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
OutbreakTools accessible using:
The main features of
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
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
simuEpi: outbreak simulation using an SIR model
and a simple model of sequence evolution.
To cite OutbreakTools, please use the reference given by
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
OutbreakTools depends on or is related to several packages. The main non-base packages OutbreakTools relies on are:
ape: phylogenetic reconstruction
ggplot2: advanced graphics
network/networkDynamics: network handling
sna: social network analysis
ggmap: various map tools for ggplot2
Other useful packages include:
EpiEstim: reproduction number estimation
adegenet: genetic data analysis
outbreaker: outbreak reconstruction using pathogen sequences
phangorn: maximum-likelihood phylogenetic reconstruction
igraph: graph theory algorithms
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