(To be submitted to the R Journal)

Use targets and capsule to recreate the paper.

• targets is the workflow system that ensures the steps required to complete the paper are completed in the right order. This is used as there is a computation (fitting many GAM models) that takes about 2-3 hours.
• capsule locks in the R package versions, including where they were downloaded from (github or CRAN, for example), so that these can be locked in. Under the hood it uses Rstudio's renv R package.

There are three steps to reproduce the paper

install.packages(
   "capsule", 
   repos = c(mm = "https://milesmcbain.r-universe.dev", getOption("repos")))

capsule::reproduce_lib()

This recreates all of the R packages used in the analysis on your computer. Importantly, this will not change where your existing R packages are installed. It is just for this repository. So no need to be concerned about this impacting other analyses you run.

capsule::run(targets::tar_make())

This runs our targets workflow using the R packages specified.

This will check if the targets are written, and if they aren't, it will re-run the necessary ones. In this case, the targets are stored in the _targets/objects folder, so the paper should just be created - it will be in paper/brolgar-paper.html or paper/brolgar-paper.pdf.

Make some changes to the paper and want to see them? Run the capsule again:

capsule::run(targets::tar_make())

And the paper will be recreated.