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

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"