Tooling

Here is an overview of all the tools used in this template - including some helpful information on how to apply them - making your R code both nicer and more robust 😉.

Managing R Installations

It's recommended to use rig - the R Installation Manager - for managing R installations.

Tools

This template uses the following tools:

• rig: R installation manager.
• renv: R project and dependency management.
• Air: R formatter and language server.
• Jarl: R linter.
• testthat: R testing suit.
• GitHub Actions: Used for running the above automatically.

Helpful Commands

• rig:
  • Install a specific R version, e.g. 4.6.1:

    rig add 4.6.1

  • Set a default R version, e.g. 4.6.1:

    rig default 4.6.1

• renv:
  • Restore an R environment:

    Rscript -e "renv::restore()"

    or

    renv::restore()

  • Snapshot an R environment:

    Rscript -e "renv::snapshot()"

    or

    renv::snapshot()

  • Install a package:

    Rscript -e "renv::install('pkg')"

    or

    renv::install("pkg")

  • Install a package from Bioconductor:

    Rscript -e "renv::install('bioc::pkg')"

    or

    renv::install("bioc::pkg")

• Air:
  • Format files:

    air format

  • Alternatively, setup air editor integration as described here.
  • Check if files are properly formatted:

    air format --check

• Jarl:
  • Lint with jarl:

    jarl check .

• testthat:
  • Test with testthat:

    Rscript -e "source('tests/testthat.R')"

• Run application:
  • CLI mode (example for this application):

    Rscript run.R -f data/characters.csv

  • Shiny mode (example for this application):

    Rscript run.R -s