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OutbreakTools (version 0.1-13)

Basic Tools for the Analysis of Disease Outbreaks

Description

Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.

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Version

Install

install.packages('OutbreakTools')

Monthly Downloads

5

Version

0.1-13

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

March 23rd, 2015

Functions in OutbreakTools (0.1-13)

make.phylo

Obtain phylogenies from outbreak data
read annotated trees

Read annotated tree files in Newick or NEXUS format
get.individuals

Retrieve individual identifiers
FluH1N1pdm2009

Dataset from the 2009 influenza A/H1N1 pandemic
obkData-class

Formal class "obkData"
auxiliary classes

Auxiliary classes for OutbreakTools
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
JSON2obkData

Import data from JSON file into OutbreakTools
OutbreakTools-package

The OutbreakTools package
get.incidence

Compute incidence
subset

Subset data in "obkData" objects
ToyOutbreak

Simulated outbreak dataset
make.tip.attributes

Obtain meta data for items in obkData objects
uniqSequences-class

Formal class "uniqSequences"
ToyOutbreakRaw

Raw simulated outbreak dataset
HorseFluRaw

Raw dataset from the Newmarket 2003 equine influenza outbreak
dna2uniqSequences

Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
plotIndividualTimeline

Plot a timeline of recorded data
plotGeo

Function to plot cases on a map
obkSequences-class

Formal class "obkSequences"
phylo2ggphy

Convert phylogenies from the class 'phylo' to the class 'ggphy'
simuEpi

Simulate an epidemic following a SIR model
get.dates

Retrieve dates data
obkContacts-class

Formal class "obkContacts"
HorseFlu

Dataset from the Newmarket 2003 equine influenza outbreak
Plot obkData

Plot outbreak data
plotggphy

Function to plot phylogenies using ggplot2
phylofromtranstree

Create phylogenetic tree from transmission tree
get.data

Access data in "obkData" objects