{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T04:40:27Z","timestamp":1774413627937,"version":"3.50.1"},"reference-count":103,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T00:00:00Z","timestamp":1730073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Modelling and Health Economics","award":["NIHR200908"],"award-info":[{"award-number":["NIHR200908"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/X020258\/1"],"award-info":[{"award-number":["MR\/X020258\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Laboratoire d\u2019Excellence Integrative Biology of Emerging Infectious Diseases program","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}]},{"name":"INCEPTION","award":["PIA\/ANR16-CONV-0005"],"award-info":[{"award-number":["PIA\/ANR16-CONV-0005"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012520","type":"journal-article","created":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T17:21:53Z","timestamp":1730136113000},"page":"e1012520","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":22,"title":["Best practices for estimating and reporting epidemiological delay distributions of infectious diseases"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7648-7041","authenticated-orcid":true,"given":"Kelly","family":"Charniga","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sang Woo","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei R.","family":"Akhmetzhanov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Cori","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan","family":"Dushoff","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Funk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katelyn M.","family":"Gostic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie M.","family":"Linton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6822-8437","authenticated-orcid":true,"given":"Adrian","family":"Lison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher E.","family":"Overton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3314-8223","authenticated-orcid":true,"given":"Juliet R. C.","family":"Pulliam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Ward","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Cauchemez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sam","family":"Abbott","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,10,28]]},"reference":[{"key":"pcbi.1012520.ref001","author":"Home | NSF NEON","journal-title":"Open Data to Understand our Ecosystems"},{"key":"pcbi.1012520.ref002","unstructured":"EarthRanger: Protecting Wildlife With Real-Time Data. [cited 2024 Aug 23]. Available from: https:\/\/www.earthranger.com\/."},{"key":"pcbi.1012520.ref003","doi-asserted-by":"crossref","first-page":"e13534","DOI":"10.7717\/peerj.13534","article-title":"A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest.","volume":"10","author":"A Paz","year":"2022","journal-title":"PeerJ"},{"key":"pcbi.1012520.ref004","doi-asserted-by":"crossref","first-page":"e1502","DOI":"10.7717\/peerj-cs.1502","article-title":"Real-time biodiversity analysis using deep-learning algorithms on mobile robotic platforms.","volume":"9","author":"S Panigrahi","year":"2023","journal-title":"PeerJ Comput Sci"},{"key":"pcbi.1012520.ref005","doi-asserted-by":"crossref","first-page":"18727","DOI":"10.1038\/s41598-024-68502-8","article-title":"Towards real-time monitoring of insect species populations.","volume":"14","author":"T Venverloo","year":"2024","journal-title":"Sci Rep."},{"key":"pcbi.1012520.ref006","first-page":"20230464","article-title":"Ongoing over-exploitation and delayed responses to environmental change highlight the urgency for action to promote vertebrate recoveries by 2030","volume":"290","author":"R Cornford","year":"2023","journal-title":"Proc Biol Sci"},{"key":"pcbi.1012520.ref007","article-title":"Estimating the incubation period of monkeypox virus during the 2022 multi-national outbreak.","author":"K Charniga","year":"2022","journal-title":"medRxiv"},{"key":"pcbi.1012520.ref008","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S1473-3099(09)70069-6","article-title":"Incubation periods of acute respiratory viral infections: a systematic review","volume":"9","author":"J