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Read command line arguments passed to an R script

Source: R/general_bash_variables.R
bash_variables.Rd

Reads command line arguments passed to an R script executed via the command line (Rscript) and return the name and value of each argument as a tibble.

Usage

bash_variables()

Value

A tibble with two columns: "name" and "value", containing the parsed command line arguments. If no arguments are provided, an empty tibble is returned.

Details

To use bash_variables, include it in an R script and run the script with Rscript and command line arguments in the format variable=value. The function parses each argument and returns a tibble with columns "name" and "value". You can then access these values as needed.

Usage:

  1. Create an R script (e.g., script.R):

    library(ecokit)

    load_packages(stringr, dplyr, purrr, tibble)

    # read command line arguments
    args <- ecokit::bash_variables()

    # Access variables from the tibble
    cat("Input:", args$value[args$name == "input_file"], "\n")
    n_iterations <- as.numeric(args$value[args$name == "n_iterations"])
    cat("Iterations:", n_iterations, "\n")

  1. Run the script:

    Rscript script.R input_file=data.csv n_iterations=100

Output:

    Input: data.csv
    Iterations: 100

Argument Format:

  • Arguments must be variable=value (e.g., input_file=data.csv).

  • Variable names must be valid R names: start with a letter or underscore, followed by letters, numbers, or underscores (e.g., max_iter, _flag).

  • Values can be any string, including empty strings (e.g., config_file=).

  • Values are assigned as character strings; convert types in the script if needed (e.g., as.numeric(n_iterations) for numbers).

Valid Commands:

    # Assigns: `data_path = "/home/data"`, `output_dir = "results"`,
    # `n_threads = "8"`.
    Rscript script.R data_path=/home/data output_dir=results n_threads=8

    # Assigns: `debug = "TRUE"`, `config_file = ""`.
    Rscript script.R debug=TRUE config_file=

    # Assigns: `model_type = "linear"`.
    Rscript script.R model_type=linear

    # No arguments; prints message: "No command line arguments provided".
    Rscript script.R

Invalid Commands (cause errors):

    # Error: "Invalid argument format... got: input_file, data.csv".
    Rscript script.R input_file data.csv

    # Error: "Invalid argument format... got: 1st_model=linear".
    Rscript script.R 1st_model=linear

    # Error: "Invalid argument format... got: input file=data.csv"
    Rscript script.R input file=data.csv

    # Error: "Variable names cannot be empty".
    Rscript script.R =data.csv

Notes:

  • The returned tibble contains the parsed arguments; you can convert values to other types as needed (e.g., as.numeric(args$value[args$name == "n_iterations"])).

Author

Ahmed El-Gabbas