├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── CDO__functions.r ├── NCO_functions.r └── ncdump.r ├── README.md └── man ├── cdo.Rd ├── cdo.dates.Rd ├── griddes.Rd ├── ncdump.Rd └── nco.Rd /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | *.Rproj 6 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: ClimateOperators 2 | Type: Package 3 | Title: Climate Operators for R 4 | Version: 0.3.2 5 | Author: Mark R. Payne 6 | Maintainer: Mark R. Payne 7 | Description: Provides a set of wrappers to support working with climate and oceanographic model outputs in R via the Climate Data Operators (CDO) and the NetCDF Operators (NCO). 8 | License: GNU 9 | LazyData: TRUE 10 | Depends: raster 11 | Suggests: lubridate 12 | RoxygenNote: 7.1.1 13 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(cdo) 4 | export(cdo.dates) 5 | export(csl) 6 | export(griddes) 7 | export(ncap2) 8 | export(ncatted) 9 | export(ncbo) 10 | export(ncdiff) 11 | export(ncdump) 12 | export(ncdump.coordinates) 13 | export(ncdump.times) 14 | export(ncecat) 15 | export(nces) 16 | export(ncks) 17 | export(ncra) 18 | export(ncrcat) 19 | export(ncrename) 20 | export(ncwa) 21 | export(set.cdo.defaults) 22 | export(set.nco.defaults) 23 | export(ssl) 24 | exportMethods(griddes) 25 | -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | # ClimateOperators 2 | 3 | # v 0.3.2 4 | 5 | * Fixed bug in `ncdump.coordinates` that failed to handle dates of format "ymd HM" 6 | 7 | # v 0.3.1 8 | 9 | * `ncdump()` function added to allow direct printing of the header information in a file. 10 | 11 | # v 0.3.0 12 | 13 | * Addition of `ncdump` functions 14 | -------------------------------------------------------------------------------- /R/CDO__functions.r: -------------------------------------------------------------------------------- 1 | #' Climate Data Operators (CDO) 2 | #' 3 | #' Provides an interface for running commands suitable for use with 4 | #' the (externally installed) Climate Data Operators (CDO) 5 | #' @param debug Doesn't run the command, but returns the command that would be run. 6 | #' @name cdo 7 | #' @export 8 | #' @examples 9 | #' # What version of CDO am I running? 10 | #' cdo("--version") 11 | #' 12 | #' # Select a variable from a CMIP5 model 13 | #' # Note, to run this in the wild, remove the debug=TRUE argument 14 | #' in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 15 | #' out.fname <- "foo.nc" 16 | #' cdo("selvar",in.fname,out.fname,debug=TRUE) 17 | #' 18 | #' # Use the defaults and csl to build up a more complex argument 19 | #' # Note, to run this in the wild, remove the debug=TRUE argument 20 | #' in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 21 | #' out.fname <- "foo.nc" 22 | #' set.cdo.defaults("--silent") 23 | #' yrs <- seq(1950,2005,by=5) #Every fifth year 24 | #' cdo(csl("selyear",yrs),in.fname,out.fname,debug=TRUE) 25 | cdo <- function(...,debug=FALSE) { 26 | #Build command 27 | cmd.args <- ssl(getOption("ClimateOperators")$cdo,list(...)) 28 | cdo.cmd <- paste("cdo",cmd.args) 29 | if(!debug) { 30 | rtn <- try(system2("cdo",cmd.args,stdout = TRUE)) 31 | if(!is.null(attr(rtn,"status"))) { 32 | stop( sprintf("CDO command failed. Status code %s. Command issued:\n %s",attr(rtn,"status"),cdo.cmd))} 33 | attr(rtn,"cdo.command") <- cdo.cmd 34 | } else { 35 | rtn <- cdo.cmd 36 | } 37 | return(rtn) 38 | } 39 | 40 | #'@export 41 | #'@rdname cdo 42 | #'@param defaults Character string supplying the defaults to be used by CDO 43 | #'@details Default options for cdo can be set at the system wide level 44 | #'using the \code{set.cdo.defaults()} command. Two of the most useful 45 | #'of these include "-O" (to overwrite files by default) and "-s" to 46 | #'silence the outputs of cdo. See the helpfiles of CDO for more. 47 | set.cdo.defaults <- function(defaults="") { 48 | opt <- getOption("ClimateOperators") 49 | opt$cdo <- defaults 50 | options("ClimateOperators"=opt) 51 | } 52 | 53 | # Comma separated list 54 | # 55 | #' @details \code{csl} converts a set of arguments into a comma separated list 56 | #' @rdname cdo 57 | #' @export 58 | csl <- function(...) { #Comma separated arguments 59 | cmd <- paste(unlist(list(...)),collapse=",") 60 | return(cmd) 61 | } 62 | 63 | # Space separated arguments 64 | # 65 | #' @details \code{ssl} converts a set of arguments into a space separated list 66 | #' @export 67 | #' @rdname cdo 68 | ssl <- function(...) { #Comma separated arguments 69 | cmd <- paste(unlist(list(...)),collapse=" ") 70 | return(cmd) 71 | } 72 | 73 | #' Extract dates from a file using CDO 74 | #' 75 | #' Extracts the timestaps from a file using CDO and coverts them to a Date format suitable for use 76 | #' elsewhere in R. It can be advantageous to use this approach, rather than, e.g. raster, when using CDO 77 | #' as your main processing tool, to ensure consistency in the approach. This is also rather handy when 78 | #' dealing with non-standard calendars that raster doesn't support. 79 | #' @param f Filename 80 | #' @export 81 | cdo.dates <- function(f) { 82 | require(lubridate) 83 | if(length(f)!=1) stop("CDO.dates function is not vectorised over input files - one at a time!") 84 | #Run command 85 | rtn <- system2("cdo",paste("--silent showdate",f),stdout=TRUE) 86 | #Process dates 87 | out <- ymd(strsplit(gsub("^ +","",rtn)," +")[[1]]) 88 | return(out) 89 | } 90 | 91 | #======================================================================== 92 | # CDO Grid Descriptor #### 93 | #======================================================================== 94 | #' Create a CDO compatable grid descriptor 95 | #' 96 | #' Creates a grid descriptor that can be used by CDO in regridding operations 97 | #' @param x Provides information to define the grid 98 | #' @export griddes 99 | #' @name griddes 100 | setGeneric("griddes", 101 | function(x, ...) 102 | standardGeneric("griddes") 103 | ) 104 | 105 | 106 | #' @export 107 | #'@rdname griddes 108 | setMethod("griddes",signature(x="Raster"), 109 | function(x,...){ 110 | #Start with the header 111 | str <- c("#", 112 | sprintf("# %s",x@title), 113 | "#") 114 | #Specify lonlat grid 115 | str <- c(str,"gridtype = lonlat", 116 | sprintf("gridsize = %i",ncell(x)), 117 | "xname = lon", 118 | "xlongname = longitude", 119 | "xunits = degrees_east", 120 | "yname = lat", 121 | "ylongname=latitude", 122 | "yunits = degrees_north") 123 | #Specify grid size and resolution 124 | str <- c(str, 125 | sprintf("xsize = %i",ncol(x)), 126 | sprintf("ysize = %i",nrow(x))) 127 | #Get coordinates information 128 | pts <- coordinates(x) 129 | str <- c(str, 130 | sprintf("xfirst = %f",min(pts[,1])), 131 | sprintf("xinc = %f",res(x)[1]), 132 | sprintf("yfirst = %f",min(pts[,2])), 133 | sprintf("yinc = %f",res(x)[2]) ) 134 | return(str) 135 | }) 136 | 137 | 138 | #' @export 139 | #'@rdname griddes 140 | #' @param res The resolution of the grid (single number of vector of two numbers) 141 | setMethod("griddes",signature(x="Extent"), 142 | function(x,res=1,...){ 143 | r <- raster(x) 144 | res(r) <- res 145 | return(griddes(r)) 146 | }) 147 | 148 | -------------------------------------------------------------------------------- /R/NCO_functions.r: -------------------------------------------------------------------------------- 1 | #' NCO operators 2 | #' 3 | #' Provides an interface to the (external to R) NetCDF Operators (NCO) 4 | #' 5 | #' @name nco 6 | #' @export 7 | #' @param ... List of arguments to be converted to a text string 8 | #' @param debug Doesn't run the command, but returns the command that would be run 9 | #' @param defaults