_DBFILE and UDUNITS_DBVAR, # based on the version of udunits detected above. # Also define preprocessor macro HAVE_LIBUDUNITS or HAVE_LIBUDUNITS2. AS_IF([test $udunits == 2], [ UDUNITS_LIB=udunits2 UDUNITS_DBFILE=udunits2.xml UDUNITS_DBVAR="UDUNITS2_XML_PATH" AC_DEFINE(HAVE_LIBUDUNITS2) ], [test $udunits == 1], [ UDUNITS_LIB=udunits UDUNITS_DBFILE=udunits.dat UDUNITS_DBVAR="UDUNITS_PATH" AC_DEFINE(HAVE_LIBUDUNITS) ], [AC_MSG_ERROR("unable to use udunits2 or udunits")] ) #-------------------------------------------------------------------------------# # Do substitution # #-------------------------------------------------------------------------------# AC_SUBST(UDUNITS_LIB) AC_SUBST(UDUNITS_DBFILE) AC_SUBST(UDUNITS_DBVAR) AC_OUTPUT(R/load.R src/Makevars) #-------------------------------------------------------------------------------# # Done # #-------------------------------------------------------------------------------# RNetCDF/tests/0000755000176200001440000000000013166006010012572 5ustar liggesusersRNetCDF/tests/RNetCDF-test.R0000644000176200001440000002537613166002735015106 0ustar liggesusers#===============================================================================# # # # Name: RNetCDF-test.R # # # # Version: 1.9-1 # # # # Purpose: Test functions to the NetCDF interface for R. # # # # Author: Pavel Michna (michna@users.r-forge.r-project.org) # # Milton Woods (mwoods@users.r-forge.r-project.org) # # # # Copyright: (C) 2010-2017 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 # # mw 02/09/14 Test 1D character arrays and character scalars # # mw 05/09/14 Test reading/writing NC_CHAR as raw bytes # # mw 26/01/16 Test utcal.nc and utinvcal.nc with POSIXct type # # # #===============================================================================# #===============================================================================# # Load library # #===============================================================================# library(RNetCDF) #===============================================================================# # Run tests # #===============================================================================# #-------------------------------------------------------------------------------# # NetCDF library functions # #-------------------------------------------------------------------------------# #--Initialize ------------------------------------------------------------------# cat("Starting NetCDF tests...\n") testfun <- function(x,y,tally=NULL) { if (is.null(tally)) { tally <- c(pass=0,fail=0) } # Compare numeric values with single precision tolerance: if (isTRUE(all.equal(x,y,tolerance=2^(-23)))) { cat("OK\n") return(tally+c(1,0)) } else { cat("failed\n") return(tally+c(0,1)) } } ## Create a new NetCDF dataset and define dimensions nc <- create.nc("foo.nc") nstation <- 5 ntime <- 2 nstring <- 32 nempty <- 0 dim.def.nc(nc, "station", nstation) dim.def.nc(nc, "time", ntime) dim.def.nc(nc, "max_string_length", nstring) dim.def.nc(nc, "empty", unlim=TRUE) ## Define variables 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")) var.def.nc(nc, "qcflag", "NC_CHAR", c("station")) var.def.nc(nc, "int0", "NC_INT", NA) var.def.nc(nc, "char0", "NC_CHAR", NA) var.def.nc(nc, "numempty", "NC_FLOAT", c("station","empty")) ## 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 <- matrix(c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9),ncol=ntime) mypackvar <- seq_len(5)*10-5 myname <- c("alfa", "bravo", "charlie", "delta", "echo") myqcflag <- "ABCDE" myint0 <- 12345 mychar0 <- "?" ## Put the data var.put.nc(nc, "time", mytime) var.put.nc(nc, "temperature", mytemperature, c(NA,1), c(NA,ntime)) var.put.nc(nc, "packvar", mypackvar, pack=TRUE) var.put.nc(nc, "name", myname, c(1,1), c(nstring,NA)) var.put.nc(nc, "qcflag", charToRaw(myqcflag)) var.put.nc(nc, "int0", myint0) var.put.nc(nc, "char0", mychar0) sync.nc(nc) ## Read tests cat("Read numeric vector ... ") x <- mytime dim(x) <- length(x) y <- var.get.nc(nc, 0) tally <- testfun(x,y) cat("Read numeric matrix ... ") x <- mytemperature y <- var.get.nc(nc, "temperature") tally <- testfun(x,y,tally) cat("Read numeric matrix slice ... ") x <- mytemperature[,2] dim(x) <- length(x) y <- var.get.nc(nc, "temperature", c(NA,2), c(NA,1)) tally <- testfun(x,y,tally) cat("Read numeric matrix empty slice ... ") x <- numeric(0) dim(x) <- c(0,1) y <- var.get.nc(nc, "temperature", c(NA,2), c(0,1),collapse=FALSE) tally <- testfun(x,y,tally) cat("Read numeric scalar ... ") x <- myint0 dim(x) <- 1 y <- var.get.nc(nc, "int0") tally <- testfun(x,y,tally) cat("Read numeric empty array ... ") x <- numeric(0) dim(x) <- c(nstation,nempty) y <- var.get.nc(nc, "numempty") tally <- testfun(x,y,tally) cat("Read 2D char array ... ") x <- myname dim(x) <- length(x) y <- var.get.nc(nc, "name") tally <- testfun(x,y,tally) cat("Read 2D char slice ... ") x <- substring(myname[2:3],1,4) dim(x) <- length(x) y <- var.get.nc(nc, "name", c(1,2), c(4,2)) tally <- testfun(x,y,tally) cat("Read 2D char slice as raw bytes ... ") x <- substring(myname[2:3],1,4) dim(x) <- length(x) x <- apply(x,MARGIN=1,FUN=charToRaw) y <- var.get.nc(nc, "name", c(1,2), c(4,2), rawchar=TRUE) tally <- testfun(x,y,tally) cat("Read 2D char slice as characters ... ") x <- myname[2:3] dim(x) <- length(x) y <- var.get.nc(nc, "name", c(1,2), c(NA,2)) tally <- testfun(x,y,tally) cat("Read empty 2D char array ... ") x <- character(0) dim(x) <- 0 y <- var.get.nc(nc, "name", NA, c(0,0),collapse=FALSE) tally <- testfun(x,y,tally) cat("Read 1D char slice ... ") x <- substring(myqcflag,2,3) dim(x) <- 1 y <- var.get.nc(nc, "qcflag", c(2), c(2)) tally <- testfun(x,y,tally) cat("Read scalar char ... ") x <- mychar0 dim(x) <- 1 y <- var.get.nc(nc, "char0") tally <- testfun(x,y,tally) cat("Read and unpack numeric array ... ") x <- mypackvar dim(x) <- length(x) y <- var.get.nc(nc, "packvar", unpack=TRUE) tally <- testfun(x,y,tally) #-- Close file -----------------------------------------------------------------# close.nc(nc) #-------------------------------------------------------------------------------# # UDUNITS calendar functions # #-------------------------------------------------------------------------------# cat("utcal.nc - numeric values ...") 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) colnames(x) <- c("year","month","day","hour","minute","second") y <- utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5)) tally <- testfun(x,y,tally) cat("utcal.nc - string values ...") 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") tally <- testfun(x,y,tally) cat("utcal.nc - POSIXct values ...") x <- ISOdatetime(c(1899,1900,1900,1900,1900,1900), c( 12, 1, 1, 1, 1, 1), c( 31, 1, 1, 1, 1, 1), c( 23, 0, 1, 2, 3, 4), c( 0, 0, 0, 0, 0, 0), c( 0, 0, 0, 0, 0, 0), tz="UTC") y <- utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5), type="c") tally <- testfun(x,y,tally) cat("utinvcal.nc - numeric values ...") x <- 6.416667 y <- utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(1900,1,1,5,25,0)) tally <- testfun(x,y,tally) cat("utinvcal.nc - string values ...") x <- 6.416667 y <- utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", "1900-01-01 05:25:00") tally <- testfun(x,y,tally) cat("utinvcal.nc - POSIXct values ...") x <- 6.416667 y <- utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", ISOdatetime(1900,1,1,5,25,0,tz="UTC")) tally <- testfun(x,y,tally) #-------------------------------------------------------------------------------# # Overall summary # #-------------------------------------------------------------------------------# cat("Summary:", tally["pass"], "pass /", tally["fail"], "fail. ") if (tally["fail"]==0) { cat("Package seems to work properly.\n") } else { cat("Some problems were detected.