commandArgs()

At present there is no official way to add arguments to R: commandArgs() 
is intended to let you retrieve the standard arguments.

This has been discussed for a long time, but there are problems with doing 
it consistently across platforms: for example Windows allows an extra 
argument, the name of a .RData file, to allow file-association to work.

What you can do reliably across platforms is to pass information in 
environment variables.  Something like

NRUNS=1000 R --vanilla < test.R > test.Rout   (Unix, sh)
Rterm NRUNS=100 --vanilla < test.R > test.Rout (Windows)

and have

nruns <- as.numeric(Sys.getenv("NRUNS"))

in the script test.R

Apologies for asking about this, but I don't quite understand how
this works after looking through the FAQ and the Help archives.

Let's say I want to pass "1000" as an argument to R.  I did the
following:

R CMD BATCH --1000 infile outfile

When I do print( commandArgs() ), I see

[1] ".../R.bin"         "--restore"
[3] "--save"            "--no-readline"
[5] "gui=none"          "--1000"

So commandArgs()[6] is the argument I want.  Does one then go on and
remove the "--" manually and cast this as numeric?  If so, what's the
usual way to do this?  Or am I not understanding this mechanism
properly?

There is no such mechanism at present.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595