epiparameter v0.2.0

new-release
Author

The Epiverse-TRACE development team

Published

July 10, 2024

We are very excited to announce the release of a new epiparameter version v0.2.0. Here is an automatically generated summary of the changes in this version.

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.

New features

  • 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.

Breaking changes

  • 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).

Bug fixes

  • DOI and PMID are lowercase throughout the package to resolve issues with older versions of R (see issue #301) (#317).

Deprecated and defunct

  • None

Acknowledgements

@Bisaloo @CarmenTamayo @DxChen0126 @adamkucharski @chartgerink @chloerice48 @cm401 @jamesmbaazam @jlessler @joshwlambert @papsti @prabasaj @sbfnk @wzmli

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Citation

BibTeX citation:
@online{epiverse-trace_development_team2024,
  author = {Epiverse-TRACE development team, The},
  title = {Epiparameter V0.2.0},
  date = {2024-07-22},
  url = {https://epiverse-trace.github.io/posts/epiparameter_v0.2.0/},
  langid = {en}
}
For attribution, please cite this work as:
Epiverse-TRACE development team, The. 2024. “Epiparameter V0.2.0.” July 22, 2024. https://epiverse-trace.github.io/posts/epiparameter_v0.2.0/.