\n") } #===============================================================================# #===============================================================================# # SCRATCH # #===============================================================================# RNetCDF/src/0000755000176200001440000000000013166006010012217 5ustar liggesusersRNetCDF/src/RNetCDF.c0000644000176200001440000022125013166006066013565 0ustar liggesusers/*=============================================================================*\ * * * Name: RNetCDF.c * * * * Version: 1.9-1 * * * * Purpose: NetCDF interface for R. * * * * Author: Pavel Michna (michna@users.r-forge.r-project.org) * * Milton Woods (mwoods@users.r-forge.r-project.org) * * * * Copyright: (C) 2004-2017 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) * * mw 05/09/14 Support reading and writing raw character arrays, * * avoid temporary arrays when reading/writing variables * * mw 08/09/14 Handle reading and writing of zero-sized arrays * * mw 01/02/15 Remove redundant ut_read_xml from R_ut_init * * mw 24/04/15 Initialise and free utunit when using udunits2, * * to fix memory errors reported by valgrind. * * Allow udunits2 headers to be in udunits2 directory. * * mw 26/01/16 Fix memory leak from abnormal exit of calendar funcs. * * mw 16/07/17 Minimise use of nc_enddef to read data from opendap. * * mw 01/10/17 Register native routines for invocation by R * * * \*=============================================================================*/ /*=============================================================================*\ * Includes * \*=============================================================================*/ #include #include #include #ifdef HAVE_UDUNITS2_UDUNITS_H #include #else #include #endif #include #include #include /*=============================================================================*\ * Macros * \*=============================================================================*/ /* Execute a netcdf function, changing to netcdf data mode if necessary. * Function return value is stored in parameter status. */ #define NC_DATAMODE(status, ncid, cmd) \ status = cmd; \ if (status == NC_EINDEFINE) { \ status = nc_enddef(ncid); \ if (status == NC_NOERR) { \ status = cmd; \ } \ } /*=============================================================================*\ * 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) { /* Some netcdf versions cannot handle zero-sized arrays */ incid = INTEGER(ncid)[0]; NC_DATAMODE(status, incid, \ nc_get_vara_double(incid, INTEGER(varid)[0], \ s_start, s_count, REAL(VECTOR_ELT(retlist, 2)))); } else { status = NC_NOERR; } /*-- Returning the list ---------------------------------------------------*/ if(status != NC_NOERR) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); } REAL(VECTOR_ELT(retlist, 0))[0] = status; UNPROTECT(2); return(retlist); } /*-----------------------------------------------------------------------------*\ * R_nc_get_vara_text() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_get_vara_text (SEXP ncid, SEXP varid, SEXP start, SEXP count, SEXP ndims, SEXP rawchar) { int i, status, incid; char *data, *tx_str; size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS]; size_t tx_len, tx_num, varsize; SEXP retlist, retlistnames; /*-- Copy dims from int to size_t, calculate number and length of strings -*/ for(i=0; i 0) { tx_num = 1; for(i=0; i 0) { SET_VECTOR_ELT(retlist, 2, allocVector(RAWSXP, varsize)); } else { SET_VECTOR_ELT(retlist, 2, allocVector(STRSXP, tx_num)); } 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("data")); setAttrib(retlist, R_NamesSymbol, retlistnames); status = -1; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Read variable from file ----------------------------------------------*/ if (INTEGER(rawchar)[0] > 0) { data = (char *) RAW(VECTOR_ELT(retlist, 2)); } else { data = (char *) R_alloc(varsize, sizeof(char)); } if (varsize > 0) { /* Some netcdf versions cannot handle zero-sized arrays */ incid = INTEGER(ncid)[0]; NC_DATAMODE(status, incid, \ nc_get_vara_text(incid, INTEGER(varid)[0], \ s_start, s_count, data)); } else { status = NC_NOERR; } /*-- Copy from C to R character vector (if specified) ---------------------*/ if (status == NC_NOERR && INTEGER(rawchar)[0] <= 0) { tx_str = (char *) R_alloc(tx_len+1, sizeof(char)); tx_str[tx_len] = '\0'; /* Final null character is never modified */ for(i=0; i 0) { /* Some netcdf versions cannot handle zero-sized arrays */ incid = INTEGER(ncid)[0]; NC_DATAMODE(status, incid, \ nc_put_vara_double(incid, INTEGER(varid)[0], \ s_start, s_count, REAL(data))); } else { status = NC_NOERR; } /*-- Returning the list ---------------------------------------------------*/ if (status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); } REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; UNPROTECT(2); return(retlist); } /*-----------------------------------------------------------------------------*\ * R_nc_put_vara_text() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_put_vara_text (SEXP ncid, SEXP varid, SEXP start, SEXP count, SEXP ndims, SEXP rawchar, SEXP data) { int i, status, incid; char *ncdata; size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS]; size_t tx_len, tx_num, varsize; SEXP retlist, retlistnames; /*-- Copy dims from int to size_t, calculate number and length of strings -*/ for(i=0; i 0) { tx_num = 1; for(i=0; i 0) { ncdata = (char *) RAW(data); } else { ncdata = (char *) R_alloc(varsize, sizeof(char)); for(i=0; i 0) { /* Some netcdf versions cannot handle zero-sized arrays */ incid = INTEGER(ncid)[0]; NC_DATAMODE(status, incid, \ nc_put_vara_text(incid, INTEGER(varid)[0], \ s_start, s_count, ncdata)); } else { status = NC_NOERR; } /*-- Returning the list ---------------------------------------------------*/ if(status != NC_NOERR) { SET_VECTOR_ELT(retlist, 1, mkString(nc_strerror(status))); } REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; UNPROTECT(2); return(retlist); } /*-----------------------------------------------------------------------------*\ * R_nc_rename_var() * \*-----------------------------------------------------------------------------*/ SEXP R_nc_rename_var (SEXP ncid, SEXP varid, SEXP varname, SEXP nameflag, SEXP newname) { int ncvarid, status, errstatus; int enddef = 0; /* Keep for possible future use as argument */ char ncvarname[NC_MAX_NAME], ncnewname[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(ncvarname, CHAR(STRING_ELT(varname, 0))); strcpy(ncnewname, CHAR(STRING_ELT(newname, 0))); ncvarid = INTEGER(varid)[0]; status = -1; errstatus = 0; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Get the variable ID if necessary -------------------------------------*/ if(INTEGER(nameflag)[0] == 1) { status = nc_inq_varid(INTEGER(ncid)[0], ncvarname, &ncvarid); if(status != NC_NOERR) { SET_VECTOR_ELT (retlist, 1, mkString(nc_strerror(status))); REAL(VECTOR_ELT(retlist, 0))[0] = status; UNPROTECT(2); return(retlist); } } /*-- 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); } /*-- Rename the variable --------------------------------------------------*/ status = nc_rename_var(INTEGER(ncid)[0], ncvarid, ncnewname); 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); } /*=============================================================================*\ * Udunits library functions * \*=============================================================================*/ /*-----------------------------------------------------------------------------*\ * R_ut_strerror() * \*-----------------------------------------------------------------------------*/ void R_ut_strerror (int errcode, char* strerror) { if (errcode == UT_EOF ) strcpy(strerror, "end-of-file encountered (udunits)"); else if(errcode == UT_ENOFILE ) strcpy(strerror, "no units-file (udunits)"); else if(errcode == UT_ESYNTAX ) strcpy(strerror, "syntax error (udunits)"); else if(errcode == UT_EUNKNOWN) strcpy(strerror, "unknown specification (udunits)"); else if(errcode == UT_EIO ) strcpy(strerror, "I/O error (udunits)"); else if(errcode == UT_EINVALID) strcpy(strerror, "invalid unit-structure (udunits)"); else if(errcode == UT_ENOINIT ) strcpy(strerror, "package not initialized (udunits)"); else if(errcode == UT_ECONVERT) strcpy(strerror, "two units are not convertable (udunits)"); else