Changelog

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

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.

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

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

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.

outbreaker2 1.1.2 (2021-01-25) Unreleased