Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014.
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).
To install the stable version from CRAN:
To install the development version from github (requires Rtools on windows and GSL headers on all platforms):
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:
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.
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])
This package re-implements and generalises the package outbreaker
It provides various functions to process input data, specify settings of the method, and even specify custom priors, likelihoods, or movement functions.
Outputs of the main function
outbreaker have a dedicated class extending the
Its engine is written in C++, interfaced via Rcpp.
Its C++ API is accessible via the function
Functionalities are documented in 4 vignettes.