if(errcode == UT_EALLOC ) strcpy(strerror, "memory allocation failure (udunits)"); else if(errcode == UT_ENOROOM ) strcpy(strerror, "insufficient room supplied (udunits)"); else if(errcode == UT_ENOTTIME) strcpy(strerror, "not a unit of time (udunits)"); else strcpy(strerror, "unknown error (udunits)"); } /*-----------------------------------------------------------------------------*\ * R_ut_calendar() * \*-----------------------------------------------------------------------------*/ SEXP R_ut_calendar (SEXP unitstring, SEXP unitcount, SEXP values) { int year, month, day, hour, minute, count, i, status; float second; double utvalue; char strerror[64]; utUnit utunit; 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)); SET_VECTOR_ELT(retlist, 2, allocMatrix(REALSXP, INTEGER(unitcount)[0], 6)); 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); status = -1; REAL(VECTOR_ELT(retlist, 0))[0] = (double)status; SET_VECTOR_ELT (retlist, 1, mkString("")); /*-- Scan unitstring ------------------------------------------------------*/ #ifdef HAVE_LIBUDUNITS2 utIni(&utunit); #endif status = utScan(CHAR(STRING_ELT(unitstring, 0)), &utunit); if(status != 0) { goto cleanup; } /*-- Check if unit is time and has origin ---------------------------------*/ if ( !utIsTime(&utunit) ) { status = UT_ENOTTIME; goto cleanup; } if ( !utHasOrigin(&utunit) ) { status = UT_EINVALID; goto cleanup; } /*-- Convert values -------------------------------------------------------*/ count = (int)INTEGER(unitcount)[0]; for(i=0; i' as shown above, and the compiler will typically search for a library called lib.so and then lib.a. But you can also specify the full pathname of a library if necessary, perhaps to force the use of a particular netcdf or udunits library on systems with multiple versions available. R CMD INSTALL Example ===================== R CMD INSTALL --configure-args="CPPFLAGS=-I/sw/include \ LDFLAGS=-L/sw/lib LIBS=-lhdf5" RNetCDF_1.9-1.tar.gz LD_LIBRARY_PATH =============== If a runtime error occurs indicating that shared libraries cannot be found, you may need to set or modify the library search path to include directories where NetCDF, HDF5 and/or UDUNITS libraries are stored. This is sometimes necessary for custom installations of the libraries. The library search path is typically influenced by the environment variable LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH for Mac OSX). For example: export LD_LIBRARY_PATH=/sw/lib:$LD_LIBRARY_PATH On some systems, it is possible to build R packages so that dependencies are found automatically at runtime. For example, some linkers provide an option such as '-rpath', which embeds the library search path when creating an executable or shared library. It may also be possible to avoid runtime dependencies by building your R package against static libraries (*.a), but this will only work if the functions in the libraries were compiled as position independent code (e.g. using the -fPIC option of gcc). R CMD check Example =================== R CMD check --install-args="--configure-args='CPPFLAGS=-I/sw/include \ LDFLAGS=-L/sw/lib'" RNetCDF_1.9-1.tar.gz Time units ========== Common udunits databases are distributed with RNetCDF, and these are used by default when RNetCDF is loaded by R. However, a different units database may be used by specifying the appropriate file in environment variables UDUNITS2_XML_PATH (udunits2) or UDUNITS_PATH (udunits1). RNetCDF/NEWS0000644000176200001440000000611113165116400012132 0ustar liggesusersVersion 1.9-1, 2017-10-04 * Allow multiple NA values in count argument of var.get.nc/var.put.nc, so that corresponding dimensions are read/written to their defined length. * Fix support for OPeNDAP (if enabled by the netcdf library) * Build Windows packages with netcdf4 library - Enable OPeNDAP in Win64 - Disable OPeNDAP in Win32, because it causes RNetCDF to crash - Thanks to Jeroen Ooms for giving us https://github.com/rwinlib/netcdf! * Register C routines for efficient access by R Version 1.8-2, 2016-02-21 * Add support for POSIXct timestamps to utcal.nc and utinvcal.nc. * Use nc-config by default in configure to find netcdf build settings. * Allow customisation of configure by variables CPPFLAGS, LDFLAGS and LIBS, and remove the following options: --with-netcdf-include, --with-netcdf-lib, --with-hdf5-lib, --with-udunits-include, --with-udunits-lib. Version 1.7-3, 2015-05-09 * Support reading/writing NC_CHAR as vectors of raw bytes * Avoid intermediate copies of array data when possible * Fix memory errors reported by valgrind for udunits2 calendar functions. * Support compilation with udunits.h inside a udunits2 sub-directory. * Add udunits data files to source package to ensure they can be found when building binary packages for Windows and Mac. Version 1.6.3-1, 2014-09-01 * Allow reading of character vector or scalar Version 1.6.2-3, 2014-06-16 * Added HDF5 licence file for distribution Version 1.6.2-2, 2014-05-27 * Corrected potential memory leak in read/write of character arrays Version 1.6.1-2, 2012-07-20 * Added function read.nc * Added packing/unpacking of data Version 1.5.3-1, 2012-02-15 * Optionally copy udunits data files during installation of RNetCDF. * When loading RNetCDF in R, initialise udunits with copied data files. Version 1.5.2-2, 2011-01-06 * configure adds tests for extra libraries used by netcdf4 on some systems. * Avoid repeated zeroing of character arrays in C interface. Version 1.5.0-1, 2010-12-30 * Add new modes (large, prefill, share) to nc_open and nc_create. * Avoid unnecessary switching of define and data modes in C library to prevent unwanted data movement within a file. * configure script accepts optional path for hdf5 (for netcdf4 library). * Added basic functional tests of package. Version 1.2-1.1, 2010-05-11 * Add build scripts for Windows. Version 1.2-1, 2006-07-26 * utcal.nc and utinvcal.nc optionally handle dates in string form. * configure script accepts optional paths for netcdf and udunits. Version 1.1-3, 2005-03-21 * Minor bugfix for detection of udunits headers in configure script. Version 1.1-2, 2005-01-04 * Return proper error status in C functions R_nc_sync and R_nc_get_vara_text. Version 1.1-1, 2004-09-19 * Add option to collapse singleton dimensions when reading arrays. * Allow reading of arrays without conversion of missing values. Version 1.0-4, 2004-09-11 * Search extra directories during configure. Version 1.0-3, 2004-08-01 * First release based on netcdf package by Thomas Lumley and ncdf package by David Pierce. RNetCDF/R/0000755000176200001440000000000013166006010011631 5ustar liggesusersRNetCDF/R/RNetCDF.R0000644000176200001440000013216513166002735013163 0ustar liggesusers#===============================================================================# # # # Name: RNetCDF.R # # # # Version: 1.9-1 # # # # Purpose: NetCDF interface for R. # # # # Author: Pavel Michna (michna@users.r-forge.r-project.org) # # Milton Woods (mwoods@users.r-forge.r-project.org) # # # # Copyright: (C) 2004-2017 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 # # mw 05/09/14 Support reading and writing raw character arrays # # mw 08/09/14 Handle reading and writing of zero-sized arrays # # mw 24/01/16 Support conversion of timestamps to/from POSIXct # # mw 29/07/17 Replace NA in count of var.get.nc and var.put.nc so that # # corresponding dimensions are read/written to end # # mw 03/10/17 Use registered entry points for .Call functions # # # #===============================================================================# #===============================================================================# # 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)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_copy_att, as.integer(ncfile.in), as.integer(varid.in), as.integer(globflag.in), as.character(attname), as.integer(ncfile.out), as.integer(varid.out), as.integer(globflag.out)) if(nc$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)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_delete_att, as.integer(ncfile), as.integer(varid), as.integer(globflag), as.character(attname)) if(nc$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)) #-- 