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Dev version #186
Dev version #186
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- use same ylim in foi plots for better readability - add environment cleanup at the end of each example
- use data simulation functionalities of the package to simulate the datasets in `foi_models.Rmd` examples - use same chunk structure in modelling to validate results - overall cleanup of the vignette
- Replace `prob_infected.stan` by two separate files for each type of model - Slight change to parameter order in `prob_infected_calculate`
…ation - Change how `stan_data` is constructed depending on type of model - Specify default behavior by type of model
- Use `age` for age-varying models and `years` in time-varying models in - `get_foi_central_estimates` - `plot_foi` - `plot_rhats`
- Update `R/stanmodels.R`
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #186 +/- ##
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- Coverage 70.07% 58.11% -11.96%
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Files 10 12 +2
Lines 1965 2488 +523
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+ Hits 1377 1446 +69
- Misses 588 1042 +454 ☔ View full report in Codecov by Sentry. |
…th the age-varying probs
- Set different init functions for log and no-log models
- Change `tsur` to `survey_year`
- Set defaults in the log and regular scale for sigma statistics - Use Cauchy distribution for sigma prior in regular scale - Use normal distribution for sigma prior in log scale
Current available options are: - `'constant'` - `'time'` - `'age'`
Add examples for: - `fit_seromodel` - `get_foi_index` - `plot_serosurvey`
NEWS.md
What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
What is the current behavior? (You can also link to an open issue here)
What is the new behavior (if this is a feature change)?
Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
Other information: