optparse Command Line Option Parsing

In optparse: Command Line Option Parser

library("knitr")
Rscript_executable <- paste(shQuote(file.path(R.home("bin"), "Rscript")), "--vanilla")
opts_knit$set(root.dir = system.file("exec", package = "optparse"))
opts_chunk$set(comment = NA, echo = FALSE)
list_file_command <- "ls"
chmod_command <- "chmod ug+x display_file.R example.R"
path_command <- "export PATH=\\$PATH:\\$(pwd)"
run_command <- function(string) suppressWarnings(cat(system(string, intern = TRUE), sep = "\n"))

optparse is a command line option parser inspired by Python's "optparse" library. Use this with Rscript to write "#!"-shebang scripts that accept short and long flags/options, generate a usage statement, and set default values for options that are not specified on the command line.

In our working directory we have two example R scripts, named "example.R" and "display_file.R" illustrating the use of the optparse package.

r paste("bash$",list_file_command)

run_command(sprintf("%s", list_file_command))
command <- "display_file.R example.R" # to show file

In order for a *nix system to recognize a "#!"-shebang line you need to mark the file executable with the chmod command, it also helps to add the directory containing your Rscripts to your path:

r paste("bash$",chmod_command)

r paste("bash$",path_command)

Here is what example.R contains:

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))

command <- "example.R --help" # same as system("Rscript example.R -h")

By default optparse will generate a help message if it encounters --help or -h on the command line. Note how %default in the example program was replaced by the actual default values in the help statement that optparse generated.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "example.R" # rely only on defaults

If you specify default values when creating your OptionParser then optparse will use them as expected.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "example.R --mean=10 --sd=10 --count=3"

Or you can specify your own values.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "example.R --quiet -c 4 --generator=\"runif\""

If you remember from the example program that --quietly had action="store_false" and dest="verbose". This means that --quietly is a switch that turns the verbose option from its default value of TRUE to FALSE. Note how the verbose and quietly options store their value in the exact same variable.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "example.R --silent -m 5"

If you specify an illegal flag then optparse will throw an error.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "example.R -c 100 -c 2 -c 1000 -c 7"

If you specify the same option multiple times then optparse will use the value of the last option specified.

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))

optparse can also recognize positional arguments if parse_args is given the option positional_arguments = c(min_pa, max_pa) where min_pa is the minimum and max_pa is the maximum number of supported positional arguments. (A single numeric corresponds to min_pa == max_pa, TRUE is equivalent to c(0, Inf), and FALSE, the default, is equivalent to 0.) Below we give an example program display_file.R, which is a program that prints out the contents of a single file (the required positional argument, not an optional argument) and which accepts the normal help option as well as an option to add line numbers to the output. Note that the positional arguments need to be placed after the optional arguments.

command <- "display_file.R --help"

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "display_file.R --add_numbers display_file.R"

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "display_file.R non_existent_file.txt"

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))
command <- "display_file.R"

r paste("bash$",command)

run_command(sprintf("%s %s 2>&1", Rscript_executable, command))

optparse documentation built on April 17, 2026, 9:06 a.m.