Character string supplying the defaults to be used by CDO 10 | #' @details Default options for nco can be set at the system wide level 11 | #'using the \code{set.nc.defaults()} command. Two of the most useful 12 | #'of these include "--overwrite" (to overwrite files by default) and 13 | #'"--netcdf4" to force NetCDF4 output. See the documentation of NCO for more. 14 | #'@examples 15 | #' # Note, to run this in the wild, remove the debug=TRUE arguments 16 | #' set.nco.defaults("--overwrite") 17 | #' in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 18 | #' out.fname <- "foo.nc" 19 | #' ncra(in.fname,out.fname,debug=TRUE) 20 | #' ncwa(in.fname,out.fname,debug=TRUE) 21 | 22 | set.nco.defaults <- function(defaults="") { 23 | opt <- getOption("ClimateOperators") 24 | opt$nco <- defaults 25 | options("ClimateOperators"=opt) 26 | } 27 | 28 | #' @export 29 | #' @rdname nco 30 | ncks <- function(...,debug=FALSE) {nco.cmd("ncks",...,debug=debug)} 31 | 32 | #' @export 33 | #' @rdname nco 34 | ncwa <- function(...,debug=FALSE) {nco.cmd("ncwa",...,debug=debug)} 35 | 36 | #' @export 37 | #' @rdname nco 38 | ncra <- function(...,debug=FALSE) {nco.cmd("ncra",...,debug=debug)} 39 | 40 | #' @export 41 | #' @rdname nco 42 | ncrcat <- function(...,debug=FALSE) {nco.cmd("ncrcat",...,debug=debug)} 43 | 44 | #' @export 45 | #' @rdname nco 46 | ncecat <- function(...,debug=FALSE) {nco.cmd("ncecat",...,debug=debug)} 47 | 48 | #' @export 49 | #' @rdname nco 50 | nces <- function(...,debug=FALSE) {nco.cmd("nces",...,debug=debug)} 51 | 52 | #' @export 53 | #' @rdname nco 54 | ncbo <- function(...,debug=FALSE) {nco.cmd("ncbo",...,debug=debug)} 55 | 56 | #' @export 57 | #' @rdname nco 58 | ncdiff <- function(...,debug=FALSE) {nco.cmd("ncdiff",...,debug=debug)} 59 | 60 | #' @export 61 | #' @rdname nco 62 | ncap2 <- function(...,debug=FALSE) {nco.cmd("ncap2",...,debug=debug)} 63 | 64 | #' @export 65 | #' @rdname nco 66 | ncrename <- function(...,debug=FALSE) {nco.cmd("ncrename",...,debug=debug)} 67 | 68 | #' @export 69 | #' @rdname nco 70 | ncatted <- function(...,debug=FALSE) {nco.cmd("ncatted",...,debug=debug)} 71 | 72 | 73 | nco.cmd <- function(cmd,...,debug) { 74 | #Build command 75 | cmd.args <- paste(c(getOption("ClimateOperators")$nco, 76 | unlist(list(...))),collapse=" ") 77 | this.cmd <-paste(cmd,cmd.args) 78 | 79 | if(!debug) { 80 | #Run the command 81 | run.time <- system.time(rtn <- system2(cmd,cmd.args)) 82 | if(rtn!=0) stop( sprintf("%s command failed with error code %s. Command issued: \n %s",cmd, rtn,this.cmd)) 83 | attr(this.cmd,"run.time") <- run.time["elapsed"] 84 | } 85 | return(this.cmd) 86 | } 87 | 88 | 89 | -------------------------------------------------------------------------------- /R/ncdump.r: -------------------------------------------------------------------------------- 1 | #' Extract metadata using ncdump 2 | #' 3 | #' ncdump is a utility provided when installing the NetCDF libraries that is very handy 4 | #' for extracting metadata information from a netcdf file 5 | #' 6 | #' @param f Path to the netcdf file to process 7 | #' 8 | #' @return `ncdump.coordinates` returns a named list of the coordinates. `ncdump.time` returns just the 9 | #' time dimension, if it exists 10 | #' @export 11 | #' @name ncdump 12 | ncdump.coordinates <- function(f) { 13 | require(lubridate) 14 | #Get ncdump output 15 | ncdump <- system2("ncdump", sprintf("-ct %s",f),stdout=TRUE) 16 | #Drop everything up to and including data: 17 | dat <- ncdump[-c(1:grep("^data:",ncdump))] 18 | #Combine and split 19 | vars.l <- strsplit(paste0(dat,collapse=""),";")[[1]] 20 | vars.dat <- strsplit(vars.l,", ") 21 | vars.dat[[length(vars.dat)]] <- NULL #Drop the last 22 | #Treat first item separately 23 | var.names <- sapply(vars.dat,function(x) gsub("^ (.