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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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Version

Install

install.packages('OutbreakTools')

Monthly Downloads

5

Version

0.1-11

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

August 11th, 2014

Functions in OutbreakTools (0.1-11)

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