Learn R Programming
⚠️There's a newer version (0.1-16) of this package.Take me there.

OutbreakTools (version 0.1-1)

basic tools for the analysis of disease outbreaks.

Description

basic tools for the analysis of disease outbreaks.

Copy Link

Version

Install

install.packages('OutbreakTools')

Monthly Downloads

5

Version

0.1-1

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

August 6th, 2014

Functions in OutbreakTools (0.1-1)

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