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, and uses a modular approach which enables fine customisation of priors, likelihoods and parameter movements (see customisation vignette).
NOTE: Correction to genetic likelihood
The genetic likelihood of the original outbreaker paper 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.
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:
$$(\kappa_i \mu)^{d(s_i,s_{\alpha_i})}(1 - \mu)^{(\kappa_i\times l(s_i, s_{\alpha_i})) - d(s_i,s_{\alpha_i})}$$
Installation
To install the stable version from CRAN:
install.packages("outbreaker2")To install the development version from github (requires Rtools on windows and GSL headers on all platforms):
devtools::install_github("reconhub/outbreaker2")To add local copies of the vignettes, you will need to specify:
devtools::install_github("reconhub/outbreaker2", build_vignettes = TRUE)Then, to load the package, use:
library("outbreaker2")Documentation
outbreaker2 is fully documented on a dedicated website.
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.
Contributors
See details of contributions here.
Contributions are welcome via pull requests.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Maintainer: Finlay Campbell (finlaycampbell93@gmail.com)