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OutbreakTools (version 0.1-11)
basic tools for the analysis of disease outbreaks.
Description
basic tools for the analysis of disease outbreaks.
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Install
install.packages('OutbreakTools')
Monthly Downloads
88
Version
0.1-11
License
GPL (>= 2)
Maintainer
Thibaut Jombart
Last Published
August 11th, 2014
Functions in OutbreakTools (0.1-11)
Search functions
uniqSequences-class
Formal class "uniqSequences"
OutbreakTools-package
The OutbreakTools package
plotIndividualTimeline
Plot a timeline of recorded data
get.individuals
Retrieve individual identifiers
plotEpi
Plot the number of susceptible, infected and recovered as a function of time
phylo2ggphy
Convert phylogenies from the class 'phylo' to the class 'ggphy'
simuEpi
Simulate an epidemic following a SIR model
HorseFluRaw
Raw dataset from the Newmarket 2003 equine influenza outbreak
Plot obkData
Plot outbreak data
plotggMST
Function to plot a minimum spanning tree of the class 'obkData'
make.phylo
Obtain phylogenies from outbreak data
read annotated trees
Read annotated tree files in Newick or NEXUS format
obkContacts-class
Formal class "obkContacts"
obkSequences-class
Formal class "obkSequences"
get.data
Access data in "obkData" objects
get.incidence
Compute incidence
obkData-class
Formal class "obkData"
HorseFlu
Dataset from the Newmarket 2003 equine influenza outbreak
get.dates
Retrieve dates data
make.tip.attributes
Obtain meta data for items in
obkData
objects
plotggphy
Function to plot phylogenies using
ggplot2
ToyOutbreak
Simulated outbreak dataset
subset
Subset data in "obkData" objects
auxiliary classes
Auxiliary classes for OutbreakTools
ToyOutbreakRaw
Raw simulated outbreak dataset
dna2uniqSequences
Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
FluH1N1pdm2009
Dataset from the 2009 influenza A/H1N1 pandemic
plotGeo
Function to plot cases on a map
JSON2obkData
Import data from JSON file into OutbreakTools
phylofromtranstree
Create phylogenetic tree from transmission tree