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

Jombart, T. et al. (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34. (doi: 10.1016/j.epidem.2014.04.003)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Hughes, Dr Joseph
• Authors: Jombart, T., Aanensen, D. M., 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, M. A., Wallinga, J., Ypma, R., and Ferguson, N.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Epidemics
• Publisher: Elsevier
• ISSN: 1755-4365
• ISSN (Online): 1878-0067
• Copyright Holders: Crown Copyright © 2014
• First Published: First published in Epidemics 7:28-34
• Publisher Policy: Reproduced under a Creative Commons License