Parsing command line arguments in R scripts

Is there any convenient way to automatically parse command line arguments passed to R scripts?

Something like perl's Getopt::Long?

There are three packages on CRAN:

• getopt: C-like getopt behavior
• optparse: a command line parser inspired by Python's optparse library
• argparse: a command line optional and positional argument parser (inspired by Python's argparse library). This package requires that a Python interpreter be installed with the argparse and json (or simplejson) modules.

Update:

• docopt: lets you define a command line interface by just giving it a description in the specific format. It is a port a docopt.py.
• argparser: cross-platform command-line argument parser written purely in R with no external dependencies. This package is useful with the Rscript front-end and facilitates turning an R script into an executable script.
• minimist: A binding to the minimist JavaScript library. This module implements the guts of optimist's argument parser without all the fanciful decoration (no external dependencies)
• optigrab: parse options from the command-line using a simple, clean syntax. It requires little or no specification and supports short and long options, GNU-, Java- or Microsoft- style syntaxes, verb commands and more.

The simplest way is to use commandArgs(). Example - save the code below as "options.R":

options <- commandArgs(trailingOnly = TRUE)
options

Run using "Rscript options.R x y z". Result:

[1] "x" "y" "z"

i.e. a list of 3 elements, one per argument.

Just to complement the Rscript answer:

edd@max:~$ r -e 'print(argv)' flim flam flom
[1] "flim" "flam" "flom"
edd@max:~$ 

We just use argv in littler. I had good luck with getopt, the older of the two available parsing packages.

May I introduce ArgumentParser in Xmisc package? It is a command line parser inspired by Python's argparse but it is Python-free.

http://cran.r-project.org/web/packages/Xmisc/vignettes/Xmisc-ArgumentParser.pdf

The getopt long is in the --parameter=argument format like so

rscript script.R --parameter1=argument1 --parameter2=argument2

It can be parsed by just using basic string packages.

Example

cli.r

library(pracma)
library(stringr)
run.arguments <- commandArgs(TRUE)
valid.run.parameters <- c( "universe", "character", "ability" )
for ( i in 1:length( run.arguments ) ) {
	if ( strcmpi( substr( run.arguments[i], 1, 2 ), "--" ) & grepl( "=", run.arguments[i], fixed = TRUE) ) {
		key.pair <- str_split( run.arguments[i], "=", simplify=TRUE )
		run.parameter <- gsub( "--", "", key.pair[1] )
		run.argument <- key.pair[2]
		if ( run.parameter %in% valid.run.parameters ) {

			# DO YOUR MAGIC HERE! Here is an example...
			cat( run.parameter, "\n" )
			cat( run.argument,  "\n\n" )

		}
	}
}

The above script was written for brevity. See the more compelling version.

Usage

rscript cli.R --universe=MCU --character="Wade Wilson"

Output

universe
MCU

character
Wade Wilson