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.

Original publication

DOI

10.1016/j.epidem.2014.04.003

Type

Journal article

Journal

Epidemics

Publication Date

06/2014

Volume

7

Pages

28 - 34

Addresses

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.

Keywords

Humans, Epidemiologic Methods, Computational Biology, Disease Outbreaks, Software, Public Health Informatics, Health Information Management