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.
c() method has been added for <epiparameter> and <multi_epiparameter> objects.aggregate() method has been added for <multi_epiparameter> to enable consensus distributions to be built utilising the mixture distribution class from {distributional} (PR #388).convert_summary_stats_to_params() can now convert from median and dispersion for a lognormal distribution (PR #378).data_dictionary.json has been enhanced to improve validation of the library of epidemiological parameters (parameters.json) (PR #379).<epiparameter> S3 methods has been added to the design_principles.Rmd vignette (PR #383).data_from_epireview.Rmd article has been improved and updated with new changes from {epireview} (@CarmenTamayo & @cm401 & @kellymccain28, PR #305 & #373).parameters.json) and to the $metadata element in <epiparameter> objects. The create_metadata() function now has a units argument to construct metadata lists (PR #391).database.Rmd vignette by adding a short citation to the reference column (@jamesmbaazam, PR #348).<epidist> class has been renamed <epiparameter> to avoid confusion with the similar R package {epidist} (PR #360).epidist in their names have been renamed to use epiparameter due to the renaming of the class (PR #360).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() (PR #381).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.) (PR #390).<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 (PR #359).create_prob_dist() has been renamed to create_prob_distribution() (PR #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} (PR #366).|>) in dependencies (PR #384).<epiparameter> (when auto_calc_params = TRUE) (PR #381).epidist_db() has been deprecated. It is replaced by epiparameter_db().The second release of the {epiparameter} R package focuses on interoperability with the {epireview} R package. Several functions have been refactored and enhanced.
This release benefited from feedback from the participants of an EpiParameter Community workshop hosted by the World Health Organisation.
The as_epidist() S3 generic has been added to the package for the coercion of other R objects into <epidist> objects. The as_epidist.data.frame() method is added, as well as the internal functions is_epireview() which determines if a <data.frame> is from {epireview}, and epireview_to_epidist() performs the conversion (#298, #334 & #335)
The epireview_core_cols.rda data is added to the package. This is used to determine whether the input to as_epidist.data.frame() is a parameter table from {epireview} as these objects do not have a recognisable class attribute (#298).
A new website only vignette (i.e. article) data_from_epireview.Rmd is added that explains how to use as_epidist() with data from {epireview} (#298 & #335).
A new vignette database.Rmd is added to the package to provide a web interface to the {epiparameter} library of epidemiological parameters. Contributed by @sbfnk (#311).
The plotting method for <epidist> objects (plot.epidist()) has been improved to better differentiate continuous from discrete or discretised distributions (#315).
epidist_db(..., single_epidist = TRUE) now prioritises parameter entries that account for right truncation (#323).
create_epidist_prob_dist() (previously named create_prob_dist()) is now exported and enables more control of discretisation settings by allowing arguments to be passed to distcrete::distcrete() via ... (#324).
The <multi_epidist> print method (print.multi_epidist()) has been improved to provides object information in the print header, the first few elements of the list or all elements if list is short, and some extra links and advice in the print footer. The design of the print method follows the design pattern of {pillar} (#326).
<epidist> objects and functions that work with <epidist> objects now work with exponential distributions (#333).
The package now has an explicit data license: CC0 in the LICENSE file.
list_distributions() has been replaced by parameter_tbl() which enhances the printing by leveraging {pillar} (#321).
The <vb_epidist> plotting method (plot.vb_epidist()) has been removed from the package. This provided minimal functionality and was unnecessarily complicating the function signature of plot.epidist() (#315).
Initial release of the {epiparameter} R package. {epiparameter} provides:
A library of epidemiological parameters extracted from the literature for a range of diseases.
Functions and classes (with class methods) to work with epidemiological parameters and distributions.
sysdata.rda, as epiparameter::multi_epidist) or as internal data (inst/extdata/parameters.json).epidist_db() function loads epidemiological parameters from the library.convert_params_to_summary_stats() & convert_summary_stats_to_params(), and extract_param()).<epidist>. This class has S3 methods to aid users easily work with these data structures. These include printing, plotting, and distribution functions for PDF/PMF, CDF, random number generation and distribution quantiles. The <epidist> class has a constructor function, a validator function, accessors (get_*()), checkers (is_*()). There is also a <vb_epidist> S3 class for vector-borne parameters, and an internal <multi_epidist> class for improved printing of lists of <epidist> objects.list_distributions() is a helper function to provide information from a list of <epidist> objects in tabular form. calc_disc_dist_quantile() calculates the quantiles of a probability distribution based on the vector of probabilities and time data.epiparameter.Rmd), one as an tutorial on converting and extracting parameters (extract_convert.Rmd), one on the protocol used to collect entries for the library of epidemiological parameters (data_protocol.Rmd), a design vignette (design_principles.Rmd), and a supplementary vignette which quantifies the bias from using the parameter extraction (extract_param()) from {epiparameter} (extract-bias.Rmd).