Basic Tools for the Analysis of Disease Outbreaks


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Documentation for package ‘OutbreakTools’ version 0.1-14

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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"