Lessler","year":"2009","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1012520.ref009","doi-asserted-by":"crossref","first-page":"e1011463","DOI":"10.1371\/journal.pcbi.1011463","article-title":"Nowcasting the 2022 mpox outbreak in England.","volume":"19","author":"CE Overton","year":"2023","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1012520.ref010","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41586-020-2488-1","article-title":"Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo\u2019","volume":"584","author":"E Lavezzo","year":"2020","journal-title":"Nature"},{"key":"pcbi.1012520.ref011","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1056\/NEJMoa1411100","article-title":"Ebola Virus Disease in West Africa\u2014The First 9 Months of the Epidemic and Forward Projections.","volume":"371","author":"WHO Ebola Response Team","year":"2014","journal-title":"N Engl J Med"},{"key":"pcbi.1012520.ref012","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1126\/science.1176062","article-title":"Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings.","volume":"324","author":"C Fraser","year":"2009","journal-title":"Science"},{"key":"pcbi.1012520.ref013","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1126\/science.aag0219","article-title":"Countering the Zika epidemic in Latin America","volume":"353","author":"NM Ferguson","year":"2016","journal-title":"Science"},{"key":"pcbi.1012520.ref014","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.1017\/S0950268822001935","article-title":"Replacement dynamics and the pathogenesis of the Alpha, Delta and Omicron variants of SARS-CoV-2","volume":"151","author":"T Ward","year":"2023","journal-title":"Epidemiol Infect"},{"key":"pcbi.1012520.ref015","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1086\/505880","article-title":"Clinical Manifestations of Human Monkeypox Influenced by Route of Infection","volume":"194","author":"MG Reynolds","year":"2006","journal-title":"J Infect Dis"},{"key":"pcbi.1012520.ref016","doi-asserted-by":"crossref","first-page":"e409","DOI":"10.1016\/S2666-5247(23)00005-8","article-title":"SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study","volume":"4","author":"S Galmiche","year":"2023","journal-title":"Lancet Microbe"},{"key":"pcbi.1012520.ref017","doi-asserted-by":"crossref","first-page":"e2113561119","DOI":"10.1073\/pnas.2113561119","article-title":"Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States","volume":"119","author":"E Cramer","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012520.ref018","doi-asserted-by":"crossref","first-page":"100705","DOI":"10.1016\/j.epidem.2023.100705","article-title":"Public health impact of the U.S. Scenario Modeling Hub","volume":"44","author":"RK Borchering","year":"2023","journal-title":"Epidemics"},{"key":"pcbi.1012520.ref019","article-title":"Modeling the impact of prioritizing first or second vaccine doses during the 2022 mpox outbreak.","author":"PA Clay","year":"2023","journal-title":"Infect Dis (except HIV\/AIDS)."},{"key":"pcbi.1012520.ref020","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.ijid.2020.02.060","article-title":"Serial interval of novel coronavirus (COVID-19) infections.","volume":"93","author":"H Nishiura","year":"2020","journal-title":"Int J Infect Dis"},{"key":"pcbi.1012520.ref021","doi-asserted-by":"crossref","first-page":"58","DOI":"10.12688\/wellcomeopenres.15788.1","article-title":"The contribution of pre-symptomatic infection to the transmission dynamics of COVID-2019 [version 1; peer review: 3 approved].","volume":"5","author":"Centre for Mathematical Modelling of Infectious Diseases nCoV Working Group","year":"2020","journal-title":"Wellcome Open Res."},{"key":"pcbi.1012520.ref022","doi-asserted-by":"crossref","first-page":"6146","DOI":"10.1073\/pnas.0307506101","article-title":"Factors that make an infectious disease outbreak controllable","volume":"101","author":"C Fraser","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012520.ref023","article-title":"Estimating epidemiological delay distributions for infectious diseases.","author":"SW Park","year":"2024","journal-title":"medRxiv"},{"key":"pcbi.1012520.ref024","doi-asserted-by":"crossref","first-page":"e073153","DOI":"10.1136\/bmj-2022-073153","article-title":"Transmission dynamics of monkeypox in the United Kingdom: contact tracing study","author":"T Ward","year":"2022","journal-title":"BMJ"},{"key":"pcbi.1012520.ref025","first-page":"409","article-title":"Using statistics and mathematical modelling to understand infectious disease outbreaks: COVID-19 as an example.","volume":"5","author":"CE Overton","year":"2020","journal-title":"Infect Dis Model."