Dev #207
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Dev #207
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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`
…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`
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