OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.

AuthorThe Hackout team (In alphabetic order: 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)
Date of publication2015-12-26 00:40:07
MaintainerThibaut Jombart <thibautjombart@gmail.com>
LicenseGPL (>= 2)
Version0.1-14
http://sites.google.com/site/therepiproject/r-pac/about

View on CRAN

Man pages

annotatedTreeReader: Read annotated tree files in Newick or NEXUS format

auxClasses: Auxiliary classes for OutbreakTools

dna2uniqSequences: Convert a DNAbin with duplicated sequences to the class...

FluH1N1pdm2009: Dataset from the 2009 influenza A/H1N1 pandemic

get.data: Access data in "obkData" objects

get.dates: Retrieve dates data

get.incidence: Compute incidence

get.individuals: Retrieve individual identifiers

HorseFlu: Dataset from the Newmarket 2003 equine influenza outbreak

HorseFluRaw: Raw dataset from the Newmarket 2003 equine influenza outbreak

importFromJSON: Import data from JSON file into OutbreakTools

make.attributes: Obtain meta data for items in 'obkData' objects

make.phylo: Obtain phylogenies from outbreak data

obkContacts: Formal class "obkContacts"

obkData: Formal class "obkData"

obkDataPlot: Plot outbreak data

obkSequences: Formal class "obkSequences"

OutbreakTools.package: The OutbreakTools package

phylo2ggphy: Convert phylogenies from the class 'phylo' to the class...

phylofromtranstree: Create phylogenetic tree from transmission tree

plotEpi: Plot the number of susceptible, infected and recovered as a...

plotGeo: Function to plot cases on a map

plotggMST: Function to plot a minimum spanning tree of the class...

plotggphy: Function to plot phylogenies using 'ggplot2'

plotIndividualTimeline: Plot a timeline of recorded data

simuEpi: Simulate an epidemic following a SIR model

subset: Subset data in "obkData" objects

ToyOutbreak: Simulated outbreak dataset

ToyOutbreakRaw: Raw simulated outbreak dataset

uniqSequences: Formal class "uniqSequences"

Files in this package

OutbreakTools
OutbreakTools/inst
OutbreakTools/inst/files
OutbreakTools/inst/files/BEAST-expl.nex
OutbreakTools/inst/doc
OutbreakTools/inst/doc/OutbreakTools.Rnw
OutbreakTools/inst/doc/OutbreakTools.pdf
OutbreakTools/inst/doc/OutbreakTools.R
OutbreakTools/NAMESPACE
OutbreakTools/data
OutbreakTools/data/ToyOutbreak.RData
OutbreakTools/data/HorseFluRaw.RData
OutbreakTools/data/FluH1N1pdm2009.RData
OutbreakTools/data/ToyOutbreakRaw.RData
OutbreakTools/data/HorseFlu.RData
OutbreakTools/R
OutbreakTools/R/utils.R OutbreakTools/R/plotggMST.R OutbreakTools/R/subset.R OutbreakTools/R/uniqSequences.R OutbreakTools/R/annotatedTreeReader.R OutbreakTools/R/plot.R OutbreakTools/R/obkData_Accessors.R OutbreakTools/R/obkData_basics.R OutbreakTools/R/obkData.R OutbreakTools/R/generics.R OutbreakTools/R/get.incidence.R OutbreakTools/R/plotGeo.R OutbreakTools/R/simuEpi.R OutbreakTools/R/importFromJSON.R OutbreakTools/R/OutbreakTools.R OutbreakTools/R/make.attributes.R OutbreakTools/R/make.phylo.R OutbreakTools/R/phylo2ggphy.R OutbreakTools/R/auxClasses.R OutbreakTools/R/dna2uniqSequences.R OutbreakTools/R/plotIndividualTimeline.R OutbreakTools/R/obkContacts.R OutbreakTools/R/zzz.R OutbreakTools/R/plotggphy.R OutbreakTools/R/obkSequences.R
OutbreakTools/vignettes
OutbreakTools/vignettes/OutbreakTools.Rnw
OutbreakTools/MD5
OutbreakTools/build
OutbreakTools/build/vignette.rds
OutbreakTools/DESCRIPTION
OutbreakTools/ChangeLog
OutbreakTools/man
OutbreakTools/man/obkDataPlot.Rd OutbreakTools/man/plotEpi.Rd OutbreakTools/man/make.phylo.Rd OutbreakTools/man/get.incidence.Rd OutbreakTools/man/get.data.Rd OutbreakTools/man/uniqSequences.Rd OutbreakTools/man/plotIndividualTimeline.Rd OutbreakTools/man/plotGeo.Rd OutbreakTools/man/get.dates.Rd OutbreakTools/man/OutbreakTools.package.Rd OutbreakTools/man/HorseFluRaw.Rd OutbreakTools/man/make.attributes.Rd OutbreakTools/man/plotggphy.Rd OutbreakTools/man/get.individuals.Rd OutbreakTools/man/HorseFlu.Rd OutbreakTools/man/obkData.Rd OutbreakTools/man/FluH1N1pdm2009.Rd OutbreakTools/man/phylofromtranstree.Rd OutbreakTools/man/plotggMST.Rd OutbreakTools/man/importFromJSON.Rd OutbreakTools/man/ToyOutbreakRaw.Rd OutbreakTools/man/annotatedTreeReader.Rd OutbreakTools/man/simuEpi.Rd OutbreakTools/man/phylo2ggphy.Rd OutbreakTools/man/obkContacts.Rd OutbreakTools/man/obkSequences.Rd OutbreakTools/man/auxClasses.Rd OutbreakTools/man/ToyOutbreak.Rd OutbreakTools/man/dna2uniqSequences.Rd OutbreakTools/man/subset.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.