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superspreading (development version)

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