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

 

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?

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 FilesR-3.0.2binRScript.exe"
%R_Script% exmpl.R 2010-01-28 example 100 > exmpl.batch 2>&1

    Alternatively, using Rterm.exe : 

    set R_TERM="C:Program FilesR-3.0.2bini386Rterm.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 FilesR-3.0.2binRScript.exe"

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

    Differences between RScript and Rterm :

  • Rscript has simpler syntax
  • Rscript automatically chooses architecture on x64 (see R Installation and Administration, 2.6 Sub-architectures for details)
  • Rscript needs options(echo=TRUE) in the .R file if you want to write the commands to the output file

    • A few points:

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

  • 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.

  • 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.

    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.

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