conmat-partial-preds

The goal of conmat-partial-preds is to generate partial dependence plots of the terms used in conmat.

Eventually these might make their way into conmat, as a way for users to understand and reason about these individual terms from conmat.

How to reproduce

Step 1: install capsule

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

capsule is an R package that provides an inversion around renv. It doesn't mean you need to setup a specific activate script, and in general I've found it slightly nicer to work with than renv.

Step 2: Reproduce the libraries used

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.

Step 3: Run the target workflow

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.

Step 4: Add new dependencies into “packages.R”?

Run:

capsule::recreate("packages.R")

Step 4: issues with recreate

If you get some weird installation error that looks like a compiler error for a package, I've found that I just need to install that given package locally...not a great fix, and definitely not smooth, but it seems to work.

Step 5 - ?

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

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

And the paper will be recreated.

Alternative installation instructions

1. Ensure you have all packages installed in packages.R.
2. Run targets::tar_make() to run the pipeline