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. . Campbell, F, Cori A, Ferguson N, Jombart T. 2019. .


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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, and uses a modular approach which enables fine customisation of priors, likelihoods and parameter movements (see customisation vignette).


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])

News

outbreaker2 1.0.1 (2018-03-06)

Minor bug fixes

  • Fixed convolution operator to keep values in log space with high kappa (thanks to @gtonkinhill)
  • C++ garbage collection fix


outbreaker2 1.0.0 (2017-11-24)

First version of outbreaker2!

  • 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 regular data.frame, with print, summary and plot methods.

  • Its engine is written in C++, interfaced via Rcpp.

  • Its C++ API is accessible via the function get_cpp_api().

  • Functionalities are documented in 4 vignettes.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("outbreaker2")

1.1.0 by Finlay Campbell, 3 months ago


Browse source code at https://github.com/cran/outbreaker2


Authors: Thibaut Jombart [aut] , Finlay Campbell [aut, cre] , Rich Fitzjohn [aut] , Gerry Tonkin-Hill [ctb] , Alexis Robert [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports utils, methods, stats, grDevices, Rcpp, ape, ggplot2, magrittr, visNetwork

Suggests coda, microbenchmark, testthat, knitr, rmarkdown, igraph, epicontacts

Linking to Rcpp

System requirements: C++11


See at CRAN