Diff of /NEWS.md [000000] .. [dfe06d]

Switch to side-by-side view

--- 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.