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+
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+
+*outbreaker2: a framework for reconstructing disease outbreaks*
+---------------------------------------------------------------
+
+Welcome to the project page of *outbreaker2*, a Bayesian framework
+ for integrating epidemiological and genetic data to reconstruct transmission
+ trees of densely sampled outbreaks. It re-implements, generalises and replaces
+ the model of [*outbreaker*](https://github.com/thibautjombart/outbreaker), and uses
+ a modular approach which enables fine customisation of priors, likelihoods
+ and parameter movements (see [customisation
+ vignette](http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html)).
+
+### NOTE: Correction to genetic likelihood
+
+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).
+
+The original genetic likelihood was:
+
+$$\mu^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}$$
+
+The corrected genetic likelihood is:
+
+$$(\kappa_i\mu)^{d(s_i,s_{\alpha_i})}(1-\kappa_i\mu)^{l(s_i,s_{\alpha_i})-d(s_i,s_{\alpha_i})}$$
+
+<br>
+
+Installation
+-------------
+
+To install the stable version from CRAN:
+
+```r
+install.packages("outbreaker2")
+```
+
+To install the development version from github (requires Rtools on windows and
+GSL headers on all platforms):
+
+
+```r
+devtools::install_github("reconhub/outbreaker2")
+```
+
+To add local copies of the vignettes, you will need to specify:
+
+```r
+devtools::install_github("reconhub/outbreaker2", build_vignettes = TRUE)
+```
+
+Then, to load the package, use:
+
+
+```r
+library("outbreaker2")
+```
+
+
+
+<br>
+
+Documentation
+-------------
+
+*outbreaker2* is fully documented on a [dedicated
+ website](http://www.repidemicsconsortium.org/outbreaker2/).
+
+It also comes with the following vignettes:
+
+- **`introduction`**: general introduction using a worked example.
+- **`overview`**: brief overview of the package's content.
+- **`customisation`**: customisation of priors, likelihoods, and movement functions.
+- **`Rcpp_API`**: documentation for the Rcpp API.
+
+
+
+<br>
+
+Contributors
+------------
+- [Thibaut Jombart](https://github.com/thibautjombart)
+- [Finlay Campbell](https://github.com/finlaycampbell)
+- [Rich Fitzjohn](https://github.com/richfitz)
+- [Gerry Tonkin-Hill](https://github.com/gtonkinhill)
+- [Alexis Robert](https://github.com/alxsrobert)
+- [Kristjan Eldjarn](https://github.com/kreldjarn)
+
+
+See details of contributions
+[here](https://github.com/reconhub/outbreaker2/graphs/contributors).
+
+Contributions are welcome via **pull requests**.
+
+Please note that this project is released with a [Contributor Code of
+Conduct](https://github.com/reconhub/outbreaker2/blob/master/CONDUCT.md). By
+participating in this project you agree to abide by its terms.
+
+**Maintainer:** Finlay Campbell (finlaycampbell93@gmail.com)