Man pages for thibautjombart/OutbreakTools
Basic Tools for the Analysis of Disease Outbreaks

annotatedTreeReaderRead annotated tree files in Newick or NEXUS format
auxClassesAuxiliary classes for OutbreakTools
dna2uniqSequencesConvert a DNAbin with duplicated sequences to the class...
FluH1N1pdm2009Dataset from the 2009 influenza A/H1N1 pandemic
get.dataAccess data in "obkData" objects
get.datesRetrieve dates data
get.incidenceCompute incidence
get.individualsRetrieve individual identifiers
HorseFluDataset from the Newmarket 2003 equine influenza outbreak
HorseFluRawRaw dataset from the Newmarket 2003 equine influenza outbreak
importFromJSONImport data from JSON file into OutbreakTools
make.attributesObtain meta data for items in 'obkData' objects
make.phyloObtain phylogenies from outbreak data
obkContactsFormal class "obkContacts"
obkDataFormal class "obkData"
obkDataPlotPlot outbreak data
obkSequencesFormal class "obkSequences"
OutbreakTools.packageThe OutbreakTools package
phylo2ggphyConvert phylogenies from the class 'phylo' to the class...
phylofromtranstreeCreate phylogenetic tree from transmission tree
plotEpiPlot the number of susceptible, infected and recovered as a...
plotGeoFunction to plot cases on a map
plotggMSTFunction to plot a minimum spanning tree of the class...
plotggphyFunction to plot phylogenies using 'ggplot2'
plotIndividualTimelinePlot a timeline of recorded data
simuEpiSimulate an epidemic following a SIR model
subsetSubset data in "obkData" objects
ToyOutbreakSimulated outbreak dataset
ToyOutbreakRawRaw simulated outbreak dataset
uniqSequencesFormal class "uniqSequences"
thibautjombart/OutbreakTools documentation built on Oct. 5, 2017, 3:06 p.m.