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OutbreakTools

Summary
OutbreakTools is the R package created during "Hackout: a hackathon for the analysis of disease outbreaks using R", which took place at the MRC Centre for Outbreak Analysis and Modeling at Imperial College, London, in January 2013. The purpose of OutbreakTools is to implement basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools.

Note: OutbreakTools replaces a package previously class epibase which caused an infringement of a deposited trademark. 


Features
  • classe 'obkData' for storing complex outbreak data including data on patients (e.g. age, sex), any type of observation/sample made on the patients (e.g. symptoms, swabs, DNA sequence collection, ...), static or dynamic contacts between patients, contextual information (e.g. weather indicators, clinical intervention, ...), and even phylogenetic trees
  • various types of graphics: timeline of samples per individuals, geographic distribution of the samples, contact networks, phylogenetic trees, minimum spanning trees
  • [in development] computation of incidence based on any time-stamped information

Screenshots
Timeline plot of pandemic influenza data
 Timeline plot of selected cases, equine influenza data

Geographic distribution of cases by sex.


Download/installation
The current version of OutbreakTools is 0.1-0 for R 3.0.2. OutbreakTools can be installed from R as other packages by typing:
install.packages("OutbreakTools", dependencies=TRUE)

See CRAN for manual downloads.

The development of OutbreakTools is currently hosted by sourceforge:


Documentation
OutbreakTools is distributed with the following documentation:


Feature request / bug report
If there is a feature you would like to suggest, or a bug you would like to report, use the ticket system on sourceforge.


Authors/contributors
OutbreakTools was initially created by the 'Hackout team'. 

The current list of contributors is:
David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caitlin Collins, Caroline Colijn, Anne Cori, Xavier Didelot, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Michael Höhle, Thibaut Jombart, Yee Loong Low, Lulla Opatowski, Andrew Rambaut, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma

OutbreakTools is maintained by Thibaut Jombart.












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