OutbreakTools.package: The OutbreakTools package

Description Details Author(s) See Also


OutbreakTools (previously known as 'epibase') is a package providing basic tools for the analysis of disease outbreaks. Its main features lie in handling possibly very different types of data within a coherent framework, represented by the class obkData (for "outbreak data"). This class allows to store and manipulate data on samples, individuals, records interventions, genetic sequences, phylogenetic trees and contact networks, most of this information being time-stamped and possibly geo-referenced.

For a more complete overview of the package, look at the tutorial vignette OutbreakTools accessible using:
vignette("OutbreakTools", package="OutbreakTools")

The main features of OutbreakTools include:

To cite OutbreakTools, please use the reference given by citation("OutbreakTools").


Package: OutbreakTools
Type: Package
Version: 0.1-0
Date: 2014-01-10
License: GPL (>=2)


Maintainer: Thibaut Jombart <[email protected]>
Developers: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma

See Also

OutbreakTools depends on or is related to several packages. The main non-base packages OutbreakTools relies on are:

Other useful packages include:

OutbreakTools documentation built on Oct. 6, 2017, 1:03 a.m.