superspreading v0.4.0 – Epiverse-TRACE: tools for outbreak analytics

We are very excited to announce the release of a new superspreading version v0.4.0. Here is an automatically generated summary of the changes in this version.

library(superspreading)

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 Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the Tidyverse style guide (#131, #134).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

Acknowledgements

@chartgerink @joshwlambert

Reuse

CC BY 4.0

Citation

BibTeX citation:

@online{epiverse-trace_development_team2025,
  author = {Epiverse-TRACE development team, The},
  title = {Superspreading V0.4.0},
  date = {2025-07-16},
  url = {https://epiverse-trace.github.io/posts/superspreading_v0.4.0/},
  langid = {en}
}

For attribution, please cite this work as:

Epiverse-TRACE development team, The. 2025. “Superspreading V0.4.0.” July 16, 2025. https://epiverse-trace.github.io/posts/superspreading_v0.4.0/.