Related Issues (20)
- Port over model tests + add testing to package functions
- Add hospital admissions only mode functionality
- Make generation of data spines in post processing separate functions HOT 1
- Remove redundant `pkg::fun()` when `importFrom(pkg, fun)` already present in NAMESPACE
- Link to package functions in documentation
- Add diagnostic flag for the maximum rhat
- Avoid the `assign(param_names[i])` construct
- Clarify role of `get_stan_data` compared to data pre-processing functions
- Remove automatic directory mode setting unless strictly needed
- Make init generation function more generic
- Make the small added value for `log_conc` configurable
- Add mermaid diagram to `model_definition.md`
- Set up caching of `wwinference.Rmd` vignette in R-cmd-check
- Forward simulation spatially correlated unadjusted reproduction number
- Add testing for key functions HOT 1
- Stan spatial functions. HOT 14
- Updating package data in spatial-ww branch.
- Add an example of a pipeline with a config
- Consider constraining site-level R(t) deviations to sum to 0 HOT 1
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