Passing multiple arguments via command line in R

Question

I am trying to pass multiple file path arguments via command line to an Rscript which can then be processed using an arguments parser. Ultimately I would want something like

Answer 1

The way you describe command line options is different from the way that most people would expect them to be used. Normally, a command line option would take a single parameter, and parameters without a preceding option are passed as arguments. If an argument would take multiple items (like a list of files), I would suggest parsing the string using strsplit().

Here's an example using optparse:

library (optparse)
option_list <- list ( make_option (c("-f","--filelist"),default="blah.txt", 
                                   help="comma separated list of files (default %default)")
                     )

parser <-OptionParser(option_list=option_list)
arguments <- parse_args (parser, positional_arguments=TRUE)
opt <- arguments$options
args <- arguments$args

myfilelist <- strsplit(opt$filelist, ",")

print (myfilelist)
print (args)

Here are several example runs:

$ Rscript blah.r -h
Usage: blah.r [options]


Options:
    -f FILELIST, --filelist=FILELIST
        comma separated list of files (default blah.txt)

    -h, --help
        Show this help message and exit


$ Rscript blah.r -f hello.txt
[[1]]
[1] "hello.txt"

character(0)
$ Rscript blah.r -f hello.txt world.txt
[[1]]
[1] "hello.txt"

[1] "world.txt"
$ Rscript blah.r -f hello.txt,world.txt another_argument and_another
[[1]]
[1] "hello.txt" "world.txt"

[1] "another_argument" "and_another"
$ Rscript blah.r an_argument -f hello.txt,world.txt,blah another_argument and_another
[[1]]
[1] "hello.txt" "world.txt" "blah"     

[1] "an_argument"      "another_argument" "and_another"     

Note that for the strsplit, you can use a regular expression to determine the delimiter. I would suggest something like the following, which would let you use commas or colons to separate your list:

myfilelist <- strsplit (opt$filelist,"[,:]")