+?) = .*$","\\1",x[1])) 24 | vars.dat <- lapply(vars.dat,function(x) gsub("^.* = (.*)$","\\1",x)) 25 | #Convert time first 26 | names(vars.dat) <- var.names 27 | if("time" %in% var.names) { 28 | time.objs <- lubridate::parse_date_time(vars.dat$time,c("ymd","ymd H","ymd HM","ymd HMS")) 29 | if(any(is.na(time.objs))) stop(paste("Failed to parse some date-times strings:", 30 | paste(vars.dat$time[is.na(time.objs)], 31 | collapse=", "))) 32 | vars.dat$time <- time.objs 33 | } 34 | #Try to convert rest to numeric 35 | for(this.var in setdiff(var.names,"time")) { 36 | this.num <- as.numeric(vars.dat[[this.var]]) 37 | if(!any(is.na(this.num))) { #Success! 38 | vars.dat[[this.var]] <- this.num 39 | } 40 | } 41 | 42 | return(vars.dat) 43 | } 44 | 45 | #' @export 46 | #' @name ncdump 47 | ncdump.times <- function(f) { 48 | all.coords <- ncdump.coordinates(f) 49 | return(all.coords$time) 50 | } 51 | 52 | #' @export 53 | #' @name ncdump 54 | ncdump <- function(f) { 55 | #Get ncdump output 56 | ncd <- system2("ncdump", sprintf("-h %s",f),stdout=TRUE) 57 | rtn <- paste(ncd,collapse="\n") 58 | cat(rtn) 59 | return(invisible(NULL)) 60 | } 61 | 62 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ClimateOperators 2 | 3 | by Mark R. Payne
4 | http://www.staff.dtu.dk/mpay
5 | @MarkPayneAtWork 6 | 7 | An R package containing wrappers to the Climate Data Operators (CDO) and the NetCDF Operators (NCO) 8 | 9 | ## Dependencies 10 | ClimateOperators acts as an R wrapper around the CDO and NCO packages - you will to download and install these from the relevant webpages first: 11 | 12 | * https://code.mpimet.mpg.de/projects/cdo/ 13 | * http://nco.sourceforge.net/ 14 | 15 | Make sure that these are available in your system path. 16 | 17 | Generally, ClimateOperators (and CDO and NCO) are intended to be used on Unix-like platforms. I expect that the package should also work on Windows and MacOS, but please note that it is untested there - *caveat emptor*. Installing CDO and NCO on these platforms is also tricky - Unix-like platforms are recommended for this type of work. 18 | 19 | ## Installation 20 | 21 | You can install this package directly from the GitHub repository using the following command: 22 | 23 | ```{R} 24 | devtools::install_github("markpayneatwork/ClimateOperators") 25 | ``` 26 | 27 | ## Some CDO examples 28 | 29 | The underlying principle of ClimateOperators is that it allows you to quickly and easily build and run CDO/NCO commands from within R. It helps to be familar with these various tools - the documentation for both is excellent, so I suggest making sure you're familar with that. 30 | 31 | Here are some basic examples to get you started. 32 | 33 | Firstly, all commands attempt to run a command by calling the relevant CDO / NCO binary. This behaviour can be overwritten using the debug option, which compiles the command (but does not run it) e.g. 34 | 35 | ```{R} 36 | cdo("--version",debug=FALSE) 37 | ``` 38 | 39 | Omitting the argument, runs the command 40 | ```{R} 41 | cdo("--version") 42 | ``` 43 | 44 | The remaining examples include the debug=TRUE command by default - in a real world situation you would remove this option. CDO commands are then built up as command line arguments 45 | ```{R} 46 | cdo("sinfo","tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc",debug=TRUE) 47 | ``` 48 | This lends itself nicely to programming: 49 | ```{R} 50 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 51 | out.fname <- "foo.nc" 52 | cdo("selvar,tos",in.fname,out.fname,debug=TRUE) 53 | ``` 54 | You can always see the command that has been built up (without running it) using the debug command 55 | ```{R} 56 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 57 | out.fname <- "foo.nc" 58 | cdo("selvar,tos",in.fname,out.fname,debug=TRUE) 