# Basic Tools for the Analysis of Disease Outbreaks

## Documentation for package ‘OutbreakTools’ version 0.1-16

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D F G H I J L M N O P R S T U

OutbreakTools-package | The OutbreakTools package

## -- A --

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"

## -- C --

characterOrNULL | Auxiliary classes for OutbreakTools
characterOrNULL-class | Auxiliary classes for OutbreakTools

## -- D --

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

## -- F --

factorNULL | Auxiliary classes for OutbreakTools
factorNULL-class | Auxiliary classes for OutbreakTools
FluH1N1pdm2009 | Dataset from the 2009 influenza A/H1N1 pandemic

## -- G --

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"

## -- H --

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

## -- I --

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

## -- J --

JSON2obkData | Import data from JSON file into OutbreakTools

## -- L --

listOrNULL | Auxiliary classes for OutbreakTools
listOrNULL-class | Auxiliary classes for OutbreakTools

## -- M --

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

## -- N --

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

## -- O --

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

## -- P --

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"

## -- R --

read.annotated.nexus | Read annotated tree files in Newick or NEXUS format
read.annotated.tree | Read annotated tree files in Newick or NEXUS format

## -- S --

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"

## -- T --

tail-method | Formal class "obkData"
tail.obkData | Formal class "obkData"
ToyOutbreak | Simulated outbreak dataset
ToyOutbreakRaw | Raw simulated outbreak dataset

## -- U --

uniqSequences | Formal class "uniqSequences"
uniqSequences-class | Formal class "uniqSequences"