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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 | Source: | 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 | Keywords: | software; free; bioinformatics; epidemiology; R; epidemics; public health; infectious disease | Document URI: | http://hdl.handle.net/1942/16879 | ISSN: | 1755-4365 | e-ISSN: | 1878-0067 | DOI: | 10.1016/j.epidem.2014.04.003 | ISI #: | 000338704900005 | Rights: | Crown Copyright © 2014 Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2015 |
Appears in Collections: | Research publications |
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Jombart et al. Epidemics 2014.pdf | Published version | 1.8 MB | Adobe PDF | View/Open |
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