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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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Version

Install

install.packages('OutbreakTools')

Monthly Downloads

5

Version

0.1-0

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

January 9th, 2014

Functions in OutbreakTools (0.1-0)

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