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OutbreakTools (version 0.1-12)
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
0.1-12
License
GPL (>= 2)
Maintainer
Thibaut Jombart
Last Published
February 6th, 2015
Functions in OutbreakTools (0.1-12)
Search functions
obkData-class
Formal class "obkData"
make.tip.attributes
Obtain meta data for items in
obkData
objects
phylofromtranstree
Create phylogenetic tree from transmission tree
obkSequences-class
Formal class "obkSequences"
ToyOutbreak
Simulated outbreak dataset
plotEpi
Plot the number of susceptible, infected and recovered as a function of time
auxiliary classes
Auxiliary classes for OutbreakTools
make.phylo
Obtain phylogenies from outbreak data
HorseFluRaw
Raw dataset from the Newmarket 2003 equine influenza outbreak
read annotated trees
Read annotated tree files in Newick or NEXUS format
FluH1N1pdm2009
Dataset from the 2009 influenza A/H1N1 pandemic
ToyOutbreakRaw
Raw simulated outbreak dataset
plotIndividualTimeline
Plot a timeline of recorded data
get.dates
Retrieve dates data
JSON2obkData
Import data from JSON file into OutbreakTools
get.data
Access data in "obkData" objects
HorseFlu
Dataset from the Newmarket 2003 equine influenza outbreak
plotggMST
Function to plot a minimum spanning tree of the class 'obkData'
OutbreakTools-package
The OutbreakTools package
subset
Subset data in "obkData" objects
obkContacts-class
Formal class "obkContacts"
phylo2ggphy
Convert phylogenies from the class 'phylo' to the class 'ggphy'
get.individuals
Retrieve individual identifiers
plotggphy
Function to plot phylogenies using
ggplot2
get.incidence
Compute incidence
uniqSequences-class
Formal class "uniqSequences"
dna2uniqSequences
Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
plotGeo
Function to plot cases on a map
Plot obkData
Plot outbreak data
simuEpi
Simulate an epidemic following a SIR model