OutbreakTools (version 0.1-0)

OutbreakTools-package: The OutbreakTools package

Description

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 usesubset) a method to subset the dataset using various criteria.
• make.phylo: create/plot phylogenies from the genes contained in anobkDataobject.
• read.annotated.nexus: read an annotated phylogeny into a phylo object.
• plotggMST: create/plot minimum spanning trees from the genes contained in anobkDataobject.
• 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 usingggplot2.
• 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").

encoding

UTF-8

Details

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

See Also

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