Passing command line arguments into R scripts

June 20, 2013

If you’d like to run an R script for processing some data from the command line (i.e. non interactively), it’s often necessary to pass some arguments into the script. For example, lets write a simple script to do column-wise statistics on files by simply reading the file and calling summary:

fn <- "somefile.csv"
df <- read.table(fn, sep = ",", header = TRUE)
print(summary(df))

Now generate some example data and run the script from the shell

> perl -e 'print "col1,col2,col3\n"; for ($i=0;$i<20;$i++) \
           {print rand() . "," . rand() * 5 . "," . rand() * 10 . "\n"}' > somefile.csv
> R -q --no-save --no-restore --slave -f summary.R
#      col1              col2             col3      
# Min.   :0.04458   Min.   :0.1185   Min.   :0.4232 
# 1st Qu.:0.25550   1st Qu.:1.8638   1st Qu.:3.4375 
# Median :0.38139   Median :2.4246   Median :5.9120 
# Mean   :0.47104   Mean   :2.3656   Mean   :5.6726 
# 3rd Qu.:0.67615   3rd Qu.:3.2736   3rd Qu.:8.3637 
# Max.   :0.98758   Max.   :4.3326   Max.   :9.8417

Obviously a hard coded file name is not very useful. Instead, let’s rewrite this to take a single argument:

args <- commandArgs(trailingOnly = TRUE)
fn <- args[1]
df <- read.table(fn, sep = ",", header = TRUE)
print(summary(df))

The trailing = TRUE option results in commandArgs only returning on the arguments after --args.

> R -q --no-save --no-restore --slave -f summary.R --args somefile.csv
#      col1              col2             col3       
# Min.   :0.01908   Min.   :0.1037   Min.   :0.01602 
# 1st Qu.:0.22552   1st Qu.:1.0515   1st Qu.:2.13243 
# Median :0.42952   Median :2.3641   Median :3.36631 
# Mean   :0.49441   Mean   :2.3710   Mean   :4.41240 
# 3rd Qu.:0.80786   3rd Qu.:3.7884   3rd Qu.:7.71034 
# Max.   :0.99459   Max.   :4.6230   Max.   :9.77731

Rscript makes this much easier:

> Rscript summary.R somefile.csv

And can also be used in a shebang line:

#! /usr/bin/env Rscript
args <- commandArgs(trailing = TRUE)
fn <- args[1]
df <- read.table(fn, sep = ",", header = TRUE)
print(summary(df))

which can then be called directly

> chmod +x summary.R
> ./summary.R somefile.csv