outbreaker2 1.1.4 (2022-12-16)

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)

outbreaker2 1.1.3 (2022-05-18)

Bug fixes

• Email addresses fixed
• Adegenet added to Suggests

outbreaker2 1.1.2 (2021-01-25)

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

outbreaker2 1.1.1 (2020-01-31)

Bug fixes

• Fixed uninitialized variable use
• Updated email addresses

outbreaker2 1.1.0 (2019-06-06)

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

outbreaker2 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

outbreaker2 1.0.0 (2017-11-24)

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.