Passing command line arguments to R CMD BATCH

Question

I have been using R CMD BATCH my_script.R from a terminal to execute an R script. I am now at the point where I would like to pass an argument to

Answer 1

My impression is that R CMD BATCH is a bit of a relict. In any case, the more recent Rscript executable (available on all platforms), together with commandArgs() makes processing command line arguments pretty easy.

As an example, here is a little script -- call it "myScript.R":

## myScript.R
args <- commandArgs(trailingOnly = TRUE)
rnorm(n=as.numeric(args[1]), mean=as.numeric(args[2]))

And here is what invoking it from the command line looks like

> Rscript myScript.R 5 100
[1]  98.46435 100.04626  99.44937  98.52910 100.78853

---

Edit:

Not that I'd recommend it, but ... using a combination of source() and sink(), you could get Rscript to produce an .Rout file like that produced by R CMD BATCH. One way would be to create a little R script -- call it RscriptEcho.R -- which you call directly with Rscript. It might look like this:

## RscriptEcho.R
args <- commandArgs(TRUE)
srcFile <- args[1]
outFile <- paste0(make.names(date()), ".Rout")
args <- args[-1]

sink(outFile, split = TRUE)
source(srcFile, echo = TRUE)

To execute your actual script, you would then do:

Rscript RscriptEcho.R myScript.R 5 100
[1]  98.46435 100.04626  99.44937  98.52910 100.78853

which will execute myScript.R with the supplied arguments and sink interleaved input, output, and messages to a uniquely named .Rout.

Edit2:
You can run Rscript verbosely and place the verbose output in a file.

Rscript --verbose myScript.R 5 100 > myScript.Rout