Question:
Is there any convenient way to automatically parse command line arguments passed to R scripts?
Something like perl's Getopt::Long?
Solution:1
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
argparseandjson(orsimplejson) 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.
Solution:2
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.
Solution:3
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.
Solution:4
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
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