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