Including arguments in R CMD BATCH mode

August 16, 2007
By

(This article was first published on Quantitative Ecology, and kindly contributed to R-bloggers)

When you have multiple computers or processors at your disposal and wish to run the same script with different arguments, use the following at the command line (here described for Linux; remove the linebreak, it is just there for display purposes):

$ R CMD BATCH --no-save --no-restore '--args a=1 b=c(2,5,6)'
test.R test.out &

Where test.R is the R script file you wish to run and test.out is a text file to include the screen output of the R terminal. A key point here is that each argument must have no spaces because --args is space delimited.

To include the variables listed in --args, adapt the following code from test.R:

##First read in the arguments listed at the command line
args=(commandArgs(TRUE))

##args is now a list of character vectors
## First check to see if arguments are passed.
## Then cycle through each element of the list and evaluate the expressions.
if(length(args)==0){
print("No arguments supplied.")
##supply default values
a = 1
b = c(1,1,1)
}else{
for(i in 1:length(args)){
eval(parse(text=args[[i]]))
}
}
print(a*2)
print(b*3)

This produces the following in test.out:

> print(a*2)
[1] 2
> print(b*3)
[1] 6 15 18

To leave a comment for the author, please follow the link and comment on his blog: Quantitative Ecology.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.