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Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

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

Author information

1
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom. Electronic address: thibautjombart@gmail.com.
2
Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
3
Immunisation, Hepatitis and Blood Safety Department, Public Health England, London, United Kingdom; Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom.
4
MRC Biostatistics Unit, Institute of Public Health, University Forvie Site, Cambridge, United Kingdom.
5
Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France.
6
Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom.
7
Department of Mathematics, Imperial College London, United Kingdom.
8
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
9
Department of Veterinary Medicine, University of Cambridge, United Kingdom.
10
Interuniversity Institute of Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium; Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
11
MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
12
Department of Mathematics, Stockholm University, Stockholm, Sweden.
13
Pharmacoepidemiology and Infectious Diseases Unit, Université de Versailles Saint Quentin EA4499/Institut Pasteur, Paris, France.
14
Institute of Evolutionary Biology, Center for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom.
15
INRA, UR546 Biostatistics and Spatial Processes, Avignon 84914, France.
16
Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA.
17
Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.

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.

KEYWORDS:

Bioinformatics; Epidemics; Epidemiology; Free; Infectious disease; Public health; R; Software

PMID:
24928667
PMCID:
PMC4058532
DOI:
10.1016/j.epidem.2014.04.003
[Indexed for MEDLINE]
Free PMC Article

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