getopt

getopt is an R package designed to be used with Rscript to write “#!”-shebang scripts that accept short and long flags/options. Many users will prefer using instead the package optparse which adds extra features (automatically generated help option and usage, support for default values, basic positional argument support).

To install the last version released on CRAN use the following command:

install.packages("getopt")

To install the development version use the following command:

install.packages("remotes")
remotes:install_github("trevorld/r-getopt")

example

An example Rscript using getopt:

#!/path/to/Rscript
library('getopt')
# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
spec = matrix(c(
  'verbose', 'v', 2, "integer",
  'help'   , 'h', 0, "logical",
  'count'  , 'c', 1, "integer",
  'mean'   , 'm', 1, "double",
  'sd'     , 's', 1, "double"
), byrow=TRUE, ncol=4)
opt = getopt(spec)

# if help was asked for print a friendly message 
# and exit with a non-zero error code
if ( !is.null(opt$help) ) {
  cat(getopt(spec, usage=TRUE))
  q(status=1)
}

# set some reasonable defaults for the options that are needed,
# but were not specified.
if ( is.null(opt$mean    ) ) { opt$mean    = 0     }
if ( is.null(opt$sd      ) ) { opt$sd      = 1     }
if ( is.null(opt$count   ) ) { opt$count   = 10    }
if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }

# print some progress messages to stderr, if requested.
if ( opt$verbose ) { write("writing...",stderr()) }

# do some operation based on user input.
cat(rnorm(opt$count,mean=opt$mean,sd=opt$sd),sep="\n")

# signal success and exit.
# q(status=0)

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