Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/16879
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dc.contributor.authorJombart, Thibaut-
dc.contributor.authorAanensen, David M.-
dc.contributor.authorBaguelin, Marc-
dc.contributor.authorBirrell, Paul-
dc.contributor.authorCauchemez, Simon-
dc.contributor.authorCamacho, Anton-
dc.contributor.authorColijn, Caroline-
dc.contributor.authorCollins, Caitlin-
dc.contributor.authorCori, Anne-
dc.contributor.authorDidelot, Xavier-
dc.contributor.authorFraser, Christophe-
dc.contributor.authorFrost, Simon-
dc.contributor.authorHENS, Niel-
dc.contributor.authorHugues, Joseph-
dc.contributor.authorHöhle, Michael-
dc.contributor.authorOpatowski, Lulla-
dc.contributor.authorRambaut, Andrew-
dc.contributor.authorRatmann, Oliver-
dc.contributor.authorSoubeyrand, Samuel-
dc.contributor.authorSuchardo, Marc A.-
dc.contributor.authorWallinga, Jacco-
dc.contributor.authorYpma, Rolf-
dc.contributor.authorFerguson, Neil-
dc.date.accessioned2014-06-13T08:17:10Z-
dc.date.available2014-06-13T08:17:10Z-
dc.date.issued2014-
dc.identifier.citationEpidemics, 7, p. 28-34-
dc.identifier.issn1755-4365-
dc.identifier.urihttp://hdl.handle.net/1942/16879-
dc.description.abstractThe 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.-
dc.description.sponsorshipWe are thankful to Tanja Stadler and two anonymous referees for their thorough reviews and useful comments. We thank Sourceforge (http://sourceforge.net/) for providing a great platform for software development. OutbreakTools has been created during "Hackout: a hackathon for the analysis of disease outbreaks in R" (http://sites.google.com/site/hackoutwiki/), an event funded by the Medical Research Council. T. Jombart and C. Collins are funded by the Medical Research Council and MIDAS. D. Aanensen is funded by the Wellcome Trust (grant 099202/Z/12/Z). M. Baguelin and A. Camacho are supported by the Wellcome Trust (project grant WR/094527). A. Camacho is also funded by the Medical Research Council (fellowship MR/J01432X/1). A. Cori thanks the NIH for funding through the NIAID cooperative agreement UM1 A1068619. M.A. Suchard is supported through National Science Foundation grants DMS 126153 and IIS 1251151. N. Hens acknowledges support from the University of Antwerp scientific chair in Evidence-Based Vaccinology, financed in 2009-2014 by a gift from Pfizer. O. Ratmann is supported by the Wellcome Trust (fellowship WR092311MF). C. Colijn acknowledges support from the Engineering and Physical Sciences Research Council (EP/I031626/1; EP/K026003/1). S. Frost is supported in part by the Royal Society, the ERSC (ES/J011266/1), and the MRC (MR/J013862/1).-
dc.language.isoen-
dc.rightsCrown Copyright © 2014 Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).-
dc.subject.othersoftware; free; bioinformatics; epidemiology; R; epidemics; public health; infectious disease-
dc.titleOutbreakTools: A new platform for disease outbreak analysis using the R software-
dc.typeJournal Contribution-
dc.identifier.epage34-
dc.identifier.spage28-
dc.identifier.volume7-
local.bibliographicCitation.jcatA1-
dc.description.notesJombart, T (reprint author), Univ London Imperial Coll Sci Technol & Med, Sch Publ Hlth, Dept Infect Dis Epidemiol, MRC Ctr Outbreak Anal & Modelling, St Marys Campus,Norfolk Pl, London W2 1PG, England. thibautjombart@gmail.com-
local.type.refereedRefereed-
local.type.specifiedArticle-
dc.identifier.doi10.1016/j.epidem.2014.04.003-
dc.identifier.isi000338704900005-
item.fullcitationJombart, 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; Suchardo, Marc A.; Wallinga, Jacco; Ypma, Rolf & Ferguson, Neil (2014) OutbreakTools: A new platform for disease outbreak analysis using the R software. In: Epidemics, 7, p. 28-34.-
item.fulltextWith Fulltext-
item.validationecoom 2015-
item.contributorJombart, Thibaut-
item.contributorAanensen, David M.-
item.contributorBaguelin, Marc-
item.contributorBirrell, Paul-
item.contributorCauchemez, Simon-
item.contributorCamacho, Anton-
item.contributorColijn, Caroline-
item.contributorCollins, Caitlin-
item.contributorCori, Anne-
item.contributorDidelot, Xavier-
item.contributorFraser, Christophe-
item.contributorFrost, Simon-
item.contributorHENS, Niel-
item.contributorHugues, Joseph-
item.contributorHöhle, Michael-
item.contributorOpatowski, Lulla-
item.contributorRambaut, Andrew-
item.contributorRatmann, Oliver-
item.contributorSoubeyrand, Samuel-
item.contributorSuchardo, Marc A.-
item.contributorWallinga, Jacco-
item.contributorYpma, Rolf-
item.contributorFerguson, Neil-
item.accessRightsOpen Access-
crisitem.journal.issn1755-4365-
crisitem.journal.eissn1878-0067-
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