Update README, extend meta analysis, extend tests#34
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Pull request overview
This PR updates project documentation and analysis tooling, and extends the test suite around dataset handling and GG-identifiability utilities.
Changes:
- Expands README overview and adds new figures for dataset coverage/grouping.
- Extends
analysis/run_meta_analysis.Rto use model weights for selecting the “best” Stan distribution and to generate LaTeX tables. - Adds/extends testthat coverage for dataset objects,
should_attempt_gg(), andmake_stan_init_fn().
Reviewed changes
Copilot reviewed 8 out of 10 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-utils.R | Adds tests for make_stan_init_fn() output structure and initialization values. |
| tests/testthat/test-should-attempt-gg.R | New test file covering should_attempt_gg() behavior, thresholds, messaging, and NA handling. |
| tests/testthat/test-datasets.R | Broadens smoke tests to all built-in datasets and refactors helper logic. |
| man/figures/pathogen_grouping.png | Adds a new figure referenced by the README. |
| analysis/run_meta_analysis.R | Uses model weights to pick best Stan model for tau reporting; generates LaTeX tables including dataset composition. |
| README.md | Adds expanded package overview and embeds dataset coverage figures. |
| R/table_utils.R | Adjusts LaTeX table column width to accommodate wider content. |
| R/ploting_utils.R | Adds shared simulation-figure builder and two exported plotting functions (main + sensitivity). |
| .Rbuildignore | Excludes analysis/ from package builds. |
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Pull request overview
Copilot reviewed 11 out of 13 changed files in this pull request and generated 2 comments.
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