Add command line arguments (R)

Copyright: Tiffany Timbers, 2023

Introduction to this repository

This is a template repository to act as a practice playground to get experience writing scripts with command line arguments.

Currently the src/count_classes.R script only works on the cancer_train.csv data set in the data directory. And it only writes the results as a csv file to the results/cancer directory. It must also be run from the root of the project to work.

You can test that the script works by running the following from the root of the project's directory:

Rscript src/count_classes.R

Exercise

Your task is to use the R package docopt to add command line arguments so that other data files can be passed to it, and so that the results can be written to other directories.

To help get you started, take a look at the docopt docs for arguments: https://github.com/docopt/docopt.R#usage.

Below, we also provide you an example of an R script that uses docopt so that it can be run at the command line to print the sum of two numbers.

"This script calculates the sum of two numbers.

Usage: sum.R <num1> <num2>
" -> doc


library(tidyverse)
library(docopt)

opt <- docopt(doc)

main <- function(num1, num2) {
  
  sum <- as.numeric(num1) + as.numeric(num2)
  paste0("The sum of ", num1, " and ", num2, " is ", sum) |> 
    print()
}

main(opt$num1, opt$num2)

To run this script from the terminal, you would navigate to the directory containing sum.R and run:

Rscript sum.R 5 7

This will lead to the script running using 5 as the value for the num1 argument, and 7 as the value for the num2 argument.
And the result being printed to the terminal:

The sum of 5 and 7 is 12

Optional/advanced exercise:

When you get the src/count_classes.R script working using positional command line arguments (as in the example above), try to improve it further by naming the arguments (we call this adding command line "options"). The docopt docs for this are here: https://github.com/docopt/docopt.R#usage

License

Add command line arguments (R) exercise contained herein are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License. See the license file for more information. If re-using/re-mixing please provide attribution and link to this webpage. The software code contained within this repository is licensed under the MIT license. See the license file for more information.