outbreaker

Disease outbreak reconstruction from epidemiological and genetic data

Welcome to the project page of outbreaker! This page is dedicated to the development of the R package outbreaker. Whenever possible, it is recommended to use the development version of the package rather than the older CRAN version. The devel version (at least the master branch) is meant to be as functional as the CRAN version, but integrates the latest new features and bug fixes.

For documentation and tutorials, see The R-epi-project.

Installing outbreaker devel

To install the development version from github (the package devtools is required):

library(devtools)
install_github("thibautjombart/outbreaker")

Note that on Windows, a toolkit (Rtools) needs to be installed separately for devtools to work. On every system, GNU scientific library also needs to be installed for outbreaker to be compiled.

Once installed, the package can be loaded using:

library("outbreaker")

Asking a question

• general questions can be asked on the R-epi forum
• for bug reports, feature requests, contributions, use github's issue system