OutbreakTools: a new platform for disease outbreak analysis using the R software.

TitleOutbreakTools: a new platform for disease outbreak analysis using the R software.
Publication TypeJournal Article
Year of Publication2014
AuthorsJombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N
JournalEpidemics
Volume7
Pagination28-34
Date Published2014 Jun
ISSN1878-0067
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.

DOI10.1016/j.epidem.2014.04.003
Alternate JournalEpidemics
PubMed ID24928667
PubMed Central IDPMC4058532
Grant List099202/Z/12/Z / / Wellcome Trust / United Kingdom
MR/J013862/1 / / Medical Research Council / United Kingdom
U54 GM088491 / GM / NIGMS NIH HHS / United States
UM1 AI068619 / AI / NIAID NIH HHS / United States
WR/094527 / / Wellcome Trust / United Kingdom
WR092311MF / / Wellcome Trust / United Kingdom
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