simulist v0.4.0

new-release
Author

The Epiverse-TRACE development team

Published

January 10, 2025

We are very excited to announce the release of a new simulist version v0.4.0. This is the first version of simulist to be on CRAN (the package can now be installed with install.packages()). Here is an automatically generated summary of the changes in this version.

A minor version release of simulist containing various minor improvements to the functions and documentation, as well as removing some triggers for warning users. There are also a few bug fixes and internal enhancements.

New features

External

  • Defaults have been added to all sim_*() arguments that previously did not have one. Allowing functions to be run without specifying any arguments (e.g. linelist <- sim_linelist()) (#149).
  • Documentation for sim_*() function arguments that accept either a function or an <epiparameter> object has been improved (#149).
  • sim_*() functions no longer warn if the user has not specified *_risk arguments and have set onset_to_* arguments to NULL (#149).
  • All vignettes now use rmarkdown::html_vignette for to correctly render the website and for maximum compatibility with {pkgdown} >= 2.1.0. This removes figure numbering and code folding (#153).

Internal

  • .add_hospitalisation() has been vectorised following .add_outcome() in PR #101 (#150).

Breaking changes

  • The function arguments infect_period and prob_infect have been renamed infectious_period and prob_infection (#143).
  • sim_*() functions now use NULL instead of NA to turn off processes (e.g. onset_to_death = NULL for no deaths) (#148).

Bug fixes

  • A new function, .sample_infect_period() is added that errors if the infectious period function generates a negative number (#142).
  • sim_linelist() no longer errors when hosp_death_risk is NULL and onset_to_death is parameterised as a delay distribution (#144).
  • .add_ct() generates the correct number of values and does not duplicate Ct values due to vector recycling (#158).
  • Update {epiparameter} usage (#159).

Deprecated and defunct

  • None

Acknowledgements

@avallecam @Bisaloo @joshwlambert @Karim-Mane @sbfnk

Reuse

Citation

BibTeX citation:
@online{epiverse-trace_development_team2025,
  author = {Epiverse-TRACE development team, The},
  title = {Simulist V0.4.0},
  date = {2025-01-10},
  url = {https://epiverse-trace.github.io/posts/simulist_v0.4.0/},
  langid = {en}
}
For attribution, please cite this work as:
Epiverse-TRACE development team, The. 2025. “Simulist V0.4.0.” January 10, 2025. https://epiverse-trace.github.io/posts/simulist_v0.4.0/.