Changes in version 0.3.0.9000                      

                 Changes in version 0.3.0 (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. 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

                        Changes in version 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

                        Changes in version 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