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, Suchard Marc A, Wallinga Jacco, Ypma Rolf, Ferguson Neil
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
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.
Epidemics. 2014 Jun;7(100):28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.
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.
传染病暴发调查依赖于对日益复杂和多样的数据进行分析，这些数据为深入了解疾病传播过程及为公共卫生政策提供依据带来了新的前景。然而，此类数据的潜力只有通过多种不同的互补方法和工具才能得以利用，且目前仍缺乏一个用于分析疾病暴发的统一平台。在本文中，我们介绍了新的R包OutbreakTools，其旨在为R语言中的暴发数据管理和分析提供基础。OutbreakTools由一群流行病学家、统计学家、建模人员和生物信息学家共同开发，实现了用于存储、处理和可视化暴发数据的类和方法。它包含真实和模拟的暴发数据集。与R语言中最近推出的一些传染病流行病学工具一起，OutbreakTools为一个新的、免费且开源的疾病暴发分析平台的出现做出了贡献。
