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OutbreakTools (version 0.1-16)

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

70

Version

0.1-16

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

October 5th, 2017

Functions in OutbreakTools (0.1-16)

FluH1N1pdm2009

Dataset from the 2009 influenza A/H1N1 pandemic
HorseFlu

Dataset from the Newmarket 2003 equine influenza outbreak
read annotated trees

Read annotated tree files in Newick or NEXUS format
auxiliary classes

Auxiliary classes for OutbreakTools
ToyOutbreak

Simulated outbreak dataset
ToyOutbreakRaw

Raw simulated outbreak dataset
dna2uniqSequences

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

Access data in "obkData" objects
HorseFluRaw

Raw dataset from the Newmarket 2003 equine influenza outbreak
OutbreakTools-package

The OutbreakTools package
get.dates

Retrieve dates data
Plot obkData

Plot outbreak data
make.tip.attributes

Obtain meta data for items in obkData objects
get.incidence

Compute incidence
phylo2ggphy

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

Create phylogenetic tree from transmission tree
get.individuals

Retrieve individual identifiers
JSON2obkData

Import data from JSON file into OutbreakTools
plotIndividualTimeline

Plot a timeline of recorded data
obkContacts-class

Formal class "obkContacts"
obkData-class

Formal class "obkData"
plotEpi

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

Function to plot cases on a map
obkSequences-class

Formal class "obkSequences"
plotggphy

Function to plot phylogenies using ggplot2
simuEpi

Simulate an epidemic following a SIR model
make.phylo

Obtain phylogenies from outbreak data
subset

Subset data in "obkData" objects
uniqSequences-class

Formal class "uniqSequences"
plotggMST

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