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)) #-- 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)$id) else varid <- variable if(is.character(variable) && variable == "NC_GLOBAL") { globflag <- 1 varid <- -1 } if(class(varid) == "try-error" || is.null(varid)) return(invisible(NULL)) #-- Determine if attribute is numeric or character -------------------------# ifelse(is.numeric(value), numflag <- 1, numflag <- 0) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_put_att, as.integer(ncfile), as.integer(varid), as.character(name), as.character(type), as.integer(length(value)), as.integer(numflag), as.integer(globflag), value) if(nc$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)$name) if(class(attname) == "try-error" || is.null(attname)) return(invisible(NULL)) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_rename_att, as.integer(ncfile), as.integer(varid), as.integer(globflag), as.character(attname), as.character(newname)) if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # close.nc() # #-------------------------------------------------------------------------------# close.nc <- function(con, ...) { #-- Check args -------------------------------------------------------------# stopifnot(class(con) == "NetCDF") #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_close, as.integer(con)) if(nc$status != 0) stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # create.nc() # #-------------------------------------------------------------------------------# create.nc <- function(filename, clobber=TRUE, large=FALSE, share=FALSE, prefill=TRUE) { #-- Convert logical values to integers -------------------------------------# iclobber <- ifelse(clobber == TRUE, 1, 0) ## Overwrite existing file (y/n) ilarge <- ifelse(large == TRUE, 1, 0) ishare <- ifelse(share == TRUE, 1, 0) iprefill <- ifelse(prefill == TRUE, 1, 0) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_create, as.character(filename), as.integer(iclobber), as.integer(ilarge), as.integer(ishare), as.integer(iprefill)) #-- Return object if no error ----------------------------------------------# if(nc$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)) 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)) #-- 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)) 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)) #-- 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)) #-- 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$type == "NC_CHAR") cat(" = \"", att.get.nc(x, i, j), "\" ;\n", sep="") else cat( " = ", att.get.nc(x, i, j), " ;\n", sep="") } } } #-------------------------------------------------------------------------------# # sync.nc() # #-------------------------------------------------------------------------------# sync.nc <- function(ncfile) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_sync, as.integer(ncfile)) if(nc$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)) 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, rawchar=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)) stopifnot(is.logical(rawchar)) stopifnot(isTRUE(na.mode %in% c(0,1,2,3))) #-- 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) # Truncate start & count to length ndims # and replace NA as described in the man page: if (isTRUE(is.na(start))) { start <- rep(1, ndims) } else if (length(start) > ndims) { start <- start[seq_len(ndims)] } stopifnot(length(start) == ndims) start[is.na(start)] <- 1 if (isTRUE(is.na(count))) { count <- rep(NA, ndims) } else if (length(count) > ndims) { count <- count[seq_len(ndims)] } stopifnot(length(count) == ndims) for (idim in seq_len(ndims)) { if (is.na(count[idim])) { diminfo <- dim.inq.nc(ncfile, varinfo$dimids[idim]) count[idim] <- ( diminfo$length - start[idim] + 1 ) } } #-- Switch from R to C convention ------------------------------------------# c.start <- rev(start-1) c.count <- rev(count) #-- C function calls -------------------------------------------------------# if(varinfo$type == "NC_CHAR") { nc <- .Call(R_nc_get_vara_text, as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(ndims), as.integer(rawchar)) } else { nc <- .Call(R_nc_get_vara_double, as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(ndims)) } #-- Adjust data ------------------------------------------------------------# if(nc$status == 0) { #-- Convert missing value to NA if defined in NetCDF file --------------# if (is.numeric(nc$data) && na.mode < 3) { tolerance <- 1*10^-5 ## Allow rounding error na.flag <- 0 missval.flag <- 0 fillval.flag <- 0 fillval <- try(att.inq.nc(ncfile, varinfo$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$name, "missing_value") na.flag <- 1 } if(na.flag == 1) { nc$data[abs(nc$data-as.numeric(na.value)) < tolerance] <- NA } } #-- Unpack variables if requested (missing values are preserved) -------# if(unpack && is.numeric(nc$data)) { 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 } } #-- Set dimensions, collapse degenerate dimensions ---------------------# if (is.character(nc$data) && ndims > 0) { # Drop string length dimension datadim <- count[-1] } else { datadim <- count } if (collapse) { # Drop singleton dimensions datadim <- datadim[datadim!=1] } if (length(datadim)<1) { # For compatibility with code written for RNetCDF<=1.6.x, # scalars and vectors always have a dimension attribute: datadim <- length(nc$data) } dim(nc$data) <- datadim #-- Return object if no error ----------------------------------------------# return(nc$data) } else stop(nc$errmsg, call.=FALSE) } #-------------------------------------------------------------------------------# # var.inq.nc() # #-------------------------------------------------------------------------------# var.inq.nc <- function(ncfile, variable) { #-- Check args -------------------------------------------------------------# stopifnot(class(ncfile) == "NetCDF") stopifnot(is.character(variable) || is.numeric(variable)) #-- Look if handle variable by name or ID ----------------------------------# varid <- -1 varname <- "" ifelse(is.character(variable), nameflag <- 1, nameflag <- 0) ifelse(is.character(variable), varname <- variable, varid <- variable) #-- C function call --------------------------------------------------------# nc <- .Call(R_nc_inq_var, as.integer(ncfile), as.integer(varid), as.character(varname), as.integer(nameflag)) #-- Return object if no error ----------------------------------------------# if(nc$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.raw(data) || is.logical(data)) stopifnot(is.numeric(start) || is.logical(start)) stopifnot(is.numeric(count) || is.logical(count)) stopifnot(is.logical(pack)) stopifnot(isTRUE(na.mode %in% c(0,1,2))) #-- Inquire the variable ---------------------------------------------------# varinfo <- try(var.inq.nc(ncfile, variable)) if(class(varinfo) == "try-error" || is.null(varinfo)) return(invisible(NULL)) ndims <- varinfo$ndims if ((is.character(data) || is.raw(data)) && varinfo$type != "NC_CHAR") { stop("R character data can only be written to NC_CHAR variable",call.=FALSE) } #-- 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" } # Truncate start & count to length ndims # and replace NA as described in the man page: if (isTRUE(is.na(start))) { start <- rep(1, ndims) } else if (length(start) > ndims) { start <- start[seq_len(ndims)] } stopifnot(length(start) == ndims) start[is.na(start)] <- 1 if (isTRUE(is.na(count))) { if (!is.null(dim(data))) { count <- dim(data) } else if (ndims==0 && length(data)==1) { count <- integer(0) } else { count <- length(data) } if (is.character(data) && ndims > 0) { strlen <- dim.inq.nc(ncfile, varinfo$dimids[1])$length count <- c(strlen, count) } } else if (length(count) > ndims) { count <- count[seq_len(ndims)] } stopifnot(length(count) == ndims) for (idim in seq_len(ndims)) { if (is.na(count[idim])) { diminfo <- dim.inq.nc(ncfile, varinfo$dimids[idim]) count[idim] <- ( diminfo$length - start[idim] + 1 ) } } #-- Check that length of data is sufficient --------------------------------# if (is.character(data) && ndims > 0) { numelem <- prod(count[-1]) } else { numelem <- prod(count) # Returns 1 if ndims==0 (scalar variable) } if (length(data) < numelem) { stop(paste("Not enough data elements (found ",length(data), ", need ",numelem,")", sep=""), call.