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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/16879

Title: OutbreakTools: A new platform for disease outbreak analysis using the R software
Authors: Jombart, Thibaut
Aanensen, David M.
Baguelin, Marc
Birrell, Paul
Cauchemez, Simon
Camacho, Anton
Colijn, Caroline
Collins, Caitlin
Cori, Anne
Didelot, Xavier
Fraser, Christophe
Frost, Simon
HENS, Niel
Hugues, Joseph
Höhle, Michael
Opatowski, Lulla
Rambaut, Andrew
Ratmann, Oliver
Soubeyrand, Samuel
Suchardo, Marc A.
Wallinga, Jacco
Ypma, Rolf
Ferguson, Neil
Issue Date: 2014
Citation: Epidemics, 7, p. 28-34
Abstract: The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools, and a unified platform for the analysis of disease outbreaks is still lacking. In this paper, we present the new R package OutbreakTools, which aims to provide a basis for outbreak data management and analysis in R. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data. It includes real and simulated outbreak datasets. Together with a number of tools for infectious disease epidemiology recently made available in R, OutbreakTools contributes to the emergence of a new, free and open-source platform for the analysis of disease outbreaks.
Notes: Jombart, T (reprint author), Univ London Imperial Coll Sci Technol & Med, Sch Publ Hlth, Dept Infect Dis Epidemiol, MRC Ctr Outbreak Anal & Modelling, St Marys Campus,Norfolk Pl, London W2 1PG, England. thibautjombart@gmail.com
URI: http://hdl.handle.net/1942/16879
DOI: 10.1016/j.epidem.2014.04.003
ISI #: 000338704900005
ISSN: 1755-4365
Category: A1
Type: Journal Contribution
Validation: ecoom, 2015
Appears in Collections: Research publications

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