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OutbreakTools (version 0.1-14)

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

0.1-14

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

December 25th, 2015

Functions in OutbreakTools (0.1-14)

dna2uniqSequences

Convert a DNAbin with duplicated sequences to the class 'uniqSequences'
get.data

Access data in "obkData" objects
get.individuals

Retrieve individual identifiers
HorseFlu

Dataset from the Newmarket 2003 equine influenza outbreak
get.dates

Retrieve dates data
obkData-class

Formal class "obkData"
JSON2obkData

Import data from JSON file into OutbreakTools
get.incidence

Compute incidence
phylo2ggphy

Convert phylogenies from the class 'phylo' to the class 'ggphy'
make.tip.attributes

Obtain meta data for items in obkData objects
plotggphy

Function to plot phylogenies using ggplot2
simuEpi

Simulate an epidemic following a SIR model
OutbreakTools-package

The OutbreakTools package
subset

Subset data in "obkData" objects
obkSequences-class

Formal class "obkSequences"
phylofromtranstree

Create phylogenetic tree from transmission tree
plotIndividualTimeline

Plot a timeline of recorded data
plotggMST

Function to plot a minimum spanning tree of the class 'obkData'
ToyOutbreakRaw

Raw simulated outbreak dataset
make.phylo

Obtain phylogenies from outbreak data
obkContacts-class

Formal class "obkContacts"
FluH1N1pdm2009

Dataset from the 2009 influenza A/H1N1 pandemic
HorseFluRaw

Raw dataset from the Newmarket 2003 equine influenza outbreak
plotGeo

Function to plot cases on a map
ToyOutbreak

Simulated outbreak dataset
auxiliary classes

Auxiliary classes for OutbreakTools
read annotated trees

Read annotated tree files in Newick or NEXUS format
uniqSequences-class

Formal class "uniqSequences"
Plot obkData

Plot outbreak data
plotEpi

Plot the number of susceptible, infected and recovered as a function of time