=FALSE) } #-- Warn if strings will be truncated --------------------------------------# if (is.character(data)) { if (ndims > 0) { strlen <- count[1] } else { strlen <- 1 } if (max(nchar(data,type="bytes")) > strlen) { warning(paste("Strings truncated to length",strlen), call.=FALSE) } } #-- Warn if array data is not conformable with count -----------------------# if (!is.null(dim(data))) { if (is.character(data)) { count_drop <- count[-1] } else { count_drop <- count } count_drop <- count_drop[count_drop!=1] dim_drop <- dim(data) dim_drop <- dim_drop[dim_drop!=1] if ((length(count_drop) != length(dim_drop)) || any(count_drop != dim_drop)) { warning(paste("Data coerced from dimensions (", paste(dim(data),collapse=","), ") to dimensions (", paste(count,collapse=","), ")", sep=""), call.=FALSE) } } #-- Pack variables if requested (missing values are preserved) -------------# if(pack && is.numeric(data)) { 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) && 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)] <- as.numeric(na.value) else stop("Found NAs but no missing value attribute", call.=FALSE) } #-- Switch from R to C convention ------------------------------------------# c.start <- rev(start-1) c.count <- rev(count) #-- C function calls -------------------------------------------------------# if(is.numeric(data)) { if (!is.double(data)) { data <- as.double(data) } nc <- .Call(R_nc_put_vara_double, as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(ndims), data) } else { stopifnot(is.character(data) || is.raw(data)) nc <- .Call(R_nc_put_vara_text, as.integer(ncfile), as.integer(varid), as.integer(c.start), as.integer(c.count), as.integer(ndims), as.integer(is.raw(data)), data) } 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)) 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" || type == "c" ) count <- length(value) #-- C function call to udunits calendar function -----------------------# ut <- .Call(R_ut_calendar, as.character(unitstring), as.integer(count), as.double(value)) #-- Return object if no error ------------------------------------------# if(ut$status == 0) { if(type == "n") { colnames(ut$value) <- c("year", "month", "day", "hour", "minute", "second") return(ut$value) } else if (type == "s") { x <- apply(ut$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 if (type == "c") { ct <- as.POSIXct( utinvcal.nc("seconds since 1970-01-01 00:00:00 +00:00",ut$value), tz="UTC", origin=ISOdatetime(1970,1,1,0,0,0,tz="UTC")) return(ct) } } else { stop(ut$errmsg, call.=FALSE) } } #-------------------------------------------------------------------------------# # utinit.nc() # #-------------------------------------------------------------------------------# utinit.nc <- function(path="") { ut <- .Call(R_ut_init, as.character(path)) 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(all(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) } else if (inherits(value,"POSIXct")) { value <- utcal.nc("seconds since 1970-01-01 00:00:00 +00:00", as.numeric(value), 'n') } 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)) #-- Return object if no error ----------------------------------------------# if(ut$status == 0) { return(ut$value) } else { stop(ut$errmsg, call.=FALSE) } } #===============================================================================# #===============================================================================# # SCRATCH # #===============================================================================# RNetCDF/R/windows/0000755000176200001440000000000013166006010013323 5ustar liggesusersRNetCDF/R/windows/load.R0000755000176200001440000000132312463263502014401 0ustar liggesusers# Assume that RNetCDF is linked with udunits2 library on Windows. ".onLoad" <- function(lib, pkg) { # Check environment for name of udunits2 database requested by user: envdb <- Sys.getenv("UDUNITS2_XML_PATH", unset=NA) if (is.na(envdb)) { # Initialise udunits2 library with database packaged in RNetCDF: datafile <- system.file("udunits", "udunits2.xml", package=pkg, lib.loc=lib) if ("udunits2" == "udunits2") { # udunits2 ignores argument passed to utInit C function Sys.setenv(UDUNITS2_XML_PATH=datafile) } utinit.nc(datafile) } else { # Initialise udunits2 library with user-specified database: utinit.nc("") } } RNetCDF/R/load.R.in0000644000176200001440000000124412463263502013313 0ustar liggesusers".onLoad" <- function(lib, pkg) { # Check environment for name of @UDUNITS_LIB@ database requested by user: envdb <- Sys.getenv("@UDUNITS_DBVAR@", unset=NA) if (is.na(envdb)) { # Initialise @UDUNITS_LIB@ library with database packaged in RNetCDF: datafile <- system.file("udunits", "@UDUNITS_DBFILE@", package=pkg, lib.loc=lib) if ("@UDUNITS_LIB@" == "udunits2") { # udunits2 ignores argument passed to utInit C function Sys.setenv(@UDUNITS_DBVAR@=datafile) } utinit.nc(datafile) } else { # Initialise @UDUNITS_LIB@ library with user-specified database: utinit.nc("") } } RNetCDF/README.md0000644000176200001440000000117313162431111012711 0ustar liggesusers# RNetCDF - Interface to NetCDF Datasets for R RNetCDF provides an R interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. This R interface is closely based on the C API of the NetCDF library, and it includes calendar conversions from the Unidata UDUNITS library. The current implementation supports operations on NetCDF datasets in classic, 64-bit offset and netcdf4-classic file formats. Work is progressing to add full support for netcdf4. An introduction to the RNetCDF package is given in http://journal.r-project.org/archive/2013-2/michna-woods.pdf . 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The R interface is closely based on the C API of the NetCDF library, and it includes calendar conversions from the Unidata UDUNITS library. The current implementation supports all operations on NetCDF datasets in classic and 64-bit offset file formats, and NetCDF4-classic format is supported for reading and modification of existing files. License: GPL (>= 2) | file LICENSE URL: http://rnetcdf.r-forge.r-project.org http://www.unidata.ucar.edu/software/netcdf/ http://www.unidata.ucar.edu/software/udunits/ NeedsCompilation: yes Repository: CRAN Repository/R-Forge/Project: rnetcdf Repository/R-Forge/Revision: 234 Repository/R-Forge/DateTimeStamp: 2017-10-06 22:45:42 Date/Publication: 2017-10-08 22:16:10 UTC Packaged: 2017-10-06 23:05:26 UTC; rforge RNetCDF/configure0000755000176200001440000042053513166006066013363 0ustar liggesusers#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.69 for RNetCDF 1.9-1. # # # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. # # # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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A dimension cannot be renamed to have the same name as another dimension.} \references{\url{http://www.unidata.ucar.edu/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("dim.rename.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/man/dim.inq.nc.Rd0000644000176200001440000000253613162431055014445 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("dim.inq.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/open.nc.Rd0000644000176200001440000000346113166002754014051 0ustar liggesusers\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. If the underlying NetCDF library supports OPeNDAP, \code{con} may be an OPeNDAP URL.} \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{TRUE}.