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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:

$$(\kappa_i \mu)^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}$$

<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 (finlaycampbell93@gmail.com)