{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T13:03:56Z","timestamp":1776258236982,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006204","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T00:00:00Z","timestamp":1529452800000}}],"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2018,6,8]],"date-time":"2018-06-08T00:00:00Z","timestamp":1528416000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["U01GM110744"],"award-info":[{"award-number":["U01GM110744"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006204","type":"journal-article","created":{"date-parts":[[2018,6,8]],"date-time":"2018-06-08T17:33:21Z","timestamp":1528479201000},"page":"e1006204","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":41,"title":["Anticipating epidemic transitions with imperfect data"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0906-441X","authenticated-orcid":true,"given":"Tobias S.","family":"Brett","sequence":"first","affiliation":[]},{"given":"Eamon B.","family":"O\u2019Dea","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8618-7280","authenticated-orcid":true,"given":"\u00c9ric","family":"Marty","sequence":"additional","affiliation":[]},{"given":"Paige B.","family":"Miller","sequence":"additional","affiliation":[]},{"given":"Andrew W.","family":"Park","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4646-1235","authenticated-orcid":true,"given":"John M.","family":"Drake","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7221-3801","authenticated-orcid":true,"given":"Pejman","family":"Rohani","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2018,6,8]]},"reference":[{"issue":"6996","key":"ref1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature02759","article-title":"The challenge of emerging and re-emerging infectious diseases","volume":"430","author":"D Morens","year":"2004","journal-title":"Nature"},{"key":"ref2","first-page":"1","article-title":"The genesis and source of the H7N9 influenza viruses causing human infections in China","author":"TTY Lam","year":"2013","journal-title":"Nature"},{"issue":"5650","key":"ref3","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1126\/science.1090350","article-title":"Are we ready for pandemic influenza?","volume":"302","author":"R Webby","year":"2003","journal-title":"Science (New York, NY)"},{"issue":"5958","key":"ref4","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1126\/science.1177345","article-title":"Epidemic dynamics at the human-animal interface","volume":"326","author":"JO Lloyd-Smith","year":"2009","journal-title":"Science"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid0101.950102","article-title":"Factors in the emergence of infectious diseases","volume":"1","author":"SS Morse","year":"1995","journal-title":"Emerging Infectious Diseases"},{"issue":"5634","key":"ref6","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1126\/science.1086726","article-title":"Measles outbreaks in a population with declining vaccine uptake","volume":"301","author":"VAA Jansen","year":"2003","journal-title":"Science"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1002993","article-title":"Inference of R<sub>0<\/sub> and transmission heterogeneity from the size distribution of stuttering chains","volume":"9","author":"S Blumberg","year":"2013","journal-title":"PLoS Computational Biology"},{"issue":"3","key":"ref8","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s12080-013-0185-5","article-title":"Theory of early warning signals of disease emergence and leading indicators of elimination","volume":"6","author":"SM O\u2019Regan","year":"2013","journal-title":"Theoretical Ecology"},{"issue":"3","key":"ref9","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1007\/s00332-012-9158-x","article-title":"A mathematical framework for critical transitions: normal forms, variance and applications","volume":"23","author":"C Kuehn","year":"2013","journal-title":"Journal of Nonlinear Science"},{"key":"ref10","doi-asserted-by":"crossref","DOI":"10.1038\/srep13190","article-title":"Early warning signs for saddle-escape transitions in complex networks","volume":"5","author":"C Kuehn","year":"2015","journal-title":"Scientific Reports"},{"issue":"5","key":"ref11","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.3934\/mbe.2016032","article-title":"Heterogeneous population dynamics and scaling laws near epidemic outbreaks","volume":"13","author":"A Widder","year":"2016","journal-title":"Mathematical Biosciences and Engineering"},{"issue":"3","key":"ref12","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s12080-015-0285-5","article-title":"Leading indicators of mosquito-borne disease elimination","volume":"9","author":"SM O\u2019Regan","year":"2016","journal-title":"Theoretical Ecology"},{"issue":"132","key":"ref13","doi-asserted-by":"crossref","first-page":"20170115","DOI":"10.1098\/rsif.2017.0115","article-title":"Anticipating the emergence of infectious diseases","volume":"14","author":"TS Brett","year":"2017","journal-title":"Journal of The Royal Society Interface"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s12976-017-0063-8","article-title":"Forecasting infectious disease emergence subject to seasonal forcing","volume":"14","author":"PB Miller","year":"2017","journal-title":"Theoretical Biology and Medical Modelling"},{"issue":"7260","key":"ref15","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature08227","article-title":"Early-warning