outbreaker2
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014.
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 ([email protected])