OutbreakTools.package: The OutbreakTools package
In OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

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:

obkData: the main class of objects storing outbreak data; this formal class is provided with a number of accessors, documented in the same page.
obkSequences: an auxiliary class for handling sequences from several genes.
obkContacts: an auxiliary class for handling possibly dynamic contact networks between individuals.
subset.obkData: (simply use subset) a method to subset the dataset using various criteria.
make.phylo: create/plot phylogenies from the genes contained in an obkData object.
read.annotated.nexus: read an annotated phylogeny into a phylo object.
plotggMST: create/plot minimum spanning trees from the genes contained in an obkData object.
dna2uniqSequences: derive unique sequences from a sequence alignment possibly containing identical genomes.
plotIndividualTimeline: graphical representation of samples as times series.
plotGeo: graphical representation of samples as geographic distributions.
plotggphy: advanced graphical representation of phylogenetic trees using ggplot2.
simuEpi: outbreak simulation using an SIR model and a simple model of sequence evolution.
datasets: HorseFlu, HorseFluRaw, ToyOutbreak, ToyOutbreakRaw, FluH1N1pdm2009

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 <t.jombart@imperial.ac.uk>
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

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