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" |
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