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OutbreakTools (version 0.1-1)
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
0.1-1
License
GPL (>= 2)
Maintainer
Thibaut Jombart
Last Published
August 6th, 2014
Functions in OutbreakTools (0.1-1)
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plotIndividualTimeline
Plot a timeline of recorded data
auxiliary classes
Auxiliary classes for OutbreakTools
Plot obkData
Plot outbreak data
plotggphy
Function to plot phylogenies using
ggplot2
phylo2ggphy
Convert phylogenies from the class 'phylo' to the class 'ggphy'
FluH1N1pdm2009
Dataset from the 2009 influenza A/H1N1 pandemic
JSON2obkData
Import data from JSON file into OutbreakTools
OutbreakTools-package
The OutbreakTools package
get.data
Access data in "obkData" objects
dna2uniqSequences
Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
obkContacts-class
Formal class "obkContacts"
get.dates
Retrieve dates data
plotGeo
Function to plot cases on a map
ToyOutbreak
Simulated outbreak dataset
simuEpi
Simulate an epidemic following a SIR model
obkData-class
Formal class "obkData"
HorseFluRaw
Raw dataset from the Newmarket 2003 equine influenza outbreak
read annotated trees
Read annotated tree files in Newick or NEXUS format
HorseFlu
Dataset from the Newmarket 2003 equine influenza outbreak
make.tip.attributes
Obtain meta data for items in
obkData
objects
make.phylo
Obtain phylogenies from outbreak data
uniqSequences-class
Formal class "uniqSequences"
get.individuals
Retrieve individual identifiers
obkSequences-class
Formal class "obkSequences"
subset
Subset data in "obkData" objects
ToyOutbreakRaw
Raw simulated outbreak dataset
get.incidence
Compute incidence
plotggMST
Function to plot a minimum spanning tree of the class 'obkData'
plotEpi
Plot the number of susceptible, infected and recovered as a function of time
phylofromtranstree
Create phylogenetic tree from transmission tree