flagr

Implements command-line flag parsing in R

Table of Contents

• About
• Installation
• Usage
  • Basic

About

Although it's fun to play with R in its REPL environment using RStudio or an interactive R session in your shell, sometimes its necessary to execute an R utility via the command line. flagr lets you write a job or script using R's strong statistical capabilities and invoke it using the command line.

This is useful if you want to specify environment configurations, model parameters, file locations, etc.

Installation

Unfortunately this package has not yet been submitted to CRAN. However, you can use devtools to install the package from GitHub:

library(devtools)
devtools::install_github("nicheinc/flagr")

Usage

Basic

test.R provides a minimal example of a script that might use flagr. Instead of sourcing the code, typical uses would load the library. For example, we might have a script like

library(flagr)

flagr <- flagr()

echo <- flagr$add_flag(
  name="echo",
  type="character",
  description="Value to echo",
  default="echo...echo...echo"
)

flagr$parse()

cat(paste0(echo, "\n"))

In a shell (pick your favorite), running the script would mean issuing

$ Rscript test.R --help

which will produce the usage message:

Usage of flagr:
-help (h) logical
    Show usage (default FALSE)
-echo character
    Value to echo (default echo...echo...echo)

Without asking for help, a typical run would look like

$ Rscript test.R 
echo...echo...echo
$

which prints the default value of the echo argument. You could also specify the value you want to get echoed back:

$ Rscript test.R --echo pickles
pickles
$

or

$ Rscript test.R -echo cherry pickles
cherry
 pickles
$
$ Rscript test.R -echo "cherry pickles"
cherry pickles
$

or

$ Rscript test.R -echo "${PATH}"
/home/nicheinc/go/bin:/usr/local/go/bin:/home/nicheinc/.local/bin:/home/nicheinc/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/nicheinc/bin

The first example illustrates basic usage in which we want the program to print exactly what we passed in to the --echo flag.

The second example shows how flagr supports single dash (-) flags as well as double dash flags (--). It also shows how flagr automatically vectorizes arguments that are separated by a space; printing the whole string cherry pickles on one line requires you to enclose it in quotes, otherwise the paste0(echo, "\n") will concatenate the vector echo=c("cherry", " pickles") with the new line character so that you get cherry\n pickles\n.

The last example shows how you can pass in variables you have defined in your shell.