superspreading v0.3.0

We are very excited to announce the release of a new superspreading version v0.3.0. This is the first version of superspreading 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.

The third minor release of the superspreading package contains enhancements to several functions and a new vignette.

We are also pleased to welcome Dillon Adam (@dcadam) as a new package author for his contributions towards this version.

New features

• The proportion_transmission() function has been expanded to incorporate a new method. The new method calculates the proportion of transmission from X% the most infectious individuals, corresponding to the Lloyd-Smith et al. (2005) calculation. The proportion_transmission() has a new method argument to toggle between the two calculations (@dcadam, #99).
• A new vignette explaining the methods in the proportion_transmission() function (#101).
• {bpmodels} is removed as a package dependency and a branching process simulation function, modified from bpmodels::chain_sim(), is added to the {superspreading} package (#103). @sbfnk is added as copyright holder and @jamesmbaazam as a contributor.
• probability_contain() is enhanced to enable to probability of containment within a certain amount of time since the outbreak started. This adds outbreak_time and generation_time arguments to probability_contain(). This addition is backwards compatible as by default the time is unlimited, outbreak_time = Inf, and no generation time is required.

Breaking changes

• The stochastic argument in probability_contain() has been renamed simulate to be consistent with other functions (#103).

Minor changes

• The proportions output of proportion_*() functions are now formatted to significant figures rather than rounding to prevent small values being rounded to zero (#102).
• Improve input checking, error messages and edge case handling for functions (#102).
• Vignettes now use rmarkdown::html_vignette instead of bookdown::html_vignette2 and as_is: true has been removed due to changes to {pkgdown} in v2.1.0. {bookdown} has been removed as a suggested package and code folding is removed from vignettes. KaTeX headers have been added to _pkgdown.yml for correct math rendering (#104 & #109).
• The get_epidist_params() internal function has been renamed get_epiparameter_params() since {epiparameter} renamed the <epidist> class to <epiparameter> (#100).
• Internal constants have been added to the package and used by functions (#111).
• Checking if the user specifies individual parameters (R and k) or provides an <epiparameter> object is now in .check_input_params() (#111).

Bug fixes

• None to {superspreading} functions.
• Update {epiparameter} use in vignette and tests (#106).

Deprecated and defunct

• None

Acknowledgements

@avallecam @Bisaloo @chartgerink @dcadam @joshwlambert