A C D F G H I J L M N O P R S T U
OutbreakTools-package | The OutbreakTools package |
as.data.frame-method | Formal class "obkContacts" |
as.data.frame.obkContacts | Formal class "obkContacts" |
as.matrix-method | Formal class "obkContacts" |
as.matrix.obkContacts | Formal class "obkContacts" |
characterOrNULL | Auxiliary classes for OutbreakTools |
characterOrNULL-class | Auxiliary classes for OutbreakTools |
data.frameOrNULL | Auxiliary classes for OutbreakTools |
data.frameOrNULL-class | Auxiliary classes for OutbreakTools |
DateOrNULL | Auxiliary classes for OutbreakTools |
DateOrNULL-class | Auxiliary classes for OutbreakTools |
dna2uniqSequences | Convert a DNAbin with duplicated sequences to the class 'uniqSequences' |
DNAbin-class | Auxiliary classes for OutbreakTools |
DNAbinOrNULL | Auxiliary classes for OutbreakTools |
DNAbinOrNULL-class | Auxiliary classes for OutbreakTools |
factorNULL | Auxiliary classes for OutbreakTools |
factorNULL-class | Auxiliary classes for OutbreakTools |
FluH1N1pdm2009 | Dataset from the 2009 influenza A/H1N1 pandemic |
get.contacts | Formal class "obkContacts" |
get.contacts-method | Formal class "obkContacts" |
get.contacts-method | Formal class "obkData" |
get.contacts.obkContacts | Formal class "obkContacts" |
get.contacts.obkData | Formal class "obkData" |
get.context | Formal class "obkData" |
get.context-method | Formal class "obkData" |
get.context.obkData | Formal class "obkData" |
get.data | Access data in "obkData" objects |
get.data-method | Access data in "obkData" objects |
get.data.obkData | Access data in "obkData" objects |
get.dates | Retrieve dates data |
get.dates-method | Retrieve dates data |
get.dates.obkContacts | Retrieve dates data |
get.dates.obkData | Retrieve dates data |
get.dates.obkSequences | Retrieve dates data |
get.dna | Formal class "obkSequences" |
get.dna-method | Formal class "obkData" |
get.dna-method | Formal class "obkSequences" |
get.dna.obkData | Formal class "obkData" |
get.dna.obkSequences | Formal class "obkSequences" |
get.incidence | Compute incidence |
get.incidence-method | Compute incidence |
get.incidence.Date | Compute incidence |
get.incidence.obkContacts | Compute incidence |
get.incidence.obkData | Compute incidence |
get.incidence.obkSequences | Compute incidence |
get.individuals | Retrieve individual identifiers |
get.individuals-method | Retrieve individual identifiers |
get.individuals.obkContacts | Retrieve individual identifiers |
get.individuals.obkData | Retrieve individual identifiers |
get.individuals.obkSequences | Retrieve individual identifiers |
get.locus | Formal class "obkSequences" |
get.locus-method | Formal class "obkData" |
get.locus-method | Formal class "obkSequences" |
get.locus.obkData | Formal class "obkData" |
get.locus.obkSequences | Formal class "obkSequences" |
get.ncontacts | Formal class "obkContacts" |
get.ncontacts-method | Formal class "obkContacts" |
get.ncontacts-method | Formal class "obkData" |
get.ncontacts.obkContacts | Formal class "obkContacts" |
get.ncontacts.obkData | Formal class "obkData" |
get.ncontext | Formal class "obkData" |
get.ncontext-method | Formal class "obkData" |
get.ncontext.obkData | Formal class "obkData" |
get.ndates | Retrieve dates data |
get.ndates-method | Retrieve dates data |
get.ndates.obkContacts | Retrieve dates data |
get.ndates.obkData | Retrieve dates data |
get.ndates.obkSequences | Retrieve dates data |
get.nindividuals | Retrieve individual identifiers |
get.nindividuals-method | Retrieve individual identifiers |
get.nindividuals.obkContacts | Retrieve individual identifiers |
get.nindividuals.obkData | Retrieve individual identifiers |
get.nindividuals.obkSequences | Retrieve individual identifiers |
get.nlocus | Formal class "obkSequences" |
get.nlocus-method | Formal class "obkData" |
get.nlocus-method | Formal class "obkSequences" |
get.nlocus.obkData | Formal class "obkData" |
get.nlocus.obkSequences | Formal class "obkSequences" |
get.nrecords | Formal class "obkData" |
get.nrecords-method | Formal class "obkData" |
get.nrecords.obkData | Formal class "obkData" |
get.nsequences | Formal class "obkSequences" |
get.nsequences-method | Formal class "obkData" |
get.nsequences-method | Formal class "obkSequences" |
get.nsequences.obkData | Formal class "obkData" |
get.nsequences.obkSequences | Formal class "obkSequences" |
get.ntrees | Formal class "obkData" |
get.ntrees-method | Formal class "obkData" |
