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

Example script/template:

#!/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$add_argument("-c", "--count", type="integer", default=5, help="Number of random normals to generate [default %(default)s]", metavar="number")
	parser$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]")
	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")
	# Please note: you can add 'required = TRUE' for parameters that are required

	# Parse command line parameters
	args <- parser$parse_args()

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

# Print inputs only if cmnd-line parameters correct and verbose 'true' (in case of errors, use 'sterr()')
if (args$verbose) {
	write("You have used the following arguments:", stdout())
	write(paste("\t--count:  ", args$count), stdout())
	write("other parameters: ...", stdout())
	write("\nStart with analysis...\n", stdout())
}
# 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]