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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).

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:

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 (f.campbell15@imperial.ac.uk)

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Version

Install

install.packages('outbreaker2')

Monthly Downloads

347

Version

1.1.0

License

MIT + file LICENSE

Maintainer

Finlay Campbell

Last Published

June 13th, 2019

Functions in outbreaker2 (1.1.0)

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