--- a +++ b/NEWS.md @@ -0,0 +1,96 @@ +outbreaker2 1.1.3 (2022-05-18) +================== + +### Bug fixes + +* Email addresses fixed +* Adegenet added to Suggests + + + +<br> +<br> + +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 + + + +<br> +<br> + +outbreaker2 1.1.1 (2020-01-31) +================== + +### Bug fixes + +* Fixed uninitialized variable use +* Updated email addresses + + + +<br> +<br> + +outbreaker2 1.1.0 (2019-06-06) +================== + +### 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 + + +<br> +<br> + +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](https://github.com/gtonkinhill/)) +* C++ garbage collection fix + + + +<br> +<br> + +outbreaker2 1.0.0 (2017-11-24) +================== + +### 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.