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" |