} \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/software/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a void NetCDF dataset nc <- create.nc("open.nc") close.nc(nc) ## Open the NetCDF dataset for writing nc <- open.nc("open.nc", write=TRUE) close.nc(nc) } \keyword{file} RNetCDF/man/close.nc.Rd0000644000176200001440000000150013162431055014201 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a void NetCDF dataset nc <- create.nc("close.nc") close.nc(nc) } \keyword{file} RNetCDF/man/utcal.nc.Rd0000644000176200001440000001130713162430743014215 0ustar liggesusers\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 \code{n} for numeric, \code{s} for string or \code{c} for POSIXct output.} } \value{If the output type is set to numeric, result is a matrix containing the corresponding date(s) and time(s), with the following columns: year, month, day, hour, minute, second. If the output type is string, result is a vector of strings in the form \code{"YYYY-MM-DD hh:mm:ss"}. Otherwise result is a vector of POSIXct values.} \details{Converts the amount, \code{value}, of the temporal unit, \code{unitstring}, into a UTC-referenced date and time. Functions \code{utcal.nc} and \code{utinvcal.nc} provide a convenient way to convert time values between the forms used by NetCDF variables and R functions. Most R functions require times to be expressed as seconds since the beginning of 1970 in the UTC time zone, typically using objects of class \code{POSIXct} or \code{POSIXlt}. NetCDF files store times in numeric variables with a wide variety of units. The units and calendar are stored in attributes of the time variable, as described by the CF Conventions. Units are expressed as a string, in the form of a time unit since a fixed date-time (e.g. ``hours since 2000-01-01 00:00:00 +00:00'', or more simply ``hours since 2000-01-01''). The conversions of times between units are performed by the UDUNITS library using 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. Conversions involving alternative calendars are not supported by UDUNITS, but they can be performed by several other R packages. } \seealso{\code{\link{utinvcal.nc}}} \references{\url{http://www.unidata.ucar.edu/software/udunits/} \url{http://cfconventions.org}} \author{Pavel Michna, Milton Woods} \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") utcal.nc("hours since 1900-01-01 00:00:00 +01:00", c(0:5), type="c") ## Create netcdf file with a time coordinate variable. # Create a time variable (using type POSIXct for convenience): nt <- 24 time_posixct <- seq(ISOdatetime(1900,1,1,0,0,0,tz="UTC"), by="hour", len=nt) # Convert time variable to specified units: time_unit <- "hours since 1900-01-01 00:00:00 +00:00" time_coord <- utinvcal.nc(time_unit, time_posixct) # Create a netcdf file: nc <- create.nc("utcal.nc") # Global attributes: att.put.nc(nc, "NC_GLOBAL", "Conventions", "NC_CHAR", "CF-1.6") att.put.nc(nc, "NC_GLOBAL", "title", "NC_CHAR", "RNetCDF example: time coordinate") att.put.nc(nc, "NC_GLOBAL", "institution", "NC_CHAR", "University of Areland") att.put.nc(nc, "NC_GLOBAL", "source", "NC_CHAR", paste("RNetCDF", installed.packages()["RNetCDF","Version"], sep="_")) att.put.nc(nc, "NC_GLOBAL", "history", "NC_CHAR", paste(Sys.time(), "File created")) att.put.nc(nc, "NC_GLOBAL", "references", "NC_CHAR", "http://www.unidata.ucar.edu/software/udunits") att.put.nc(nc, "NC_GLOBAL", "comment", "NC_CHAR", "Uses attributes recommended by http://cfconventions.org") # Define time coordinate and attributes: dim.def.nc(nc, "time", nt) var.def.nc(nc, "time", "NC_INT", "time") att.put.nc(nc, "time", "long_name", "NC_CHAR", "time") att.put.nc(nc, "time", "units", "NC_CHAR", time_unit) # Calendar is optional (gregorian is the default): att.put.nc(nc, "time", "calendar", "NC_CHAR", "gregorian") # Write the data: var.put.nc(nc, "time", time_coord) close.nc(nc) ## Read time coordinate from netcdf file: # Open the file prepared earlier: nc <- open.nc("utcal.nc") # Read time coordinate and attributes: time_coord2 <- var.get.nc(nc, "time") time_unit2 <- att.get.nc(nc, "time", "units") close.nc(nc) # Convert the time variable to POSIXct: time_posixct2 <- utcal.nc(time_unit2, time_coord2, "c") # Compare with original POSIXct variable: stopifnot(all.equal(time_posixct, time_posixct2)) } \keyword{utilities} RNetCDF/man/att.put.nc.Rd0000644000176200001440000000433713162431055014506 0ustar liggesusers\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/software/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("att.put.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/read.nc.Rd0000644000176200001440000000347513162431055014024 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("read.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.Rd0000644000176200001440000000351013162431055014405 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("dim.def.nc") dim.def.nc(nc, "station", 5) dim.def.nc(nc, "time", unlim=TRUE) close.nc(nc) } \keyword{file} RNetCDF/man/var.def.nc.Rd0000644000176200001440000000451413162431055014431 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("var.def.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/var.put.nc.Rd0000644000176200001440000001371513162431221014501 0ustar liggesusers\name{var.put.nc} \alias{var.put.nc} \title{Write Data to 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 NetCDF variable.} \item{data}{An R vector or array of data to be written to the NetCDF variable. Values are taken from \code{data} in the order of R vector elements, so that leftmost indices vary fastest over an array.} \item{start}{A vector of indices specifying the element where writing starts along each dimension of \code{variable}. Indices are numbered from 1 onwards, and the order of dimensions is shown by \code{\link[RNetCDF]{print.nc}} (array elements are stored sequentially with leftmost indices varying fastest). By default (\code{start=NA}), all dimensions of \code{variable} are written from the first element onwards. Otherwise, \code{start} must be a vector whose length is not less than the number of dimensions in \code{variable} (excess elements are ignored). Any \code{NA} values in vector \code{start} are set to 1.} \item{count}{A vector of integers specifying the number of values to write along each dimension of \code{variable}. The order of dimensions is the same as for \code{start}. By default (\code{count=NA}), \code{count} is set to \code{dim(data)} for an array or \code{length(data)} for a vector. Otherwise, \code{count} must be a vector whose length is not less than the number of dimensions in \code{variable} (excess elements are ignored). Any \code{NA} value in vector \code{count} indicates that the corresponding dimension should be written from the \code{start} index to the end of the dimension. Note that an unlimited dimension initially has zero length, and the dimension is extended by setting the corresponding element of \code{count} greater than the current length.} \item{na.mode}{Set the mode for handling missing values (\code{NA}) in numeric variables: 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 performed by the NetCDF library, so that numeric values in R are automatically converted to the correct type of NetCDF variable. However, text represented by R types \code{raw} and \code{character} can only be written to NetCDF type \code{NC_CHAR}. The dimensions of R \code{raw} variables map directly to NetCDF dimensions, but \code{character} variables have an implied dimension corresponding to the string length. This implied dimension must be defined explicitly as the fastest-varying dimension of the \code{NC_CHAR} variable, and it must be included as the first element of arguments \code{start} and \code{count} taken by this function. Values of \code{NA} are supported in numeric variables if the variable's missing value attribute (as defined in \code{na.mode}) is set. They are converted to the corresponding value before writing 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 variable is represented as a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The \code{start} and \code{count} arguments of this routine indicate where the writing starts and the number of values to write along each dimension. 