},{"key":"pcbi.1012520.ref026","doi-asserted-by":"crossref","first-page":"20180670","DOI":"10.1098\/rsif.2018.0670","article-title":"Estimation in emerging epidemics: biases and remedies.","volume":"16","author":"T Britton","year":"2019","journal-title":"J R Soc Interface"},{"key":"pcbi.1012520.ref027","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1177\/09622802211023955","article-title":"Estimating a time-to-event distribution from right-truncated data in an epidemic: A review of methods.","volume":"31","author":"SR Seaman","year":"2022","journal-title":"Stat Methods Med Res"},{"key":"pcbi.1012520.ref028","doi-asserted-by":"crossref","first-page":"e1008409","DOI":"10.1371\/journal.pcbi.1008409","article-title":"Practical considerations for measuring the effective reproductive number, Rt.","volume":"16","author":"KM Gostic","year":"2020","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1012520.ref029","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1126\/science.abc9004","article-title":"Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions","volume":"369","author":"ST Ali","year":"2020","journal-title":"Science"},{"key":"pcbi.1012520.ref030","article-title":"epiparameter.","author":"JW Lambert","year":"2023"},{"key":"pcbi.1012520.ref031","article-title":"epireview.","author":"R Nash"},{"key":"pcbi.1012520.ref032","volume-title":"WorldHealthOrganization\/collaboratory-epiparameter-community.","year":"2023"},{"key":"pcbi.1012520.ref033","doi-asserted-by":"crossref","first-page":"e039652","DOI":"10.1136\/bmjopen-2020-039652","article-title":"Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research","volume":"10","author":"C McAloon","year":"2020","journal-title":"BMJ Open"},{"key":"pcbi.1012520.ref034","first-page":"S1473309923005157","article-title":"Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review","author":"G Cuomo-Dannenburg","year":"2023","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1012520.ref035","article-title":"Lassa fever outbreaks, mathematical models, and disease parameters: a systematic review and meta-analysis.","author":"P Doohan","year":"2024","journal-title":"medRxiv."},{"key":"pcbi.1012520.ref036","doi-asserted-by":"crossref","first-page":"818","DOI":"10.3201\/eid2904.221622","article-title":"Serial Interval and Incubation Period Estimates of Monkeypox Virus Infection in 12 Jurisdictions, United States, May\u2013August 2022","volume":"29","author":"ZJ Madewell","year":"2023","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1012520.ref037","doi-asserted-by":"crossref","first-page":"c6580","DOI":"10.1136\/bmj.c6580","article-title":"Mother to child transmission of HIV among Zimbabwean women who seroconverted postnatally: prospective cohort study","volume":"341","author":"JH Humphrey","year":"2010","journal-title":"BMJ"},{"key":"pcbi.1012520.ref038","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1001\/jama.1995.03530020061033","article-title":"Risk Factors for Tuberculosis in HIV-lnfected Persons: A Prospective Cohort Study","volume":"274","author":"G Antonucci","year":"1995","journal-title":"JAMA"},{"key":"pcbi.1012520.ref039","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1093\/infdis\/jit828","article-title":"The Source of Respiratory Syncytial Virus Infection In Infants: A Household Cohort Study In Rural Kenya","volume":"209","author":"PK Munywoki","year":"2014","journal-title":"J Infect Dis"},{"key":"pcbi.1012520.ref040","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1093\/aje\/kws402","article-title":"The Serial Intervals of Seasonal and Pandemic Influenza Viruses in Households in Bangkok, Thailand","volume":"177","author":"JW Levy","year":"2013","journal-title":"Am J Epidemiol"},{"key":"pcbi.1012520.ref041","first-page":"25","article-title":"Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.","volume":"2020","author":"TW Russell","journal-title":"Eurosurveillance"},{"key":"pcbi.1012520.ref042","unstructured":"Centers for Disease Control and Prevention. Introduction to Public Health. In: Public Health 101 Series. 