DNAbin-class            Auxiliary classes for OutbreakTools
FluH1N1pdm2009          Dataset from the 2009 influenza A/H1N1 pandemic
HorseFlu                Dataset from the Newmarket 2003 equine
                        influenza outbreak
HorseFluRaw             Raw dataset from the Newmarket 2003 equine
                        influenza outbreak
JSON2obkData            Import data from JSON file into OutbreakTools
OutbreakTools-package   The OutbreakTools package
ToyOutbreak             Simulated outbreak dataset
ToyOutbreakRaw          Raw simulated outbreak dataset
dna2uniqSequences       Convert a DNAbin with duplicated sequences to
                        the class 'uniqSequences'
get.data                Access data in "obkData" objects
get.dates               Retrieve dates data
get.incidence           Compute incidence
get.individuals         Retrieve individual identifiers
make.phylo              Obtain phylogenies from outbreak data
make.tip.attributes     Obtain meta data for items in 'obkData' objects
obkContacts-class       Formal class "obkContacts"
obkData-class           Formal class "obkData"
obkSequences-class      Formal class "obkSequences"
phylo2ggphy             Convert phylogenies from the class 'phylo' to
                        the class 'ggphy'
phylofromtranstree      Create phylogenetic tree from transmission tree
plot.obkData            Plot outbreak data
plotEpi                 Plot the number of susceptible, infected and
                        recovered as a function of time
plotGeo                 Function to plot cases on a map
plotIndividualTimeline
                        Plot a timeline of recorded data
plotggMST               Function to plot a minimum spanning tree of the
                        class 'obkData'
plotggphy               Function to plot phylogenies using 'ggplot2'
read.annotated.tree     Read annotated tree files in Newick or NEXUS
                        format
simuEpi                 Simulate an epidemic following a SIR model
subset,obkData-method   Subset data in "obkData" objects
uniqSequences-class     Formal class "uniqSequences"
