OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

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.

Version: 0.1-13
Depends: R (≥ 3.0.0), methods, ggplot2, network, knitr
Imports: utils, RColorBrewer, ape, reshape2, sna, plyr, ggmap, scales, rjson, networkDynamic, RCurl
Suggests: EpiEstim
Published: 2015-03-23
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://sites.google.com/site/therepiproject/r-pac/about
NeedsCompilation: no
Materials: ChangeLog
In views: Phylogenetics
CRAN checks: OutbreakTools results

Downloads:

Reference manual: OutbreakTools.pdf
Vignettes: Handling disease outbreak data
Package source: OutbreakTools_0.1-13.tar.gz
Windows binaries: r-devel: OutbreakTools_0.1-13.zip, r-release: OutbreakTools_0.1-13.zip, r-oldrel: OutbreakTools_0.1-13.zip
OS X Snow Leopard binaries: r-release: OutbreakTools_0.1-13.tgz, r-oldrel: OutbreakTools_0.1-13.tgz
OS X Mavericks binaries: r-release: OutbreakTools_0.1-13.tgz
Old sources: OutbreakTools archive

Reverse dependencies:

Reverse imports: repijson