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/software/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("var.put.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 subsets of the data: var.put.nc(nc, "time", mytime, start=2, count=1) var.put.nc(nc, "temperature", mytemperature[3:4,2], start=c(3,2), count=c(2,1)) var.put.nc(nc, "name", myname[3:4], start=c(NA,3), count=c(NA,2)) sync.nc(nc) ## Put all of the data: 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/var.inq.nc.Rd0000644000176200001440000000331313162431055014456 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("var.inq.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/print.nc.Rd0000644000176200001440000000316713162431055014243 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("print.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/sync.nc.Rd0000644000176200001440000000261313162431055014056 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("sync.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/att.delete.nc.Rd0000644000176200001440000000241613162431055015134 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("att.delete.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/file.inq.nc.Rd0000644000176200001440000000324413162431055014610 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("file.inq.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/att.inq.nc.Rd0000644000176200001440000000366113162431055014464 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("att.inq.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.rename.nc.Rd0000644000176200001440000000274713162431055015150 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("att.rename.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/utinvcal.nc.Rd0000644000176200001440000000277313162430743014741 0ustar liggesusers\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}{Dates to convert as a numeric vector or array, or a vector of strings or POSIXct values.} } \value{A vector containing the amount(s) of the temporal unit(s) corresponding to the given date(s).} \details{Uses the UDUNITS library to convert a UTC-referenced date and time into the amount, \code{value}, of the temporal unit, \code{unitstring}. If the dates are given in string form, the structure must be exactly \code{"YYYY-MM-DD hh:mm:ss"}. A vector of POSIXct values is also accepted as input. These are converted to the specified units by a linear transformation, without an intermediate separation into date components. } \seealso{\code{\link{utcal.nc}}} \references{\url{http://www.unidata.ucar.edu/software/udunits/}} \author{Pavel Michna, Milton Woods} \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") utinvcal.nc("hours since 1900-01-01 00:00:00 +01:00", ISOdatetime(1900,1,1,5,25,0,tz="UTC")) ## An example of reading and writing a netcdf time coordinate ## is given in the help for utcal.nc } \keyword{utilities} RNetCDF/man/00RNetCDF.Rd0000644000176200001440000000505412651011205014023 0ustar liggesusers\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/software/netcdf/} \url{http://www.unidata.ucar.edu/software/udunits/} } \note{The NetCDF and the UDUNITS library must be already installed on the system.} \author{Pavel Michna} \keyword{file} RNetCDF/man/att.get.nc.Rd0000644000176200001440000000331013162431055014443 0ustar liggesusers\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/software/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("att.get.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/var.rename.nc.Rd0000644000176200001440000000216713162431055015144 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create a new NetCDF dataset and define two dimensions nc <- create.nc("var.rename.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/utinit.nc.Rd0000644000176200001440000000167312651011205014414 0ustar liggesusers\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/software/udunits/}} \author{Pavel Michna} \examples{ ## NOTE: The user will normally never need to call this function utinit.nc() } \keyword{utilities} RNetCDF/man/var.get.nc.Rd0000644000176200001440000001576513162431221014457 0ustar liggesusers\name{var.get.nc} \alias{var.get.nc} \title{Read Data from 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, rawchar=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 NetCDF variable.} \item{start}{A vector of indices specifying the element where reading starts along each dimension of \code{variable}. Indices are numbered from 1 onwards, and the order of dimensions is shown by \code{\link[RNetCDF]{print.nc}} (array elements are stored sequentially with leftmost indices varying fastest). By default (\code{start=NA}), all dimensions of \code{variable} are read from the first element onwards. Otherwise, \code{start} must be a vector whose length is not less than the number of dimensions in \code{variable} (excess elements are ignored). Any \code{NA} values in vector \code{start} are set to 1.} \item{count}{A vector of integers specifying the number of values to read along each dimension of \code{variable}. The order of dimensions is the same as for \code{start}. By default (\code{count=NA}), all dimensions of \code{variable} are read from \code{start} to end. Otherwise, \code{count} must be a vector whose length is not less than the number of dimensions in \code{variable} (excess elements are ignored). Any \code{NA} value in vector \code{count} indicates that the corresponding dimension should be read from the \code{start} index to the end of the dimension.} \item{na.mode}{Set the mode for handling missing values (\code{NA}) in numeric variables: 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}.} \item{rawchar}{This option only relates to NetCDF variables of type \code{NC_CHAR}. When \code{rawchar} is \code{FALSE} (default), a NetCDF variable of type \code{NC_CHAR} is converted to a \code{character} array in R. The \code{character} values are from the fastest-varying dimension of the NetCDF variable, so that the R \code{character} array has one fewer dimensions than the \code{NC_CHAR} array. If \code{rawchar} is \code{TRUE}, the bytes of \code{NC_CHAR} data are read into an R \code{raw} array of the same shape.} } \details{This function returns the value of a variable. Numeric variables are always returned in R double precision, no matter what precision they have in the on-disk dataset. NetCDF variables of type \code{NC_CHAR} are returned as R \code{character} or \code{raw} variables, as specified by argument \code{rawchar}. Values of \code{NA} are supported in numeric variables. 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}, values are read from each variable without alteration. Data in a NetCDF variable is represented as a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The \code{start} and \code{count} arguments of this routine indicate where the reading starts and the number of values to read along each dimension. 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{An array with dimensions determined by \code{count} and a data type that depends on the type of \code{variable}. For NetCDF variables of type \code{NC_CHAR}, the R type is either \code{character} or \code{raw}, as specified by argument \code{rawchar}. All other NetCDF variables are returned to R as type \code{numeric} (double precision). The dimension order in the R array is reversed relative to the order reported by NetCDF commands such as \code{ncdump}, because NetCDF arrays are stored in row-major (C) order whereas R arrays are stored in column-major (Fortran) order. Arrays of type \code{character} drop the fastest-varying dimension of the corresponding \code{NC_CHAR} array, because this dimension corresponds to the length of the individual \code{character} elements. For example, an \code{NC_CHAR} array with dimensions (5,10) would be returned as a \code{character} vector containing 5 elements, each with a maximum length of 10 characters.