signals for critical transitions","volume":"461","author":"M Scheffer","year":"2009","journal-title":"Nature"},{"issue":"6033","key":"ref16","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1126\/science.1203672","article-title":"Early warnings of regime shifts: a whole-ecosystem experiment","volume":"332","author":"SR Carpenter","year":"2011","journal-title":"Science"},{"issue":"3","key":"ref17","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/s12080-009-0060-6","article-title":"Spatial correlation as leading indicator of catastrophic shifts","volume":"3","author":"V Dakos","year":"2010","journal-title":"Theoretical Ecology"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"e92097","DOI":"10.1371\/journal.pone.0092097","article-title":"Early warning signals of ecological transitions: methods for spatial patterns","volume":"9","author":"S Kefi","year":"2014","journal-title":"PloS One"},{"issue":"38","key":"ref19","doi-asserted-by":"crossref","first-page":"14308","DOI":"10.1073\/pnas.0802430105","article-title":"Slowing down as an early warning signal for abrupt climate change","volume":"105","author":"V Dakos","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6085","key":"ref20","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1126\/science.1219805","article-title":"Generic indicators for loss of resilience before a tipping point leading to population collapse","volume":"336","author":"L Dai","year":"2012","journal-title":"Science"},{"issue":"7314","key":"ref21","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/nature09389","article-title":"Early warning signals of extinction in deteriorating environments","volume":"467","author":"JM Drake","year":"2010","journal-title":"Nature"},{"key":"ref22","article-title":"Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering","author":"SH Strogatz","year":"2001"},{"key":"ref23","article-title":"The Elements of Stochastic Processes with Applications to the Natural Sciences","volume":"vol. 25","author":"NTJ Bailey","year":"1990"},{"key":"ref24","article-title":"Stochastic Processes in Physics and Chemistry","author":"NG van Kampen","year":"1981"},{"issue":"2","key":"ref25","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1111\/1467-9868.00177","article-title":"Statistical studies of infectious disease incidence","volume":"61","author":"NG Becker","year":"1999","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"issue":"1","key":"ref26","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1471-2458-14-147","article-title":"Measuring underreporting and under-ascertainment in infectious disease datasets: a comparison of methods","volume":"14","author":"CL Gibbons","year":"2014","journal-title":"BMC Public Health"},{"issue":"9","key":"ref27","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1093\/aje\/155.9.866","article-title":"Completeness of notifiable infectious disease reporting in the United States: an analytical literature review","volume":"155","author":"TJ Doyle","year":"2002","journal-title":"American Journal of Epidemiology"},{"issue":"7206","key":"ref28","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/nature07084","article-title":"Inapparent infections and cholera dynamics","volume":"454","author":"AA King","year":"2008","journal-title":"Nature"},{"issue":"6","key":"ref29","doi-asserted-by":"crossref","first-page":"e1002172","DOI":"10.1371\/journal.pbio.1002172","article-title":"Unraveling the transmission ecology of polio","volume":"13","author":"M Martinez-Bakker","year":"2015","journal-title":"PLoS Biol"},{"issue":"12","key":"ref30","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1098\/rsif.2006.0161","article-title":"Comparative estimation of the reproduction number for pandemic influenza from daily case notification data","volume":"4","author":"G Chowell","year":"2007","journal-title":"Journal of the Royal Society Interface"},{"issue":"5543","key":"ref31","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1126\/science.1065973","article-title":"Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape","volume":"294","author":"MJ Keeling","year":"2001","journal-title":"Science"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1056\/NEJMp1605367","article-title":"Zika and the risk of microcephaly","volume":"375","author":"MA Johansson","year":"2016","journal-title":"New England Journal of Medicine"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","article-title":"A general method for numerically simulating the stochastic time evolution of coupled chemical reactions","volume":"22","author":"DT Gillespie","year":"1976","journal-title":"Journal of Computational Physics"},{"issue":"22","key":"ref34","doi-asserted-by":"crossref","first-page":"2152","DOI":"10.1056\/NEJMms1215400","article-title":"Contagious diseases in the United States from 1888 to the present","volume":"369","author":"WG Van Panhuis","year":"2013","journal-title":"The New England journal of medicine"},{"issue":"7","key":"ref35","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.2105\/AJPH.83.7.1011","article-title":"Reporting efficiency during a measles outbreak in New York City, 1991","volume":"83","author":"SF Davis","year":"1993","journal-title":"American Journal of Public Health"},{"issue":"5","key":"ref36","doi-asserted-by":"crossref","first-page":"868","DOI":"10.2105\/AJPH.84.5.868-a","article-title":"The