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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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Version

Install

install.packages('OutbreakTools')

Monthly Downloads

5

Version

0.1-12

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

February 6th, 2015

Functions in OutbreakTools (0.1-12)

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