optparse (version 0.8)

optparse-package: Command line option parser

Description

Goal is to create an R package of a command line parser inspired by Python's optparse library.

Details

optparse is primarily intended to be used with Rscript. It facilitates writing #! shebang scripts that accept short and long flags/options. It can also be used from Rdirectly, but is probably less useful in this context.

See package vignette for a more detailed example.

Notes on naming convention in package: 1. An option is one of the shell-split input strings. 2. A flag is a type of option. a flag can be defined as having no argument (defined below), a required argument, or an optional argument. 3. An argument is a type of option, and is the value associated with a flag. 4. A long flag is a type of flag, and begins with the string --. If the long flag has an associated argument, it may be delimited from the long flag by either a trailing =, or may be the subsequent option. 5. A short flag is a type of flag, and begins with the string -. If a short flag has an associated argument, it is the subsequent option. short flags may be bundled together, sharing a single leading "-", but only the final short flag is able to have a corresponding argument.

References

Python's optparse library, which this package is based on, is described here: http://docs.python.org/library/optparse.html

See Also

getopt

Examples

#!/path/to/Rscript
        # specify our desired options in a list
        # by default ``OptionParser`` will automatically add an help option equivalent to 
        # ``make_option(c("-h", "--help"), action="store_true", default=FALSE, 
        #               help="Show this help message and exit")``
        option_list <- list( 
                make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
                    help="Print lots of output [default]"),
                make_option(c("-q", "--quietly"), action="store_false", 
                    dest="verbose", help="Print little output"),
                make_option(c("-c", "--count"), action="store", type="integer", default=10, 
                    help="Number of random normals to generate [default %default]"),
                make_option(c("-m", "--mean"), action="store", type="numeric", default=0,
                    help="Mean of random normals [default %default]"),
                make_option(c("-s", "--sd"), action="store", type="numeric", default=1,
                    help="Standard deviation of random normals [default %default]")
                )
                                                
        # get command line options, if not found set to specified defaults, 
        # and if help option encountered print help and exit
        opt <- parse_args(OptionParser(option_list))

        # print some progress messages to stderr if "quietly" wasn't requested
        if ( opt$verbose ) { write("writing...", stderr()) }

        # do some operations based on user input
        cat(paste(rnorm(opt$count, mean=opt$mean, sd=opt$sd), collapse="\n"))
        cat("\n")

    <testonly>if (require("RUnit")) {


            parser <- OptionParser( option_list = list( make_option(c("-q", "--quietly"), action="store_false", dest="verbose"),
                                                make_option("--verbose", action="store_true", dest="verbose", default=TRUE),
                                                make_option(c("-f", "--filename"), action="store", metavar="file")))
                                            
            # verbose should be false
            checkEquals(parse_args(parser, "-q"), list(verbose = FALSE, help = FALSE))
            checkException(checkEquals(parse_args(parser, "-q"), list(verbose = TRUE, help = FALSE)))
            print_help(parser)
        }</testonly>