title: OutbreakTools: a new platform for disease outbreak analysis using the R software.
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.
authors.affiliation: 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.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Jombart
authors.affiliation: 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.
authors.forename: David M
authors.initials: DM
authors.lastname: Aanensen
authors.affiliation: 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.
authors.forename: Marc
authors.initials: M
authors.lastname: Baguelin
authors.affiliation: MRC Biostatistics Unit, Institute of Public Health, University Forvie Site, Cambridge, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Birrell
authors.affiliation: Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Cauchemez
authors.affiliation: Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom.
authors.forename: Anton
authors.initials: A
authors.lastname: Camacho
authors.affiliation: Department of Mathematics, Imperial College London, United Kingdom.
authors.forename: Caroline
authors.initials: C
authors.lastname: Colijn
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Caitlin
authors.initials: C
authors.lastname: Collins
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Anne
authors.initials: A
authors.lastname: Cori
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, United Kingdom.
authors.forename: Simon
authors.initials: S
authors.lastname: Frost
authors.affiliation: 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.
authors.forename: Niel
authors.initials: N
authors.lastname: Hens
authors.affiliation: 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.
authors.forename: Joseph
authors.initials: J
authors.lastname: Hugues
authors.affiliation: Department of Mathematics, Stockholm University, Stockholm, Sweden.
authors.forename: Michael
authors.initials: M
authors.lastname: Höhle
authors.affiliation: Pharmacoepidemiology and Infectious Diseases Unit, Université de Versailles Saint Quentin EA4499/Institut Pasteur, Paris, France.
authors.forename: Lulla
authors.initials: L
authors.lastname: Opatowski
authors.affiliation: Institute of Evolutionary Biology, Center for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Oliver
authors.initials: O
authors.lastname: Ratmann
authors.affiliation: INRA, UR546 Biostatistics and Spatial Processes, Avignon 84914, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Soubeyrand
authors.affiliation: 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.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.affiliation: Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
authors.forename: Jacco
authors.initials: J
authors.lastname: Wallinga
authors.affiliation: Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
authors.forename: Rolf
authors.initials: R
authors.lastname: Ypma
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.
authors.forename: Neil
authors.initials: N
authors.lastname: Ferguson
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004196:Disease Outbreaks / Q000517:prevention & control / Q000706:statistics & numerical data*; D004812:Epidemiologic Methods; D063025:Health Information Management / Q000379:methods* / Q000458:organization & administration; D006801:Humans; D040442:Public Health Informatics / Q000379:methods*; D012984:Software
keywords: Bioinformatics; Epidemics; Epidemiology; Free; Infectious disease; Public health; R; Software