OutbreakTools (previously known as 'epibase') is a package
providing basic tools for the analysis of disease outbreaks. Its main
features lie in handling possibly very different types of data within
a coherent framework, represented by the class '>obkData
(for "outbreak data"). This class allows to store and manipulate data
on samples, individuals, records interventions, genetic sequences,
phylogenetic trees and contact networks, most of this information
being time-stamped and possibly geo-referenced.
For a more complete overview of the package, look at the tutorial
vignette OutbreakTools accessible using:
vignette("OutbreakTools", package="OutbreakTools")
The main features of OutbreakTools include:
'>obkData: the main class of objects storing outbreak data; this formal class is provided with a number of accessors, documented in the same page.
'>obkSequences: an auxiliary class for handling sequences from several genes.
'>obkContacts: an auxiliary class for handling possibly dynamic contact networks between individuals.
subset.obkData: (simply use subset) a
method to subset the dataset using various criteria.
make.phylo: create/plot phylogenies from the genes
contained in an '>obkData object.
read.annotated.nexus: read an annotated phylogeny
into a phylo object.
plotggMST: create/plot minimum spanning trees
from the genes contained in an '>obkData object.
dna2uniqSequences: derive unique sequences from
a sequence alignment possibly containing identical genomes.
plotIndividualTimeline: graphical representation
of samples as times series.
plotGeo: graphical representation of samples
as geographic distributions.
plotggphy: advanced graphical representation of
phylogenetic trees using ggplot2.
simuEpi: outbreak simulation using an SIR model
and a simple model of sequence evolution.
datasets: HorseFlu,
HorseFluRaw, ToyOutbreak,
ToyOutbreakRaw, FluH1N1pdm2009
To cite OutbreakTools, please use the reference given by
citation("OutbreakTools").
| Package: | OutbreakTools |
| Type: | Package |
| Version: | 0.1-0 |
| Date: | 2014-01-10 |
OutbreakTools depends on or is related to several packages. The main non-base packages OutbreakTools relies on are:
ape: phylogenetic reconstruction
ggplot2: advanced graphics
network/networkDynamics: network handling
sna: social network analysis
ggmap: various map tools for ggplot2
Other useful packages include:
EpiEstim: reproduction number estimation
adegenet: genetic data analysis
outbreaker: outbreak reconstruction using pathogen sequences
phangorn: maximum-likelihood phylogenetic reconstruction
igraph: graph theory algorithms