epiparameter v0.3.0

We are very excited to announce the release of a new epiparameter version v0.3.0. Here is an automatically generated summary of the changes in this version.

The third minor release of the {epiparameter} R package contains a range of updates and improvements to the package. The principal aim of this release is to simplify, clarify and enhance the classes and class methods when working with epidemiological parameters in R.

The are a large number of breaking changes in this release, primarily functions and function arguments being renamed or restructured, see the Breaking changes section for an overview.

New features

• The library of epidemiological parameters has been updated to include 3 new Chikungunya parameter entries. The Mpox parameters previously missing from the Guzzetta et al. entry have been added (#346 & #374).
• A c() method has been added for <epiparameter> and <multi_epiparameter> objects (#368).
• An aggregate() method has been added for <multi_epiparameter> to enable consensus distributions to be built utilising the mixture distribution class from {distributional} (#388).
• Infrastructure has been added to the package to allow translations of messages/warnings/errors printed to the console. (@Bisaloo, #367).
• convert_summary_stats_to_params() can now convert from median and dispersion for a lognormal distribution (#378).
• The data_dictionary.json has been enhanced to improve validation of the library of epidemiological parameters (parameters.json) (#379).
• An interactive network showing all of the <epiparameter> S3 methods has been added to the design_principles.Rmd vignette (#383).
• The data_from_epireview.Rmd article has been improved and updated with new changes from {epireview} (@CarmenTamayo & @cm401 & @kellymccain28, #305 & #373).
• Parameter units have been added to every entry in the {epiparameter} library (parameters.json) and to the $metadata element in <epiparameter> objects. The create_metadata() function now has a units argument to construct metadata lists (#391).
• Improved database.Rmd vignette by adding a short citation to the reference column (@jamesmbaazam, #348).
• The family() method for <epiparameter> has been improved to allow access to distribution names for transformed (e.g. mixture and truncated distributions) and untransformed (e.g. gamma and lognormal) distributions with a new argument base_dist and a new internal function .distributional_family() (#398).
• as_epiparameter() can now work with the SARS parameters from {epireview} (#407).

Breaking changes

• The <epidist> class has been renamed <epiparameter> to avoid confusion with the similar R package {epidist} (#360).
• Many functions that used epidist in their names have been renamed to use epiparameter due to the renaming of the class (#360).
• The function signatures of epiparameter() and new_epiparameter() functions (previously epidist() and new_epidist()) have been updated to collapse the prob_dist, prob_dist_params, discretise and truncation arguments into prob_distribution, which accepts the output of create_prob_distribution() (#381).
• The epi_dist argument has been renamed epi_name. This is to clarify that {epiparameter} can work with epidemiological parameters that take a variety of forms (e.g. point estimates, ranges, probability distributions, etc.) (#390).
• The <vb_epidist> class and it’s methods have been removed from the package. It was not being used and was increasing the complexity and maintenance load of the package (#359).
• create_prob_dist() has been renamed to create_prob_distribution() (#381).
• validate_epiparameter() (previously validate_epidist()) has been renamed assert_epiparameter(), and test_epiparameter() has been added, with the aim to harmonise design with {contactmatrix} and the messages and errors have been improved (#366 & #402).
• The minimum version of R required by the package is now 4.1.0 due to the use of the base R pipe (|>) in dependencies, and the R-CMD-check workflow on GitHub actions now explicitly runs on the minimum version of R stated in the DESCRIPTION (#384 & #405).

Bug fixes

• Epidemiological parameter entries in the library stored with lognormal distributions, parameterised as median and dispersion are now converted to meanlog and sdlog correctly when creating an <epiparameter> (when auto_calc_params = TRUE) (#381).

Deprecated and defunct

• epidist_db() has been deprecated. It is replaced by epiparameter_db() (#360 & #399).

Acknowledgements

@Bisaloo @CarmenTamayo @adamkucharski @avallecam @chartgerink @jamesmbaazam @joshwlambert