2014 [cited 2024 Jan 9]. Available from: https:\/\/www.cdc.gov\/training\/publichealth101\/surveillance.html."},{"key":"pcbi.1012520.ref043","doi-asserted-by":"crossref","first-page":"944","DOI":"10.15585\/mmwr.mm7235a2","article-title":"Possible Exposures Among Mpox Patients Without Reported Male-to-Male Sexual Contact\u2014Six U.S. Jurisdictions, November 1\u2013December 14, 2022.","volume":"72","author":"JD Sharpe","year":"2023","journal-title":"MMWR Morb Mortal Wkly Rep."},{"key":"pcbi.1012520.ref044","doi-asserted-by":"crossref","first-page":"2769","DOI":"10.1002\/sim.3659","article-title":"Estimating incubation period distributions with coarse data.","volume":"28","author":"NG Reich","year":"2009","journal-title":"Stat Med"},{"key":"pcbi.1012520.ref045","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1038\/s41592-022-01563-7","article-title":"Survival analysis\u2014time-to-event data and censoring.","volume":"19","author":"T Dey","year":"2022","journal-title":"Nat Methods"},{"key":"pcbi.1012520.ref046","doi-asserted-by":"crossref","first-page":"e2011548118","DOI":"10.1073\/pnas.2011548118","article-title":"Forward-looking serial intervals correctly link epidemic growth to reproduction numbers","volume":"118","author":"SW Park","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012520.ref047","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/S1473-3099(20)30243-7","article-title":"Estimates of the severity of coronavirus disease 2019: a model-based analysis","volume":"20","author":"R Verity","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1012520.ref048","article-title":"coarseDataTools: Analysis of Coarsely Observed Data.","author":"NG Reich","year":"2021"},{"key":"pcbi.1012520.ref049","article-title":"Estimating delay distributions accounting for common biases.","author":"SW Park","year":"2023"},{"key":"pcbi.1012520.ref050","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1146\/annurev.publhealth.18.1.83","article-title":"CENSORING ISSUES IN SURVIVAL ANALYSIS.","volume":"18","author":"K-M Leung","year":"1997","journal-title":"Annu Rev Public Health."},{"key":"pcbi.1012520.ref051","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.3201\/eid2206.150579","article-title":"Extended Human-to-Human Transmission during a Monkeypox Outbreak in the Democratic Republic of the Congo","volume":"22","author":"LD Nolen","year":"2016","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1012520.ref052","doi-asserted-by":"crossref","first-page":"780","DOI":"10.4269\/ajtmh.1973.22.780","article-title":"Clinical presentation of lassa fever cases during the hospital epidemic at Zorzor, Liberia, March-April 1972","volume":"22","author":"PE Mertens","year":"1973","journal-title":"Am J Trop Med Hyg"},{"key":"pcbi.1012520.ref053","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1136\/pgmj.49.574.542","article-title":"Marburg virus disease.","volume":"49","author":"G. Martini","year":"1973","journal-title":"Postgrad Med J"},{"key":"pcbi.1012520.ref054","first-page":"247","article-title":"Ebola haemorrhagic fever in Sudan, 1976.","volume":"56","author":"WHO International Study Team","year":"1978","journal-title":"Bull World Health Organ"},{"key":"pcbi.1012520.ref055","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1742-7622-4-2","article-title":"Early efforts in modeling the incubation period of infectious diseases with an acute course of illness.","volume":"4","author":"H. Nishiura","year":"2007","journal-title":"Emerg Themes Epidemiol"},{"key":"pcbi.1012520.ref056","first-page":"27","article-title":"Estimated incubation period for monkeypox cases confirmed in the Netherlands, May 2022 Eurosurveillance.","author":"F Miura","year":"2022"},{"key":"pcbi.1012520.ref057","article-title":"The timing of COVID-19 transmission.","author":"L Ferretti","year":"2020","journal-title":"Epidemiology"},{"key":"pcbi.1012520.ref058","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1186\/s12889-021-10868-9","article-title":"Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID\u2212 19 in Ireland using contact tracing data.","volume":"21","author":"CG McAloon","year":"2021","journal-title":"BMC Public Health."