outbreaker2 1.1.2 (2021-01-25) Unreleased

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) 2020-02-07

Bug fixes

  • Fixed uninitialized variable use
  • Updated email addresses

outbreaker2 1.1.0 (2019-06-06) 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

outbreaker2 1.0.1 (2018-03-06) 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) Unreleased

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.