59 | ``` 60 | CDO (and NCO) often base their arguments on the back of comma-separated or space-separated lists. These can be built quickly and easily using the csl() and ssl() commands respectively. Putting this together makes for a more realistic CDO command: 61 | ```{R} 62 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 63 | out.fname <- "foo.nc" 64 | var <- "tos" 65 | cdo(csl("selvar",var),in.fname,out.fname,debug=TRUE) 66 | ``` 67 | 68 | Default (system-wide) options to CDO and NCO can also be supplied e.g. 69 | ```{R} 70 | set.cdo.defaults("--silent") 71 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 72 | out.fname <- "foo.nc" 73 | var <- "tos" 74 | cdo(csl("selvar",var),in.fname,out.fname,debug=TRUE) 75 | ``` 76 | 77 | ## Some NCO examples 78 | 79 | NCO is conceptually identical, except there are functions for each of the operators. 80 | ```{R} 81 | set.nco.defaults("--overwrite") 82 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 83 | out.fname <- "foo.nc" 84 | ncra(in.fname,out.fname,debug=TRUE) 85 | ncwa(in.fname,out.fname,debug=TRUE) 86 | ``` 87 | ## More help 88 | 89 | For more help, see the list of supported functions in the package help 90 | ```{R} 91 | help(package="ClimateOperators") 92 | ``` 93 | Questions, queries, comments or theories are always welcome via the GitHub repository. Push-requests are especially welcome! 94 | -------------------------------------------------------------------------------- /man/cdo.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/CDO__functions.r 3 | \name{cdo} 4 | \alias{cdo} 5 | \alias{set.cdo.defaults} 6 | \alias{csl} 7 | \alias{ssl} 8 | \title{Climate Data Operators (CDO)} 9 | \usage{ 10 | cdo(..., debug = FALSE) 11 | 12 | set.cdo.defaults(defaults = "") 13 | 14 | csl(...) 15 | 16 | ssl(...) 17 | } 18 | \arguments{ 19 | \item{debug}{Doesn't run the command, but returns the command that would be run.} 20 | 21 | \item{defaults}{Character string supplying the defaults to be used by CDO} 22 | } 23 | \description{ 24 | Provides an interface for running commands suitable for use with 25 | the (externally installed) Climate Data Operators (CDO) 26 | } 27 | \details{ 28 | Default options for cdo can be set at the system wide level 29 | using the \code{set.cdo.defaults()} command. Two of the most useful 30 | of these include "-O" (to overwrite files by default) and "-s" to 31 | silence the outputs of cdo. See the helpfiles of CDO for more. 32 | 33 | \code{csl} converts a set of arguments into a comma separated list 34 | 35 | \code{ssl} converts a set of arguments into a space separated list 36 | } 37 | \examples{ 38 | # What version of CDO am I running? 39 | cdo("--version") 40 | 41 | # Select a variable from a CMIP5 model 42 | # Note, to run this in the wild, remove the debug=TRUE argument 43 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 44 | out.fname <- "foo.nc" 45 | cdo("selvar",in.fname,out.fname,debug=TRUE) 46 | 47 | # Use the defaults and csl to build up a more complex argument 48 | # Note, to run this in the wild, remove the debug=TRUE argument 49 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 50 | out.fname <- "foo.nc" 51 | set.cdo.defaults("--silent") 52 | yrs <- seq(1950,2005,by=5) #Every fifth year 53 | cdo(csl("selyear",yrs),in.fname,out.fname,debug=TRUE) 54 | } 55 | -------------------------------------------------------------------------------- /man/cdo.dates.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/CDO__functions.r 3 | \name{cdo.dates} 4 | \alias{cdo.dates} 5 | \title{Extract dates from a file using CDO} 6 | \usage{ 7 | cdo.dates(f) 8 | } 9 | \arguments{ 10 | \item{f}{Filename} 11 | } 12 | \description{ 13 | Extracts the timestaps from a file using CDO and coverts them to a Date format suitable for use 14 | elsewhere in R. It can be advantageous to use this approach, rather than, e.g. raster, when using CDO 15 | as your main processing tool, to ensure consistency in the approach. This is also rather handy when 16 | dealing with non-standard calendars that raster doesn't support. 