},{"key":"pcbi.1012520.ref059","article-title":"Incubation-period estimates of Omicron (BA.1) variant from Taiwan, December 2021\u2013January 2022, and its comparison to other SARS-CoV-2 variants: a statistical modeling, systematic search and meta-analysis.","author":"AR Akhmetzhanov","year":"2023","journal-title":"Infect Dis (except HIV\/AIDS)"},{"key":"pcbi.1012520.ref060","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1186\/1471-2334-14-539","article-title":"The distribution of incubation and relapse times in experimental human infections with the malaria parasite Plasmodium vivax.","volume":"14","author":"AA Lover","year":"2014","journal-title":"BMC Infect Dis"},{"key":"pcbi.1012520.ref061","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.jtbi.2011.06.015","article-title":"The correlation between infectivity and incubation period of measles, estimated from households with two cases","volume":"284","author":"D Klinkenberg","year":"2011","journal-title":"J Theor Biol"},{"key":"pcbi.1012520.ref062","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1093\/jrsssc\/qlad011","article-title":"Faecal shedding models for SARS-CoV-2 RNA among hospitalised patients and implications for wastewater-based epidemiology","volume":"72","author":"T Hoffmann","year":"2023","journal-title":"J R Stat Soc Ser C Appl Stat"},{"key":"pcbi.1012520.ref063","article-title":"epinowcast\/epinowcast: Epinowcast 0.2.2.","author":"S Abbott","year":"2023","journal-title":"Zenodo"},{"key":"pcbi.1012520.ref064","doi-asserted-by":"crossref","first-page":"e79134","DOI":"10.7554\/eLife.79134","article-title":"The unmitigated profile of COVID-19 infectiousness.","volume":"11","author":"R Sender","year":"2022","journal-title":"Elife"},{"key":"pcbi.1012520.ref065","unstructured":"Gamma distribution. Wikipedia. 2024. Available from: https:\/\/en.wikipedia.org\/w\/index.php?title=Gamma_distribution&oldid=1210997995."},{"key":"pcbi.1012520.ref066","unstructured":"Log-normal distribution. Wikipedia. 2024. Available from: https:\/\/en.wikipedia.org\/w\/index.php?title=Log-normal_distribution&oldid=1210518171."},{"key":"pcbi.1012520.ref067","article-title":"EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters.","author":"S Abbott","year":"2023"},{"key":"pcbi.1012520.ref068","article-title":"epitrix: Small Helpers and Tricks for Epidemics Analysis.","author":"T Jombart","year":"2023"},{"key":"pcbi.1012520.ref069","article-title":"mixR: Finite Mixture Modeling for Raw and Binned Data.","author":"Y. Yu","year":"2021"},{"key":"pcbi.1012520.ref070","doi-asserted-by":"crossref","first-page":"150019","DOI":"10.1038\/sdata.2015.19","article-title":"A review of epidemiological parameters from Ebola outbreaks to inform early public health decision-making.","volume":"2","author":"MD Van Kerkhove","year":"2015","journal-title":"Sci Data"},{"key":"pcbi.1012520.ref071","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/328719a0","article-title":"Incubation period of AIDS in patients infected via blood transfusion","volume":"328","author":"GF Medley","year":"1987","journal-title":"Nature"},{"key":"pcbi.1012520.ref072","article-title":"Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates.","author":"A Lison","year":"2023"},{"key":"pcbi.1012520.ref073","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1093\/ije\/dyt043","article-title":"Markov Chain Monte Carlo: an introduction for epidemiologists.","volume":"42","author":"G Hamra","year":"2013","journal-title":"Int J Epidemiol."},{"key":"pcbi.1012520.ref074","volume-title":"A student\u2019s guide to Bayesian statistics","author":"B. Lambert","year":"2018"},{"key":"pcbi.1012520.ref075","unstructured":"RStan: the R interface to Stan. [cited 2024 Apr 10]. Available from: https:\/\/mc-stan.org\/rstan\/articles\/rstan.html."