Make covariance recovery easier to maintain and test
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 50/100
- Issue type
- Refactor
- Clarity
- Clearly specified
- Activity status
- Quiet
- Domain
- documentation, testing
Research direction
Start by reading R/model_exchangeable_covariance.R and its tests to map which helpers read fitted-model results, match model terms, compute, and format output. Check issues #27–#32 first: the issue requires those correctness fixes to land before any file moves, and moves must stay separate from behavior changes. Done means helpers split into focused files with existing tests passing numerically unchanged, a new fitted-brms test matching an independent covariance calculation, and one internal reference for attr(data, "dyadMLM") linked from .github/CONTRIBUTING.md.
Written by the indexing model from the issue text.
Description
Make covariance recovery easier to maintain and test. Preserve public functions and arguments, numerical results, and statistical meaning.
Tasks
- Split covariance recovery into focused files. Move helpers from
R/model_exchangeable_covariance.Rinto files for reading fitted-model results, matching and checking model terms, calculations, and output. Run existing tests and preserve their numerical results. - Test fitted
glmmTMBandbrmsmodels. Keep the fittedglmmTMBtests and add a check using posterior draws from a fittedbrmsmodel. Check that model results are read correctly, coefficients and draws remain in order, and recovered covariance matches an independent calculation without dyadMLM's extraction helpers. Retain fast tests with supplied results. Record package versions and run expensive checks separately where needed. - Document what preparation stores with the data. Combine the existing preparation help and developer notes into one concise internal reference. Describe the fields, types, and object shapes in
attr(data, "dyadMLM"), including thegenerated_columnstable of generated columns. Explain what each preparation stage reads, writes, and guarantees. Link the reference from.github/CONTRIBUTING.md.
Address correctness fixes #27–#32 first, especially silent wrong results. Keep file moves separate from behavior changes. Help-page improvements remain in #26.
- Dominant language
- R
- Stars
- 1
- Forks
- 2
- Avg merge
- 9h 28m
- Merged PRs (30d)
- 21
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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