I'm experimenting with project structures for my current research. I used to use two distinct projects for the same research:
- One project (A) for the actual analyses, manuscript, data, etc.
- Another project (B) built as an R package for ad-hoc helper functions used in project A.
I've recently read about research compendiums, which seem to be a better alternative to keep everything related to the same research in one place.
I've a few questions regarding non-standard directory/file names and renv/DESCRIPTION's imports.
1:
My project has a scripts/ (for analyses) and data/ (for raw and processed data sets) directories. data/ contains .parquet files (locally) and a README.md (to keep the project structure on GitHub since I don't commit data to the GitHub repo).
This makes R CMD Check unhappy, either because of unexpected directory names (e.g. scripts) or unallowed file formats in data/.
Is there any recommended way to handle this? E.g., should I simply ignore CMD check warnings in this case? Or should I put the data sets in a custom directory, e.g. _data/, which will only generate a note as opposed to a warning? Or maybe put every non-standard directories/files below inst/?
2:
I use the DESCRIPTION Imports field to specify the required packages both for the analyses and helper functions. Some of these packages are only required to run the analyses or render the manuscript. Having packages not used in files below R/ also generates a R CMD Check note which I should probably just ignore.
But out of curiosity, is it preferable to use Imports only for packages helper functions depend on, and renv for the rest? Or keep everything in Imports and use renv on top of it?
Note that I'll most likely rely on devtools::load_all() rather than install and load the project as an actual package to use helper functions.