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README.Rmd
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[](https://travis-ci.org/reconhub/outbreaker2)
[](https://ci.appveyor.com/project/thibautjombart/outbreaker2/branch/master)
[](https://codecov.io/github/reconhub/outbreaker2?branch=master)
[](https://cran.r-project.org/package=outbreaker2)
[](https://www.r-pkg.org:443/pkg/outbreaker2)
[](https://cran.r-project.org/package=outbreaker2)
*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:
$$(\kappa_i \mu)^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}$$
<br>
Installation
-------------
To install the stable version from CRAN:
```{r, eval = FALSE}
install.packages("outbreaker2")
```
To install the development version from github (requires Rtools on windows and
GSL headers on all platforms):
```{r, eval = FALSE}
devtools::install_github("reconhub/outbreaker2")
```
To add local copies of the vignettes, you will need to specify:
```{r, eval = FALSE}
devtools::install_github("reconhub/outbreaker2", build_vignettes = TRUE)
```
Then, to load the package, use:
```{r, eval = FALSE}
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 ([email protected])