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OutbreakTools (version 0.1-0)
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
0.1-0
License
GPL (>= 2)
Maintainer
Thibaut Jombart
Last Published
January 9th, 2014
Functions in OutbreakTools (0.1-0)
Search functions
HorseFluRaw
Raw dataset from the Newmarket 2003 equine influenza outbreak
plotggphy
Function to plot phylogenies using
ggplot2
Plot obkData
Plot outbreak data
get.dates
Retrieve dates data
FluH1N1pdm2009
Dataset from the 2009 influenza A/H1N1 pandemic
JSON2obkData
Import data from JSON file into OutbreakTools
get.individuals
Retrieve individual identifiers
plotggMST
Function to plot a minimum spanning tree of the class 'obkData'
HorseFlu
Dataset from the Newmarket 2003 equine influenza outbreak
read annotated trees
Read annotated tree files in Newick or NEXUS format
uniqSequences-class
Formal class "uniqSequences"
obkSequences-class
Formal class "obkSequences"
ToyOutbreakRaw
Raw simulated outbreak dataset
OutbreakTools-package
The OutbreakTools package
phylo2ggphy
Convert phylogenies from the class 'phylo' to the class 'ggphy'
obkData-class
Formal class "obkData"
auxiliary classes
Auxiliary classes for OutbreakTools
plotEpi
Plot the number of susceptible, infected and recovered as a function of time
simuEpi
Simulate an epidemic following a SIR model
make.tip.attributes
Obtain meta data for items in
obkData
objects
get.data
Access data in "obkData" objects
dna2uniqSequences
Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
get.incidence
Compute incidence
obkContacts-class
Formal class "obkContacts"
make.phylo
Obtain phylogenies from outbreak data
phylofromtranstree
Create phylogenetic tree from transmission tree
subset
Subset data in "obkData" objects
plotGeo
Function to plot cases on a map
ToyOutbreak
Simulated outbreak dataset
plotIndividualTimeline
Plot a timeline of recorded data