# test.R:

cat("-- reading arguments\n", sep = "");
cmd_args = commandArgs();
for (arg in cmd_args) cat("  ", arg, "\n", sep="");
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# command line:

R --slave --no-save --no-restore --no-environ --silent --args arg1=abc
+ < test.R
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# output from R:

-- reading arguments
  /home/aardvark/lib/R/bin/exec/R
  --slave
  --no-save
  --no-restore
  --no-environ
  --silent
  --args
  arg1=abc
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Thank you very much! This is precisely what I was looking for =)
Now I need to tweak it a bit for my needs. Thank you soooooooooo much!

---

Smoothie, smoothie, hundre prosent naturlig!

very late answer, maybe the library is newer than your question, but what about optparse or getopt?

install.packages('optparse')
?optparse
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I tried to get it working (I come from Python and I'm used to the syntax) but in the end I settled for the easier (and working) 'getopt' solution:

install.packages('getopt')
.
.
.
  if(require("getopt", quietly=TRUE)) {
    opt <- getopt(matrix(c('path', 'p', 1, "character"),
                         ncol=4, byrow=TRUE))
    if(!is.null(opt$path))
      path <- opt$path
  }
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However, have you considered using Perl to generate your R command input file with whatever parameters you need, then load that new command file into R?

> cat 644967.pl
#!/usr/bin/env perl
 
use warnings;
use strict;
 
my $x = shift;
my $cmd_file = 'cmd.txt';
open my $OUT_FH, '>', $cmd_file or die "Can not open $cmd_file $!\n";
print $OUT_FH <<"EOF";
x <- c(1:$x)
y <- c(x^2)
png(filename="plot.png", bg="transparent")
plot(x, y)
dev.off()
EOF
close $OUT_FH or die "Can not close $cmd_file $!\n";
 
>
> ./644967.pl 13
>
> cat cmd.txt
x <- c(1:13)
y <- c(x^2)
png(filename="plot.png", bg="transparent")
plot(x, y)
dev.off()
>
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Thank you both
I have considered doing it this way (writing an R file). I just felt I was not far from the R solution. I know this is not the best place to be asking an R question but I have had useful advice to all my questions in the past I am always compelled to ask here first
Once again, thank you

---

Smoothie, smoothie, hundre prosent naturlig!

##In a file called test_args.R
args <- commandArgs()

print (args)
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which you can run from the shell

cat test_args.R | R --slave --args all your base
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which prints

[1] "usr/lib64/R/bin/exec/R" "--slave"
[3] "--args"                 "all"
[5] "your"                   "base"
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Thank you all for your input! I did eventually work it out and my solution looks like so:

# 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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This creates the image file image.png which contains a plot of an exponential curve =)
The variable Args contains the following:

[1] "/usr/lib/R/bin/exec/R" 
[2] "--slave" 
[3] "--args"               
[4] "100"
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We only require the 4th element for our graph. You can add more arguments and just pick them off accordingly =)
I hope someone else finds this useful.

---

Smoothie, smoothie, hundre prosent naturlig!

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 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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