superspreading 0.4.0

The fourth minor release of the superspreading package contains new functionality, a new vignette and various minor improvements to documentation.

With this release the development status of the package has been updated from experimental to stable.

New features

• The probability_emergence() function has been added to calculate the probability that a pathogen introduced to humans can evolve and emerge to cause a sustained human-to-human outbreak, implementing and extending the framework of Antia et al. (2003) (#124, #133).

• A new vignette, emergence.Rmd, has been added that covers the functionality of probability_emergence() and reproduces the two figures from Antia et al. (2003) as well as a figure using the multiple introductions extension (#124, #133).

• Alt-text has been added to all plots across all vignettes (#129).

Breaking changes

• The percent_transmission argument in proportion_transmission() has been renamed to prop_transmission (#130).

Minor changes

• An .aspell/ folder is added to the package including defaults.R and superspreading.rds to supply a wordlist to the CRAN spell checking to avoid quoting names in the DESCRIPTION (#127).

• Package and function documentation has been updated. Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the Tidyverse style guide (#131, #134).

• Internal code style has been updated to adhere to current best practice (#125).

• The package lifecycle badge has been updated from experimental to stable. CRAN status, CRAN downloads, repo status and Zenodo DOI badges have been added to the README (#119, #132).

• The {pkgdown} development: mode has been set to auto now the package is hosted on CRAN (#118).

Bug fixes

• None

Deprecated and defunct

• None