Merge dev into main #127
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Merge dev into main #127
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This commit changes the removed preloaded dataset `serodata` for the identical `chagas2012`.
…ule. This change is meant to simplify `fit_seromodel()`. This commit also changes the name of the stanfit object in the output of `fit_seromodel()` from `fit` to `seromodel_fit`.
… .RDS and updates test_visualization accordingly
* Enabling CMD check when doing pull request on `dev` * Removed tidyverse dependency
* refac: `fit_seromodel` returns a stanfit object
`fit_seromodel` returns a stanfit object now, which induces changes all across the pachage
- `seromodel_object$seromodel_fit -> seromodel_object`:
* `get_foi_central_estimates`
* `extract_seromodel_summary`
* `plot_seroprev_fitted`
* `plot_foi`
* `plot_rhats`
* `plot_seromodel`
* `get_table_rhats`
- add `serodata` as input:
* `get_foi_central_estimates`
* `extract_seromodel_summary`
* `plot_seroprev_fitted`
* `plot_seromodel`
* `plot_rhats`
* `plot_foi`
* `get_table_rhats`
- use of `exposure_years` (this suggest adding a function for this purpose):
* `get_foi_central_estimates`
* `get_table_rhats`
- minor corrections:
* `plot_seromodel` -> correction to exception
* tests(refac): re-generate .RDS files used in tests
* tests(refac): update tests according to 7be19f9
- change `model_object$seromodel_fit` to `model_object`
- add `serodata` as input where needed
- minor syntax changes to test_issue_47.R
* fix examples
Fix examples of functions across the package in accordance to the
new output of `fit_seromodel`.
Updated examples:
- `get_table_rhats`
- `get_foi_central_estimates`
- `get_prev_expanded`
- `extract_seromodel_summary`
- `plot_seroprev_fitted`
- `plot_foi`
- `plot_rhats`
- `plot_seromodel`
- `plot_info_table`
* refac: replace `get_exposure_ages` for `get_cohort_ages`
add `get_cohort_ages`: this function serves as replacement for
`get_exposure_ages` and also includes the information of
`exposure_years`, which was being used in some functions.
Affected functions:
- `fit_seromodel`
- `get_exposure_matrix`
- `get_table_rhats`
* test: add test for `get_cohort_ages` to the test_modelling.R
* refac: replace `serodata` for `cohort_ages` where needed
Affected functions:
- `get_table_rhats`
- `get_foi_central_estimates`
- `extract_seromodel_summary`
- `plot_foi`
- `plot_rhats`
- `plot_seromodel`
* doc: update documentation
use @inheritParams to simplify documentation
* add comment to exception in `fit_seromodel`
* refac: specify argument `parameter_name`
Explicitely specify argument `parameter_name = "logLikelihood"`
in `loo::loo`
* change condition to check whether sampling is done or not
* doc: update vignettes according to changes
* doc: update documentation and examples
parameter `seromodel_object` description correction in `get_foi_central_estimates`
add input check for `age_mean_f` in `serodata` in the following functions - `prepare_serodata` - `prepare_bin_data`
* Added argument matching in fit_seromodel() * Added allowed options to arg foi_model * Added input validation to prepare_serodata() * Fixed the check for required columns * Regenerated the docs --------- Co-authored-by: ntorresd <[email protected]>
To keep a reasonable repo size
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