} \references{\url{http://www.unidata.ucar.edu/software/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("var.get.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(3,1), c(1,1)) var.get.nc(nc, "temperature", c(3,2)) 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/att.copy.nc.Rd0000644000176200001440000000435713162431055014652 0ustar liggesusers\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/software/netcdf/}} \author{Pavel Michna} \examples{ ## Create two new NetCDF datasets and define two dimensions nc.1 <- create.nc("att.copy1.nc") nc.2 <- create.nc("att.copy2.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/create.nc.Rd0000644000176200001440000000350313162431055014344 0ustar liggesusers\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{TRUE}.} \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/software/netcdf/}} \author{Pavel Michna, Milton Woods} \examples{ ## Create a void NetCDF dataset nc <- create.nc("create.nc") close.nc(nc) } \keyword{file} RNetCDF/configure.win0000755000176200001440000000000012462141463014133 0ustar liggesusersRNetCDF/cleanup0000755000176200001440000000014513166006066013020 0ustar liggesusers#!/bin/sh rm -rf *.cache rm -f ./config.* rm -f ./src/Makevars ./R/load.R rm -f ./src/*.so ./src/*.o RNetCDF/tools/0000755000176200001440000000000013166006010012570 5ustar liggesusersRNetCDF/tools/winlibs.R0000644000176200001440000000064313162431163014374 0ustar liggesusers# Build against imagemagick static website. VERSION <- commandArgs(TRUE) if(!file.exists(sprintf("../windows/netcdf-%s/include/netcdf.h", VERSION))){ if(getRversion() < "3.3.0") setInternet2() download.file(sprintf("https://github.com/rwinlib/netcdf/archive/v%s.zip", VERSION), "lib.zip", quiet = TRUE) dir.create("../windows", showWarnings = FALSE) unzip("lib.zip", exdir = "../windows") unlink("lib.zip") } RNetCDF/LICENSE0000644000176200001440000002720213162431001012436 0ustar liggesusersThis file is intended to clarify ownership, copyrights and licenses. Where possible individual files also carry brief copyright notices. RNetCDF ======= All files except those indicated later are Copyright (C) 2004-2017 Pavel Michna. They are licensed under the terms of the GNU General Public 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. See http://www.r-project.org/Licenses/GPL-2 for license details. NetCDF ====== The documentation of RNetCDF is based on the "NetCDF User's Guide for C", and installation of RNetCDF requires linking with the Unidata NetCDF library. These uses of NetCDF are allowed by the NetCDF copyright: Copyright 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 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, although this is not an obligation. 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. UDUNITS ======= RNetCDF may be linked with the UDUNITS (version 1.x) library. To simplify distribution of RNetCDF in binary form, data files required by UDUNITS are included with RNetCDF, subject to the following license: (C) Copyright 1992,1995 UCAR/Unidata Permission to use, copy, modify, and distribute this software and its documentation for any purpose without fee is hereby granted, provided that the above copyright notice appears in all copies, that both that copyright notice and this permission notice appear in supporting documentation, and that the name of UCAR/Unidata not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. UCAR makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. It is provided with no support and without obligation on the part of UCAR or Unidata, to assist in its use, correction, modification, or enhancement. UDUNITS2 ======== RNetCDF may be linked with the UDUNITS2 library. To simplify distribution of RNetCDF in binary form, data files required by UDUNITS2 are included with RNetCDF, subject to the following license: Copyright 2014 University Corporation for Atmospheric Research and contributors. All rights reserved. This software was developed by the Unidata Program Center of the University Corporation for Atmospheric Research (UCAR) . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3) Neither the names of the development group, the copyright holders, nor the names of contributors may be used to endorse or promote products derived from this software without specific prior written permission. 4) This license shall terminate automatically and you may no longer exercise any of the rights granted to you by this license as of the date you commence an action, including a cross-claim or counterclaim, against the copyright holders or any contributor alleging that this software infringes a patent. This termination provision shall not apply for an action alleging patent infringement by combinations of this software with other software or hardware. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. NCSA HDF5 ========= Although the RNetCDF package does not use HDF5 directly, if statically linked to a build of netcdf with the netcdf4 feature enabled, it will link in code from HDF5. The license for such code is given below: Copyright Notice and License Terms for HDF5 (Hierarchical Data Format 5) Software Library and Utilities ----------------------------------------------------------------------------- HDF5 (Hierarchical Data Format 5) Software Library and Utilities Copyright 2006-2014 by The HDF Group. NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities Copyright 1998-2006 by the Board of Trustees of the University of Illinois. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted for any purpose (including commercial purposes) provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or materials provided with the distribution. 3. In addition, redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change. 4. All publications or advertising materials mentioning features or use of this software are asked, but not required, to acknowledge that it was developed by The HDF Group and by the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign and credit the contributors. 5. Neither the name of The HDF Group, the name of the University, nor the name of any Contributor may be used to endorse or promote products derived from this software without specific prior written permission from The HDF Group, the University, or the Contributor, respectively. DISCLAIMER: THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no event shall The HDF Group or the Contributors be liable for any damages suffered by the users arising out of the use of this software, even if advised of the possibility of such damage. ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Contributors: National Center for Supercomputing Applications (NCSA) at the University of Illinois, Fortner Software, Unidata Program Center (netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment Corporation (DEC). ----------------------------------------------------------------------------- Portions of HDF5 were developed with support from the Lawrence Berkeley National Laboratory (LBNL) and the United States Department of Energy under Prime Contract No. DE-AC02-05CH11231. ----------------------------------------------------------------------------- Portions of HDF5 were developed with support from the University of California, Lawrence Livermore National Laboratory (UC LLNL). The following statement applies to those portions of the product and must be retained in any redistribution of source code, binaries, documentation, and/or accompanying materials: This work was partially produced at the University of California, Lawrence Livermore National Laboratory (UC LLNL) under contract no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy (DOE) and The Regents of the University of California (University) for the operation of UC LLNL. DISCLAIMER: This work was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately- owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California, and shall not be used for advertising or product endorsement purposes. ----------------------------------------------------------------------------- Pavel Michna