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Dev version #186
Dev version #186
Commits on May 9, 2024
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doc: use chunks functionality in
use_cases.Rmd
examples- use same ylim in foi plots for better readability - add environment cleanup at the end of each example
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doc: replace
data(simdata_*)
by corresponding code to simulate data- 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
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Commits on May 10, 2024
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feat: add age-varying normal model
av_normal
- Replace `prob_infected.stan` by two separate files for each type of model - Slight change to parameter order in `prob_infected_calculate`
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feat: modify
fit_seromodel
to allow for age-varying model implement……ation - Change how `stan_data` is constructed depending on type of model - Specify default behavior by type of model
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fix: use years or ages in plots depending on the type of model
- Use `age` for age-varying models and `years` in time-varying models in - `get_foi_central_estimates` - `plot_foi` - `plot_rhats`
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feat: add age-varying normal model
av_normal
- Update `R/stanmodels.R`
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Commits on Jul 31, 2024
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#169 started to add in age-varying simulation but there's an error wi…
…th the age-varying probs
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#169 added master simulate function. Bug for sample_size_by_individua…
…l_age_random needs sorting
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#169 corrected probability_exact_time_varying function (which now doe…
…s not use an exposure matrix)
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fix(i169): correct age binning for data simulation function
- Correct tests accordingly - Avoids using `cut`
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#169 corrected mistake which meant (previously) age and time model se…
…ropositivities were the same
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doc: make sure old vignettes work as expected
(provisional) Manually change variable names to use visualization functions. This will be remove after the refactorization of the package.
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doc: syntax changes to 'simulating_serosurveys.Rmd'
- Use different names for foi data frames on each example - Minor text and syntax changes to improve vignette's aesthetics
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doc: add analytical solution line to seroprevalence plots in 'simulat…
…ing_serosurveys.Rmd'
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doc: changes to code chunks options
- Set theme to 'theme_bw()' - Set 'echo=FALSE' on plotting code chunks - Set 'fig.align="center"' on plotting code chunks
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Commits on Sep 9, 2024
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feat: add working version of
fit_seromodel
using functional specifi……cation of priors
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feat: introduce 'summarise_loo_estimate' to simplify 'summarise_serom…
…odel' This function allows to extact an specific loo estimate for model parameters like 'seroreversion_rate' or 'foi'. This introduce changes in: - 'summarise_seromodel' - 'plot_summary' - 'plot_seromodel'
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fix: replace validation function by
checkmate::assert_names()
- Remove two validation functions
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feat: modify R modules to allow log-scale model implementation
- Add `sf_cauchy()` to set sigma prior in tv log modules - Add `is_log_foi` parameter to `fit_seromodel` - Add corresponding defaults
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feat: set default behavior for sampling initialization
- Set different init functions for log and no-log models
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fix: simplify loaded datasets structure and update column NAMESPACE
- Change `tsur` to `survey_year`
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feat: enable sigma prior specification for all foi_models
- 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
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fix: add error whenever a not supported
model_type
is specifiedCurrent available options are: - `'constant'` - `'time'` - `'age'`
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doc: add some examples in functions' documentation
Add examples for: - `fit_seromodel` - `get_foi_index` - `plot_serosurvey`
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