Changes in version 1.1.4 (2025-12-17)                  

Bug fixes

  - Added negative_si option to create_config to allow ancestries with
    negative serial intervals to be immediately discarded.
  - Removed C++11 SystemRequirements specification (R 4.0+ defaults to
    C++11)

                 Changes in version 1.1.3 (2022-05-23)                  

Bug fixes

  - Email addresses fixed
  - Adegenet added to Suggests

                 Changes in version 1.1.2 (2021-02-09)                  

New features

  - Custom likelihoods now support local likelihood calculations via the
    optional i argument; this will speed up likelihood calculations by
    avoiding global calculations where these are unnecessary

Bug fixes

  - Random index shuffling in cpp_move_swap_cases to ensure correct
    mixing
  - Negative serial intervals now allowed in can_be_ances
  - ID labels fix in plotting functions

                 Changes in version 1.1.1 (2020-02-07)                  

Bug fixes

  - Fixed uninitialized variable use
  - Updated email addresses

                 Changes in version 1.1.0 (2019-06-13)                  

Bug fixes

  - The genetic likelihood of the original outbreaker paper was found to
    contain a minor mistake in accounting for unobserved generations of
    infection. As of June 7th 2019, outbreaker2 will use the correct
    genetic likelihood published here.

New features

  - outbreaker2 now accepts epicontacts objects for contact data
  - Contact tracing data can be directed or not by toggling ctd_directed
  - Cyclical consensus trees can now be avoided by using method =
    'decyle' in summary.outbreaker_chains
  - Added support for case-labelling in plot.outbreaker_chains
  - Added progress bar

                 Changes in version 1.0.1 (2018-03-06)                  

Minor bug fixes

  - Fixed convolution operator to keep values in log space with high
    kappa (thanks to @gtonkinhill)
  - C++ garbage collection fix

                        Changes in version 1.0.0                        

First version of outbreaker2!

  - This package re-implements and generalises the package outbreaker

  - It provides various functions to process input data, specify
    settings of the method, and even specify custom priors, likelihoods,
    or movement functions.

  - Outputs of the main function outbreaker have a dedicated class
    extending the regular data.frame, with print, summary and plot
    methods.

  - Its engine is written in C++, interfaced via Rcpp.

  - Its C++ API is accessible via the function get_cpp_api().

  - Functionalities are documented in 4 vignettes.