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

Here's another way to process command line args, using R CMD BATCH. My approach, which builds on an earlier answer here, lets you specify arguments at the command line and, in your R script, give some or all of them default values.

Here's an R file, which I name test.R:

defaults <- list(a=1, b=c(1,1,1)) ## default values of any arguments we might pass

## parse each command arg, loading it into global environment
for (arg in commandArgs(TRUE))
  eval(parse(text=arg))

## if any variable named in defaults doesn't exist, then create it
## with value from defaults
for (nm in names(defaults))
  assign(nm, mget(nm, ifnotfound=list(defaults[[nm]]))[[1]])

print(a)
print(b)

At the command line, if I type

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

then within R we'll have a = 2 and b = c(2,5,6). But I could, say, omit b, and add in another argument c:

R CMD BATCH --no-save --no-restore '--args a=2 c="hello"' test.R

Then in R we'll have a = 2, b = c(1,1,1) (the default), and c = "hello".

Finally, for convenience we can wrap the R code in a function, as long as we're careful about the environment:

## defaults should be either NULL or a named list
parseCommandArgs <- function(defaults=NULL, envir=globalenv()) {
  for (arg in commandArgs(TRUE))
    eval(parse(text=arg), envir=envir)

  for (nm in names(defaults))
    assign(nm, mget(nm, ifnotfound=list(defaults[[nm]]), envir=envir)[[1]], pos=envir)
}

## example usage:
parseCommandArgs(list(a=1, b=c(1,1,1)))