How can I read command line parameters from an R script?

user_140823 0
Viewed 181910

I've got a R script for which I'd like to be able to supply several command-line parameters (rather than hardcode parameter values in the code itself). The script runs on Windows.

I can't find info on how to read parameters supplied on the command-line into my R script. I'd be surprised if it can't be done, so maybe I'm just not using the best keywords in my Google search...

Any pointers or recommendations?

r parameters command-line
10 Answers

Dirk's answer here is everything you need. Here's a minimal reproducible example.

I made two files: exmpl.bat and exmpl.R.

  • exmpl.bat:

    set R_Script="C:\Program Files\R-3.0.2\bin\RScript.exe"
%R_Script% exmpl.R 2010-01-28 example 100 > exmpl.batch 2>&1

    Alternatively, using Rterm.exe:

    set R_TERM="C:\Program Files\R-3.0.2\bin\i386\Rterm.exe"
%R_TERM% --no-restore --no-save --args 2010-01-28 example 100 < exmpl.R > exmpl.batch 2>&1

  • exmpl.R:

    options(echo=TRUE) # if you want see commands in output file
args <- commandArgs(trailingOnly = TRUE)
print(args)
# trailingOnly=TRUE means that only your arguments are returned, check:
# print(commandArgs(trailingOnly=FALSE))

start_date <- as.Date(args[1])
name <- args[2]
n <- as.integer(args[3])
rm(args)

# Some computations:
x <- rnorm(n)
png(paste(name,".png",sep=""))
plot(start_date+(1L:n), x)
dev.off()

summary(x)

Save both files in the same directory and start exmpl.bat. In the result you'll get:

  • example.png with some plot
  • exmpl.batch with all that was done

You could also add an environment variable %R_Script%:

"C:\Program Files\R-3.0.2\bin\RScript.exe"

and use it in your batch scripts as %R_Script% <filename.r> <arguments>

Differences between RScript and Rterm:

user_1687470

A few points:

  1. Command-line parameters are accessible via commandArgs(), so see help(commandArgs) for an overview.

  2. You can use Rscript.exe on all platforms, including Windows. It will support commandArgs(). littler could be ported to Windows but lives right now only on OS X and Linux.

  3. There are two add-on packages on CRAN -- getopt and optparse -- which were both written for command-line parsing.

Edit in Nov 2015: New alternatives have appeared and I wholeheartedly recommend docopt.

user_1433050

Add this to the top of your script: 

args<-commandArgs(TRUE)

Then you can refer to the arguments passed as args[1], args[2] etc.

Then run 

Rscript myscript.R arg1 arg2 arg3

If your args are strings with spaces in them, enclose within double quotes.

user_2208910

you need littler (pronounced 'little r')

Dirk will be by in about 15 minutes to elaborate ;)

user_377510

In bash, you can construct a command line like the following:

$ z=10
$ echo $z
10
$ Rscript -e "args<-commandArgs(TRUE);x=args[1]:args[2];x;mean(x);sd(x)" 1 $z
 [1]  1  2  3  4  5  6  7  8  9 10
[1] 5.5
[1] 3.027650
$

You can see that the variable $z is substituted by bash shell with "10" and this value is picked up by commandArgs and fed into args[2], and the range command x=1:10 executed by R successfully, etc etc.

user_5688120
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