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.

Install the latest version of this package by entering the following in R:
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)

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"


as.data.frame.obkContacts Man page
as.data.frame,obkContacts-method Man page
as.matrix.obkContacts Man page
as.matrix,obkContacts-method Man page
characterOrNULL Man page
characterOrNULL-class Man page
data.frameOrNULL Man page
data.frameOrNULL-class Man page
DateOrNULL Man page
DateOrNULL-class Man page
dna2uniqSequences Man page
DNAbin-class Man page
DNAbinOrNULL Man page
DNAbinOrNULL-class Man page
factorNULL Man page
factorNULL-class Man page
FluH1N1pdm2009 Man page
get.contacts Man page
get.contacts.obkContacts Man page
get.contacts,obkContacts-method Man page
get.contacts.obkData Man page
get.contacts,obkData-method Man page
get.context Man page
get.context.obkData Man page
get.context,obkData-method Man page
get.data Man page
get.data.obkData Man page
get.data,obkData-method Man page
get.dates Man page
get.dates.obkContacts Man page
get.dates,obkContacts-method Man page
get.dates.obkData Man page
get.dates,obkData-method Man page
get.dates.obkSequences Man page
get.dates,obkSequences-method Man page
get.dna Man page
get.dna.obkData Man page
get.dna,obkData-method Man page
get.dna.obkSequences Man page
get.dna,obkSequences-method Man page
get.id Man page
get.id,obkSequences-method Man page
get.incidence Man page
get.incidence.Date Man page
get.incidence,Date-method Man page
get.incidence.obkContacts Man page
get.incidence,obkContacts-method Man page
get.incidence.obkData Man page
get.incidence,obkData-method Man page
get.incidence.obkSequences Man page
get.incidence,obkSequences-method Man page
get.individuals Man page
get.individuals.obkContacts Man page
get.individuals,obkContacts-method Man page
get.individuals.obkData Man page
get.individuals,obkData-method Man page
get.individuals.obkSequences Man page
get.individuals,obkSequences-method Man page
get.locus Man page
get.locus.obkData Man page
get.locus,obkData-method Man page
get.locus.obkSequences Man page
get.locus,obkSequences-method Man page
get.ncontacts Man page
get.ncontacts.obkContacts Man page
get.ncontacts,obkContacts-method Man page
get.ncontacts.obkData Man page
get.ncontacts,obkData-method Man page
get.ncontext Man page
get.ncontext.obkData Man page
get.ncontext,obkData-method Man page
get.ndates Man page
get.ndates.obkContacts Man page
get.ndates,obkContacts-method Man page
get.ndates.obkData Man page
get.ndates,obkData-method Man page
get.ndates.obkSequences Man page
get.ndates,obkSequences-method Man page
get.nindividuals Man page
get.nindividuals.obkContacts Man page
get.nindividuals,obkContacts-method Man page
get.nindividuals.obkData Man page
get.nindividuals,obkData-method Man page
get.nindividuals.obkSequences Man page
get.nindividuals,obkSequences-method Man page
get.nlocus Man page
get.nlocus.obkData Man page
get.nlocus,obkData-method Man page
get.nlocus.obkSequences Man page
get.nlocus,obkSequences-method Man page
get.nrecords Man page
get.nrecords.obkData Man page
get.nrecords,obkData-method Man page
get.nsequences Man page
get.nsequences.obkData Man page
get.nsequences,obkData-method Man page
get.nsequences.obkSequences Man page
get.nsequences,obkSequences-method Man page
get.ntrees Man page
get.ntrees.obkData Man page
get.ntrees,obkData-method Man page
get.records Man page
get.records.obkData Man page
get.records,obkData-method Man page
get.sequences Man page
get.sequences.obkData Man page
get.sequences,obkData-method Man page
get.sequences.obkSequences Man page
get.sequences,obkSequences-method Man page
get.trees Man page
get.trees.obkData Man page
get.trees,obkData-method Man page
head.obkData Man page
head,obkData-method Man page
HorseFlu Man page
HorseFluRaw Man page
initialize,obkContacts-method Man page
initialize,obkData-method Man page
initialize,obkSequences-method Man page
initialize,uniqSequences-method Man page
integerOrNULL Man page
integerOrNULL-class Man page
JSON2obkData Man page
listOrNULL Man page
listOrNULL-class Man page
make.individual.attributes Man page
make.phylo Man page
make.phylo.obkData Man page
make.phylo,obkData-method Man page
make.sequence.attributes Man page
make.tip.attributes Man page
matrixOrNULL Man page
matrixOrNULL-class Man page
multiPhylo-class Man page
multiPhyloOrNULL Man page
multiPhyloOrNULL-class Man page
network-class Man page
networkDynamic-class Man page
networkDynamicOrNetwork-class Man page
networkDynamicOrNetworkOrNULL-class Man page
numericOrNULL Man page
numericOrNULL-class Man page
obkContacts Man page
[,obkContacts,ANY,ANY-method Man page
obkContacts-class Man page
[,obkContacts-method Man page
obkContactsOrNULL Man page
obkContactsOrNULL-class Man page
obkData Man page
obkData-class Man page
obkSequences Man page
obkSequences-class Man page
obkSequencesOrNULL-class Man page
OutbreakTools Man page
OutbreakTools-package Man page
phylo2ggphy Man page
phylo-class Man page
phylofromtranstree Man page
plotEpi Man page
plotGeo Man page
plotggMST Man page
plotggphy Man page
plotIndividualTimeline Man page
plot.obkContacts Man page
plot,obkContacts,ANY-method Man page
plot,obkContacts-method Man page
plot.obkData Man page
plot,obkData,ANY-method Man page
plot,obkData-method Man page
POSIXctOrNULL Man page
POSIXctOrNULL-class Man page
print.obkContacts Man page
read.annotated.nexus Man page
read.annotated.tree Man page
show.obkContacts Man page
show,obkContacts-method Man page
show,obkData-method Man page
show,obkSequences-method Man page
simuEpi Man page
subset.obkContacts Man page
subset,obkContacts-method Man page
subset.obkData Man page
subset,obkData-method Man page
subset.obkSequences Man page
subset,obkSequences-method Man page
summary.obkData Man page
summary,obkData-method Man page
tail.obkData Man page
tail,obkData-method Man page
ToyOutbreak Man page
ToyOutbreakRaw Man page
uniqSequences Man page
uniqSequences-class Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

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