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| 1 | +--- |
| 2 | +title: "superspreading v0.4.0" |
| 3 | +author: |
| 4 | + - name: "The Epiverse-TRACE development team" |
| 5 | +date: "2025-07-16" |
| 6 | +categories: [new-release] |
| 7 | +code-link: true |
| 8 | +--- |
| 9 | + |
| 10 | +<!-- markdownlint-disable-next-line --> |
| 11 | +We are very excited to announce the release of a new [superspreading](https://epiverse-trace.github.io/superspreading) version v0.4.0. |
| 12 | +Here is an automatically generated summary of the changes in this version. |
| 13 | + |
| 14 | +```{r} |
| 15 | +library(superspreading) |
| 16 | +``` |
| 17 | + |
| 18 | +The fourth minor release of the _superspreading_ package contains new functionality, a new vignette and various minor improvements to documentation. |
| 19 | + |
| 20 | +With this release the development status of the package has been updated from _experimental_ to _stable_. |
| 21 | + |
| 22 | +## New features |
| 23 | + |
| 24 | +* 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)](https://doi.org/10.1038/nature02104) (#124, #133). |
| 25 | + |
| 26 | +* 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)](https://doi.org/10.1038/nature02104) as well as a figure using the multiple introductions extension (#124, #133). |
| 27 | + |
| 28 | +* Alt-text has been added to all plots across all vignettes (#129). |
| 29 | + |
| 30 | +## Breaking changes |
| 31 | + |
| 32 | +* The `percent_transmission` argument in `proportion_transmission()` has been renamed to `prop_transmission` (#130). |
| 33 | + |
| 34 | +## Minor changes |
| 35 | + |
| 36 | +* 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). |
| 37 | + |
| 38 | +* 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 Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the [Tidyverse style guide](https://style.tidyverse.org/documentation.html) (#131, #134). |
| 39 | + |
| 40 | +* Internal code style has been updated to adhere to current best practice (#125). |
| 41 | + |
| 42 | +* 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). |
| 43 | + |
| 44 | +* The {pkgdown} `development: mode` has been set to `auto` now the package is hosted on CRAN (#118). |
| 45 | + |
| 46 | +## Bug fixes |
| 47 | + |
| 48 | +* None |
| 49 | + |
| 50 | +## Deprecated and defunct |
| 51 | + |
| 52 | +* None |
| 53 | + |
| 54 | +## Acknowledgements |
| 55 | + |
| 56 | +[@chartgerink](https://github.com/chartgerink) [@joshwlambert](https://github.com/joshwlambert) |
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