outbreaker2 1.1.3 (2022-05-18)

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### Bug fixes

* Email addresses fixed

* Adegenet added to Suggests

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outbreaker2 1.1.2 (2021-01-25)

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### 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

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outbreaker2 1.1.1 (2020-01-31)

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### Bug fixes

* Fixed uninitialized variable use

* Updated email addresses

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outbreaker2 1.1.0 (2019-06-06)

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### Bug fixes

* The genetic likelihood of the [original *outbreaker* paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003457) 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](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006930).

### 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

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outbreaker2 1.0.1 (2018-03-06)

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### Minor bug fixes

* Fixed convolution operator to keep values in log space with high kappa (thanks to [@gtonkinhill](https://github.com/gtonkinhill/))

* C++ garbage collection fix

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outbreaker2 1.0.0 (2017-11-24)

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### First version of outbreaker2!

* This package re-implements and generalises the package

  [*outbreaker*](https://CRAN.R-project.org/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.