Template for R scripts

R scripts

Please use the following example/template for R-scripts. Note:

• Please add a short description of the script's purpose after the #DOC-directive at the second line of the script.

• Then define constants

• Retrieve command line parameters as shown in example

• Now load functions (path may depend on command line parameters)

• Rest of your script

  #!/usr/bin/env Rscript DOC = "This script illustrates how R can parse arguments if called from the command line."

  Define your constants here

    #-- const1 = "first"   --#
    #-- const2 = "second"  --#
  

  Retrieve command line parameters

    suppressPackageStartupMessages(library("argparse"))
  
    # Create parser object
    parser <- ArgumentParser(description = DOC)
  
    parser$add_argument("-v", "--verbose", action="store_true", default=TRUE, help="Print extra output [default]")
    parser$add_argument("-q", "--quietly", action="store_false", dest="verbose", help="Print little output")
    parser$add_argument("-c", "--count", type="integer", default=5, help="Number of random normals to generate [default %(default)s]", metavar="number")
    parser$add_argument("--generator", default="rnorm", help = "Function to generate random deviates [default \"%(default)s\"]")
    parser$add_argument("--mean", default=0, type="double", help="Mean if generator == \"rnorm\" [default %(default)s]")
    parser$add_argument("--sd", default=1, type="double", metavar="standard deviation", help="Standard deviation if generator == \"rnorm\" [default %(default)s]")
    # Please note: you can add 'required = TRUE' for parameters that are required
  
    args <- parser$parse_args()
  

  Load your functions here

    #-- Example: source("main.functions.R") --#
  

  Print some progress messages to stderr if "quietly" wasn't requested

  if ( args$verbose ) { write("Writing some verbose output to standard error...\n", stderr()) }

  Do some operations based on user input

  if("rnorm" == args$generator) { cat(paste(rnorm(args$count, mean=args$mean, sd=args$sd), collapse="\n")) } else { cat(paste(do.call(args$generator, list(args$count)), collapse="\n")) } cat("\n")

If you'd save this script as demo.R, make it executable (chmod +x demo.R), running

./demo.R -h

will give the following result.

usage: ./demo.R [-h] [-v] [-q] [-c number] [--generator GENERATOR]
                [--mean MEAN] [--sd standard deviation]

This script illustrates how R can parse arguments if called from the command line.

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         Print extra output [default]
  -q, --quietly         Print little output
  -c number, --count number
                        Number of random normals to generate [default 5]
  --generator GENERATOR
                        Function to generate random deviates [default "rnorm"]
  --mean MEAN           Mean if generator == "rnorm" [default 0]
  --sd standard deviation
                        Standard deviation if generator == "rnorm" [default 1]