17 | } 18 | -------------------------------------------------------------------------------- /man/griddes.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/CDO__functions.r 3 | \name{griddes} 4 | \alias{griddes} 5 | \alias{griddes,Raster-method} 6 | \alias{griddes,Extent-method} 7 | \title{Create a CDO compatable grid descriptor} 8 | \usage{ 9 | griddes(x, ...) 10 | 11 | \S4method{griddes}{Raster}(x, ...) 12 | 13 | \S4method{griddes}{Extent}(x, res = 1, ...) 14 | } 15 | \arguments{ 16 | \item{x}{Provides information to define the grid} 17 | 18 | \item{res}{The resolution of the grid (single number of vector of two numbers)} 19 | } 20 | \description{ 21 | Creates a grid descriptor that can be used by CDO in regridding operations 22 | } 23 | -------------------------------------------------------------------------------- /man/ncdump.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ncdump.r 3 | \name{ncdump} 4 | \alias{ncdump} 5 | \alias{ncdump.coordinates} 6 | \alias{ncdump.times} 7 | \title{Extract metadata using ncdump} 8 | \usage{ 9 | ncdump.coordinates(f) 10 | 11 | ncdump.times(f) 12 | 13 | ncdump(f) 14 | } 15 | \arguments{ 16 | \item{f}{Path to the netcdf file to process} 17 | } 18 | \value{ 19 | `ncdump.coordinates` returns a named list of the coordinates. `ncdump.time` returns just the 20 | time dimension, if it exists 21 | } 22 | \description{ 23 | ncdump is a utility provided when installing the NetCDF libraries that is very handy 24 | for extracting metadata information from a netcdf file 25 | } 26 | -------------------------------------------------------------------------------- /man/nco.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/NCO_functions.r 3 | \name{nco} 4 | \alias{nco} 5 | \alias{set.nco.defaults} 6 | \alias{ncks} 7 | \alias{ncwa} 8 | \alias{ncra} 9 | \alias{ncrcat} 10 | \alias{ncecat} 11 | \alias{nces} 12 | \alias{ncbo} 13 | \alias{ncdiff} 14 | \alias{ncap2} 15 | \alias{ncrename} 16 | \alias{ncatted} 17 | \title{NCO operators} 18 | \usage{ 19 | set.nco.defaults(defaults = "") 20 | 21 | ncks(..., debug = FALSE) 22 | 23 | ncwa(..., debug = FALSE) 24 | 25 | ncra(..., debug = FALSE) 26 | 27 | ncrcat(..., debug = FALSE) 28 | 29 | ncecat(..., debug = FALSE) 30 | 31 | nces(..., debug = FALSE) 32 | 33 | ncbo(..., debug = FALSE) 34 | 35 | ncdiff(..., debug = FALSE) 36 | 37 | ncap2(..., debug = FALSE) 38 | 39 | ncrename(..., debug = FALSE) 40 | 41 | ncatted(..., debug = FALSE) 42 | } 43 | \arguments{ 44 | \item{defaults}{Character string supplying the defaults to be used by CDO} 45 | 46 | \item{...}{List of arguments to be converted to a text string} 47 | 48 | \item{debug}{Doesn't run the command, but returns the command that would be run} 49 | } 50 | \description{ 51 | Provides an interface to the (external to R) NetCDF Operators (NCO) 52 | } 53 | \details{ 54 | Default options for nco can be set at the system wide level 55 | using the \code{set.nc.defaults()} command. Two of the most useful 56 | of these include "--overwrite" (to overwrite files by default) and 57 | "--netcdf4" to force NetCDF4 output. See the documentation of NCO for more. 58 | } 59 | \examples{ 60 | # Note, to run this in the wild, remove the debug=TRUE arguments 61 | set.nco.defaults("--overwrite") 62 | in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc" 63 | out.fname <- "foo.nc" 64 | ncra(in.fname,out.fname,debug=TRUE) 65 | ncwa(in.fname,out.fname,debug=TRUE) 66 | } 67 | --------------------------------------------------------------------------------