reporting efficiency of measles by hospitals in Los Angeles County, 1986 and 1989","volume":"84","author":"D Ewert","year":"1994","journal-title":"American journal of public health"},{"key":"ref37","doi-asserted-by":"crossref","DOI":"10.1515\/9781400841035","article-title":"Modeling infectious diseases in humans and animals","author":"MJ Keeling","year":"2008"},{"issue":"1","key":"ref38","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1214\/08-AOAS201","article-title":"Time series analysis via mechanistic models","volume":"3","author":"C Bret\u00f3","year":"2009","journal-title":"The Annals of Applied Statistics"},{"issue":"8","key":"ref39","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.patrec.2005.10.010","article-title":"An introduction to ROC analysis","volume":"27","author":"T Fawcett","year":"2006","journal-title":"Pattern Recognition Letters"},{"key":"ref40","first-page":"869","article-title":"Encyclopedia of machine learning","author":"PA Flach","year":"2011"},{"key":"ref41","article-title":"Springer Series in Statistics","author":"T Hastie","year":"2001"},{"issue":"6967","key":"ref42","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/nature02104","article-title":"The role of evolution in the emergence of infectious diseases","volume":"426","author":"R Antia","year":"2003","journal-title":"Nature"},{"issue":"12","key":"ref43","article-title":"Statistical inference for Partially Observed Markov Processes via the R Package pomp","volume":"69","author":"AA King","year":"2016","journal-title":"Journal of Statistical Software"},{"key":"ref44","doi-asserted-by":"crossref","unstructured":"O\u2019Dea E. spaero: Software for Project AERO; 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/CRAN.R-project.org\/package=spaero\" xlink:type=\"simple\">https:\/\/CRAN.R-project.org\/package=spaero<\/ext-link>.","DOI":"10.32614\/CRAN.package.spaero"},{"issue":"7348","key":"ref45","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/473446a","article-title":"Lessons from polio eradication","volume":"473","author":"HJ Larson","year":"2011","journal-title":"Nature"},{"issue":"5296","key":"ref46","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1126\/science.275.5296.65","article-title":"Disease extinction and community size: modeling the persistence of measles","volume":"275","author":"MJ Keeling","year":"1997","journal-title":"Science"},{"issue":"9","key":"ref47","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1093\/aje\/kwu209","article-title":"Serial intervals of respiratory infectious diseases: a systematic review and analysis","volume":"180","author":"MA Vink","year":"2014","journal-title":"American Journal of Epidemiology"},{"issue":"5627","key":"ref48","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1126\/science.1086616","article-title":"Transmission dynamics and control of severe acute respiratory syndrome","volume":"300","author":"M Lipsitch","year":"2003","journal-title":"Science"},{"issue":"3","key":"ref49","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1097\/EDE.0b013e31819d1092","article-title":"Estimation of the serial interval of influenza","volume":"20","author":"BJ Cowling","year":"2009","journal-title":"Epidemiology (Cambridge, Mass)"},{"key":"ref50","article-title":"Estimation of MERS-coronavirus reproductive number and case fatality rate for the spring 2014 Saudi Arabia outbreak: insights from publicly available data","volume":"6","author":"MS Majumder","year":"2014","journal-title":"PLoS Currents"},{"issue":"1","key":"ref51","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/s12916-014-0196-0","article-title":"Transmission dynamics and control of Ebola virus disease (EVD): a review","volume":"12","author":"G Chowell","year":"2014","journal-title":"BMC Medicine"},{"issue":"3","key":"ref52","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.epidem.2011.10.001","article-title":"The decline and resurgence of pertussis in the US","volume":"3","author":"P Rohani","year":"2011","journal-title":"Epidemics"},{"issue":"7470","key":"ref53","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature12515","article-title":"The genesis and source of the H7N9 influenza viruses causing human infections in China","volume":"502","author":"TTY Lam","year":"2013","journal-title":"Nature"},{"issue":"25","key":"ref54","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES2015.20.25.21163","article-title":"Preliminary epidemiologic assessment of MERS-CoV outbreak in South Korea, May\u2014June 2015","volume":"20","author":"BJ Cowling","year":"2015","journal-title":"Eurosurveillance"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006204","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T00:00:00Z","timestamp":1529452800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006204","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,7]],"date-time":"2024-07-07T10:53:07Z","timestamp":1720349587000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006204"}},"subtitle":[],"editor":[{"given":"Mercedes","family":"Pascual","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,8]]},"references-count":54,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2018,6,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006204","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006204","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,8]]}}}