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() and probability_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> as numeric when the new argument format_prop is set to FALSE (#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 and pop_control arguments replace control and control_type arguments in probability_contain(); and the argument default for num_init_infect is removed (#70).
• Changed epidist argument to offspring_dist to follow Epiverse style (affects several functions) (#64).
• Argument in proportion_transmission() has been renamed from sim to simulate (#81).

Minor changes

• New package hex logo (#73).
• Updated continuous integration and package infrastructure (#67).
• Improved function documentation (#63).
• Optimisation now uses optim() by default (#82).
• Testing suite now uses snapshot testing for regression tests (#84).

Bug fixes

• None to {superspreading} functions.
• Update {epiparameter} use in vignette and tests (#62).

Deprecated and defunct

• None

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.

Breaking changes

• None

Bug fixes

• None

Deprecated and defunct

• None