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.

Author
The 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 publication
2015-12-26 00:40:07
Maintainer
Thibaut Jombart <thibautjombart@gmail.com>
License
GPL (>= 2)
Version
0.1-14
URLs

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