Final version of ddsynth_data and additons of more analysis.#32
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Pull request overview
This PR expands the analysis/reporting tooling around the incubation-period synthesis workflow, updates dataset definitions, and refines simulation-study reporting outputs.
Changes:
- Refactors the simulation study vignette summary table and adds a second summary table stratified by data availability.
- Adds new analysis scripts for (1) classical meta-analysis via
{meta}and (2) per-pathogen supplementary figure generation. - Updates the main Stan analysis runner (more pathogens/subgroups, GG/gamma heuristics, resume logic), plus supporting table/map utilities and dataset entries.
Reviewed changes
Copilot reviewed 8 out of 9 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
vignettes/simulation_study.Rmd |
Refactors performance summary table generation and adds a “By Data Availability” table. |
pathogen_grouping.html |
Adds a standalone HTML diagram asset. |
analysis/run_meta_analysis.R |
New script to run classical meta-analyses and generate forest plots + pooled summary outputs. |
analysis/make_supplementary_figures.R |
New script to generate multi-panel supplementary PDFs per pathogen from main Stan results. |
analysis/main_analysis.R |
Updates the main Stan fitting workflow (load_all usage, expanded registry/subgroups, heuristics, force rerun/skip controls, resume optimizations). |
R/table_utils.R |
Adds subgroup label and hides tau in tables when n_datasets < 5. |
R/map_utils.R |
Updates size legend labeling to show outbreak size rather than log-scale label. |
R/ddsynth_datasets.R |
Updates/extends several dataset entries (notably Cholera/COVID/Flu). |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Expanding frequency tables with rep(..., freq_count) can allocate very large vectors (e.g., large surveillance datasets) and is avoidable. Prefer computing weighted mean/variance directly from freq_value/freq_count (and from midpoints for interval-censored) to reduce memory/time and avoid potential OOM issues.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…into stan_model_changes
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Pull request overview
Copilot reviewed 8 out of 9 changed files in this pull request and generated 2 comments.
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