# test.R
# Parse and use command line arguments
# Invoke % R --slave --args 100 < test.R 

Args <- commandArgs();      # retrieve args
x <- c(1:as.real(Args[4])); # get the 4th argument
y <- c(x^2);                # work out square
png(filename="image.png");  # create image file
plot(x,y);                  # plot image
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[1] "/usr/lib/R/bin/exec/R" 
[2] "--slave" 
[3] "--args"               
[4] "100"
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Yes, this was very useful and worked right away! Thanks a lot!

That works fine, but there's a slightly neater way to do it; if you provide a TRUE value to the commandArgs function, it ignores any commandline parameters before (and including) --args.
So with Args <- commandArgs(TRUE), Args[1] is "100", and is the only element of the vector.

It's also possible to use a simpler syntax to call the script on the command line, which implicitly assumes that any arguments are given after the script name:
Rscript test.R 100

Cheers,
Julio

In Bash shell

# a=1
# b=10
# Rscript -e "args<-commandArgs(TRUE);x=args[1]:args[2];x;mean(x);sd(x
+)" $a $b
 [1]  1  2  3  4  5  6  7  8  9 10
[1] 5.5
[1] 3.027650
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So you can control variables on the command line R script and you can feed these variables into R itself using commandArgs(TRUE), and manipulate the variables as args1 and args2. So if I imagine if you are doing a system call in perl, you can also construct a similar Rscript on the command line, and get the output accordingly, which you can manipulate further within perl (or any other script).

Here is simple function to parse unix way of parsing argument from R.

#
#
# EXAMPLE:
# R --test=mydata.csv
#> getopt('test')
#[1] "mydata.csv"

# getting numeric argument
# R --N=123
#> getopt('N',numeric=T)
#[1] 123
#

getopt <- function(argname, numeric = F)
  {
    args <- commandArgs()  
    argexp = sprintf('^--%s=',argname)
    idx <- regexpr(argexp, args);

    ret <- NA
    
    if ( any(idx > 0) )
    { # found matching argument  
    found <- args[idx > 0]
    value <- strsplit(found,"=")
    ret <- unlist(value)[2]
    }

    if ( numeric )
    ret <- as.numeric(ret)

    ret
  }
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cheers, c.okugami

In Rscript/R

require(plyr)

## get and parse any commandline options/args
cmd.args <- commandArgs(trailingOnly=TRUE)

## this assumes trailingOnly in commandArgs()
mk.cmd.args.list <- function(args) {
  if (length(args)>1) {
    split.list <- strsplit( args[-1], '\\=' )  ## exclude "--args"
    values <- llply( split.list, '[[', 2 )
    names(values) <- laply( split.list, '[[', 1 )
    values } else list()  ## the possible returns 
}
cmd.args.list <- mk.cmd.args.list(cmd.args)
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