superspreading 0.4.0
CRAN release: 2025-07-15
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 ofprobability_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 inproportion_transmission()
has been renamed toprop_transmission
(#130).
Minor changes
An
.aspell/
folder is added to the package includingdefaults.R
andsuperspreading.rds
to supply a wordlist to the CRAN spell checking to avoid quoting names in theDESCRIPTION
(#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 Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the Tidyverse style guide (#131, #134).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 toauto
now the package is hosted on CRAN (#118).
superspreading 0.3.0
CRAN release: 2025-01-27
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. Theproportion_transmission()
has a newmethod
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 addsoutbreak_time
andgeneration_time
arguments toprobability_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 inprobability_contain()
has been renamedsimulate
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 ofbookdown::html_vignette2
andas_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 renamedget_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
andk
) 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).
superspreading 0.2.0
Second minor release of superspreading. This release enhances functions added in v0.1.0 and adds two new exported functions, and two new vignettes.
New features
- A new function (
calc_network_R()
) to estimate the reproduction number for heterogeneous networks and a vignette outlining use cases for the function from existing epidemiological literature is added (#71). -
probability_epidemic()
andprobability_extinct()
now have individual-level and population-level control in a joint framework (#70). -
proportion_*()
functions can now return proportion columns of the output<data.frame>
asnumeric
when the new argumentformat_prop
is set toFALSE
(#72). - A new design principles vignette to document package development is added (#68).
- Added a helper function (
ic_tbl()
) to improve model comparison tables (#65). -
probability_*()
functions now accept dynamic dots ({rlang} is added as a dependency) (#82).
Breaking changes
-
ind_control
andpop_control
arguments replacecontrol
andcontrol_type
arguments inprobability_contain()
; and the argument default fornum_init_infect
is removed (#70). - Changed
epidist
argument tooffspring_dist
to follow Epiverse style (affects several functions) (#64). - Argument in
proportion_transmission()
has been renamed fromsim
tosimulate
(#81).
Bug fixes
- None to {superspreading} functions.
- Update {epiparameter} use in vignette and tests (#62).
superspreading 0.1.0
Initial release of superspreading, an R package to estimate individual-level variation in disease transmission and provide summary metrics for superspreading events.
New features
- Offspring distributions, not available in base R, to fit to transmission data.
- Functions to calculate the probability an infectious disease will cause an epidemic, go extinct or be contained.
- Summary metric functions to calculate proportion of cases that cause a certain proportion of secondary transmission, as well as which proportion of cases are within clusters of a certain size.
- Three vignettes, including: an introduction to the package, estimating individual-level transmission from data, and the effect of superspreading on epidemic risk.
- Unit tests and documentation files.
- Continuous integration workflows for R package checks, rendering the README.md, calculating test coverage, and deploying the pkgdown website.