R/NCO_functions.r

In markpayneatwork/ClimateOperators: Climate Operators for R

#' NCO operators
#'
#' Provides an interface to the (external to R) NetCDF Operators (NCO)
#'
#' @name nco
#' @export
#' @param ... List of arguments to be converted to a text string
#' @param debug Doesn't run the command, but returns the command that would be run
#' @param defaults Character string supplying the defaults to be used by CDO
#' @details Default options for nco can be set at the system wide level
#'using the \code{set.nc.defaults()} command. Two of the most useful
#'of these include "--overwrite" (to overwrite files by default) and
#'"--netcdf4" to force NetCDF4 output. See the documentation of NCO for more.
#'@examples
#' # Note, to run this in the wild, remove the debug=TRUE arguments
#' set.nco.defaults("--overwrite")
#' in.fname <- "tos_Omon_IPSL-CM5A-LR_historical_r1i1p1_185001-200512.nc"
#' out.fname <- "foo.nc"
#' ncra(in.fname,out.fname,debug=TRUE)
#' ncwa(in.fname,out.fname,debug=TRUE)

set.nco.defaults <- function(defaults="") {
  opt <- getOption("ClimateOperators")
  opt$nco <- defaults
  options("ClimateOperators"=opt)
}

#' @export
#' @rdname nco
ncks <- function(...,debug=FALSE) {nco.cmd("ncks",...,debug=debug)}

#' @export
#' @rdname nco
ncwa <- function(...,debug=FALSE) {nco.cmd("ncwa",...,debug=debug)}

#' @export
#' @rdname nco
ncra <- function(...,debug=FALSE) {nco.cmd("ncra",...,debug=debug)}

#' @export
#' @rdname nco
ncrcat <- function(...,debug=FALSE) {nco.cmd("ncrcat",...,debug=debug)}

#' @export
#' @rdname nco
ncecat <- function(...,debug=FALSE) {nco.cmd("ncecat",...,debug=debug)}

#' @export
#' @rdname nco
nces <- function(...,debug=FALSE) {nco.cmd("nces",...,debug=debug)}

#' @export
#' @rdname nco
ncbo <- function(...,debug=FALSE) {nco.cmd("ncbo",...,debug=debug)}

#' @export
#' @rdname nco
ncdiff <- function(...,debug=FALSE) {nco.cmd("ncdiff",...,debug=debug)}

#' @export
#' @rdname nco
ncap2 <- function(...,debug=FALSE) {nco.cmd("ncap2",...,debug=debug)}

#' @export
#' @rdname nco
ncrename <- function(...,debug=FALSE) {nco.cmd("ncrename",...,debug=debug)}

#' @export
#' @rdname nco
ncatted <- function(...,debug=FALSE) {nco.cmd("ncatted",...,debug=debug)}


nco.cmd <- function(cmd,...,debug) {
  #Build command
  cmd.args <- paste(c(getOption("ClimateOperators")$nco,
                      unlist(list(...))),collapse=" ")
  this.cmd <-paste(cmd,cmd.args)

  if(!debug) {
    #Run the command
    run.time <- system.time(rtn <- system2(cmd,cmd.args))
    if(rtn!=0) stop( sprintf("%s command failed with error code %s. Command issued: \n %s",cmd, rtn,this.cmd))
    attr(this.cmd,"run.time") <- run.time["elapsed"]
  }
  return(this.cmd)
}