2013-07-02

Parse arguments of an R script

R can be used also as a scripting tool. We just need to add shebang in the first line of a file (script):

#!/usr/bin/Rscript

and then the R code should follow.

Often we want to pass arguments to such a script, which can be collected in the script by the commandArgs() function. Then we need to parse the arguments and conditional on them do something. I came with a rather general way of parsing these arguments using simply these few lines:

## Collect arguments
args <- commandArgs(TRUE)
 
## Default setting when no arguments passed
if(length(args) < 1) {
  args <- c("--help")
}
 
## Help section
if("--help" %in% args) {
  cat("
      The R Script
 
      Arguments:
      --arg1=someValue   - numeric, blah blah
      --arg2=someValue   - character, blah blah
      --arg3=someValue   - logical, blah blah
      --help              - print this text
 
      Example:
      ./test.R --arg1=1 --arg2="output.txt" --arg3=TRUE \n\n")
 
  q(save="no")
}
 
## Parse arguments (we expect the form --arg=value)
parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
argsL <- as.list(as.character(argsDF$V2))
names(argsL) <- argsDF$V1
 
## Arg1 default
if(is.null(args$arg1)) {
  ## do something
}
 
## Arg2 default
if(is.null(args$arg2)) {
  ## do something
}
 
## Arg3 default
if(is.null(args$arg3)) {
  ## do something
}
 
## ... your code here ...
Created by Pretty R at inside-R.org

It is some work, but I find it pretty neat and use it for quite a while now. I do wonder what others have come up for this task. I hope I did not miss some very general solution.

2 comments:

nxskok said...

I use package "batch". I run R from the command line like this:

R --vanilla --args w 0.5 mg 10 < test.r

then inside test.r is

library(batch)
parseCommandArgs()

and after that, in my namespace, w is 0.5 and mg is 10.

I don't know whether that's easier or harder than your way, but it seems to work for me.

dickoa said...

Great post but you might consider also the more general optparse package