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. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
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:
The corrected genetic likelihood is:
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@example.com)
Functions in outbreaker2
|bind_to_function||Encloses argument in a function's environment|
|outbreaker||outbreaker2: main function for reconstructing disease outbreaks|
|print.outbreaker_chains||Basic methods for processing outbreaker results|
|sim_ctd||Simulate contact data from a transmission tree|
|chains_pal||Color palettes used in outbreaker|
|create_param||Initializes outputs for outbreaker|
|custom_likelihoods||Customise likelihood functions for outbreaker|
|custom_moves||Customise samplers for outbreaker|
|custom_priors||Customise priors for outbreaker|
|create_config||Set and check parameter settings of outbreaker|
|fake_outbreak||Small simulated outbreak|
|outbreaker_data||Process input data for outbreaker|
|get_cpp_api||Access internal C++ rountines used in outbreaker2|
|outbreaker_package||outbreaker2: a platform for disease outbreak reconstruction|
Vignettes of outbreaker2
Last month downloads
|License||MIT + file LICENSE|
|Packaged||2019-06-13 10:17:09 UTC; fc1915|
|Date/Publication||2019-06-13 15:40:02 UTC|
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