get.ntrees.obkData | Formal class "obkData" |
get.records | Formal class "obkData" |
get.records-method | Formal class "obkData" |
get.records.obkData | Formal class "obkData" |
get.sequences | Formal class "obkSequences" |
get.sequences-method | Formal class "obkData" |
get.sequences-method | Formal class "obkSequences" |
get.sequences.obkData | Formal class "obkData" |
get.sequences.obkSequences | Formal class "obkSequences" |
get.trees | Formal class "obkData" |
get.trees-method | Formal class "obkData" |
get.trees.obkData | Formal class "obkData" |
head-method | Formal class "obkData" |
head.obkData | Formal class "obkData" |
HorseFlu | Dataset from the Newmarket 2003 equine influenza outbreak |
HorseFluRaw | Raw dataset from the Newmarket 2003 equine influenza outbreak |
initialize-method | Formal class "obkContacts" |
initialize-method | Formal class "obkData" |
initialize-method | Formal class "obkSequences" |
initialize-method | Formal class "uniqSequences" |
integerOrNULL | Auxiliary classes for OutbreakTools |
integerOrNULL-class | Auxiliary classes for OutbreakTools |
JSON2obkData | Import data from JSON file into OutbreakTools |
listOrNULL | Auxiliary classes for OutbreakTools |
listOrNULL-class | Auxiliary classes for OutbreakTools |
make.individual.attributes | Obtain meta data for items in 'obkData' objects |
make.phylo | Obtain phylogenies from outbreak data |
make.phylo-method | Obtain phylogenies from outbreak data |
make.phylo.obkData | Obtain phylogenies from outbreak data |
make.sequence.attributes | Obtain meta data for items in 'obkData' objects |
make.tip.attributes | Obtain meta data for items in 'obkData' objects |
matrixOrNULL | Auxiliary classes for OutbreakTools |
matrixOrNULL-class | Auxiliary classes for OutbreakTools |
multiPhylo-class | Auxiliary classes for OutbreakTools |
multiPhyloOrNULL | Auxiliary classes for OutbreakTools |
multiPhyloOrNULL-class | Auxiliary classes for OutbreakTools |
network-class | Formal class "obkContacts" |
networkDynamic-class | Formal class "obkContacts" |
networkDynamicOrNetwork-class | Formal class "obkContacts" |
networkDynamicOrNetworkOrNULL-class | Formal class "obkContacts" |
numericOrNULL | Auxiliary classes for OutbreakTools |
numericOrNULL-class | Auxiliary classes for OutbreakTools |
obkContacts | Formal class "obkContacts" |
obkContacts-class | Formal class "obkContacts" |
obkContactsOrNULL | Formal class "obkContacts" |
obkContactsOrNULL-class | Formal class "obkContacts" |
obkData | Formal class "obkData" |
obkData-class | Formal class "obkData" |
obkSequences | Formal class "obkSequences" |
obkSequences-class | Formal class "obkSequences" |
obkSequencesOrNULL-class | Formal class "obkSequences" |
OutbreakTools | The OutbreakTools package |
phylo-class | Auxiliary classes for OutbreakTools |
phylo2ggphy | Convert phylogenies from the class 'phylo' to the class 'ggphy' |
phylofromtranstree | Create phylogenetic tree from transmission tree |
plot-method | Formal class "obkContacts" |
plot-method | Plot outbreak data |
plot.obkContacts | Formal class "obkContacts" |
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 |
plotggMST | Function to plot a minimum spanning tree of the class 'obkData' |
plotggphy | Function to plot phylogenies using 'ggplot2' |
plotIndividualTimeline | Plot a timeline of recorded data |
POSIXctOrNULL | Auxiliary classes for OutbreakTools |
POSIXctOrNULL-class | Auxiliary classes for OutbreakTools |
print.obkContacts | Formal class "obkContacts" |
read.annotated.nexus | Read annotated tree files in Newick or NEXUS format |
read.annotated.tree | Read annotated tree files in Newick or NEXUS format |
show-method | Formal class "obkContacts" |
show-method | Formal class "obkData" |
show-method | Formal class "obkSequences" |
show.obkContacts | Formal class "obkContacts" |
simuEpi | Simulate an epidemic following a SIR model |
subset-method | Subset data in "obkData" objects |
subset.obkContacts | Subset data in "obkData" objects |
subset.obkData | Subset data in "obkData" objects |
subset.obkSequences | Subset data in "obkData" objects |
summary-method | Formal class "obkData" |
summary.obkData | Formal class "obkData" |
tail-method | Formal class "obkData" |
tail.obkData | Formal class "obkData" |
ToyOutbreak | Simulated outbreak dataset |
ToyOutbreakRaw | Raw simulated outbreak dataset |
uniqSequences | Formal class "uniqSequences" |
uniqSequences-class | Formal class "uniqSequences" |