},{"key":"pcbi.1012520.ref076","article-title":"Stan Modeling Language Users Guide and Reference Manual Version 2.34","author":"Stan Development Team","year":"2022"},{"key":"pcbi.1012520.ref077","doi-asserted-by":"crossref","first-page":"15693","DOI":"10.1073\/pnas.0600816103","article-title":"Uncertainty in predictions of disease spread and public health responses to bioterrorism and emerging diseases","volume":"103","author":"BD Elderd","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012520.ref078","doi-asserted-by":"crossref","first-page":"e1003793","DOI":"10.1371\/journal.pmed.1003793","article-title":"Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines.","volume":"18","author":"S Pollett","year":"2021","journal-title":"PLoS Med."},{"key":"pcbi.1012520.ref079","first-page":"20","article-title":"Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2015.","volume":"2015","author":"BJ Cowling","journal-title":"Eurosurveillance"},{"key":"pcbi.1012520.ref080","first-page":"30","article-title":"SARS-CoV-2 Incubation Period during Omicron BA.5\u2013Dominant Period, Japan","author":"H-Y Cheng","year":"2024","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1012520.ref081","article-title":"Time Scales of Human Mpox Transmission in The Netherlands","author":"F Miura","year":"2023","journal-title":"J Infect Dis"},{"key":"pcbi.1012520.ref082","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1186\/s12859-018-2330-z","article-title":"outbreaker2: a modular platform for outbreak reconstruction","volume":"19","author":"F Campbell","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1012520.ref083","doi-asserted-by":"crossref","first-page":"e1004613","DOI":"10.1371\/journal.pcbi.1004613","article-title":"Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.","volume":"11","author":"M Hall","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1012520.ref084","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1002\/sim.3136","article-title":"A likelihood-based method for real-time estimation of the serial interval and reproductive number of an epidemic.","volume":"27","author":"L Forsberg White","year":"2008","journal-title":"Stat Med"},{"key":"pcbi.1012520.ref085","doi-asserted-by":"crossref","first-page":"e0148061","DOI":"10.1371\/journal.pone.0148061","article-title":"Estimation of the Basic Reproductive Number and Mean Serial Interval of a Novel Pathogen in a Small Well-Observed Discrete Population.","volume":"11","author":"KM Wu","year":"2016","journal-title":"PLoS ONE"},{"key":"pcbi.1012520.ref086","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1186\/s12879-023-08407-5","article-title":"Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants.","volume":"23","author":"ZJ Madewell","year":"2023","journal-title":"BMC Infect Dis"},{"key":"pcbi.1012520.ref087","article-title":"Prior Choice Recommendations.","author":"Stan Development Team.","journal-title":"GitHub"},{"key":"pcbi.1012520.ref088","doi-asserted-by":"crossref","first-page":"882","DOI":"10.4269\/ajtmh.13-0403","article-title":"Incubation Periods of Mosquito-Borne Viral Infections: A Systematic Review","volume":"90","author":"KE Rudolph","year":"2014","journal-title":"Am J Trop Med Hyg"},{"key":"pcbi.1012520.ref089","doi-asserted-by":"crossref","first-page":"e2221887120","DOI":"10.1073\/pnas.2221887120","article-title":"Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2","volume":"120","author":"SW Park","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012520.ref090","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.3201\/eid2712.210505","article-title":"Coronavirus Disease Contact Tracing Outcomes and Cost, Salt Lake County, Utah, USA, March\u2013May 2020","volume":"27","author":"VL Fields","year":"2021","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1012520.ref091","doi-asserted-by":"crossref","first-page":"e012660","DOI":"10.1136\/bmjgh-2023-012660","article-title":"The cost of public health interventions to respond to the 10th Ebola outbreak in the Democratic Republic of the Congo","volume":"8","author":"W Zeng","year":"2023","journal-title":"BMJ Glob Health"},{"key":"pcbi.1012520.ref092","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1111\/biom.12194","article-title":"Bayesian nowcasting during the STEC O104:H4 outbreak in Germany, 2011","volume":"70","author":"M H\u00f6hle","year":"2014","journal-title":"Biometrics"},{"key":"pcbi.1012520.ref093","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1097\/EDE.0000000000001050","article-title":"Nowcasting the Number of New Symptomatic Cases During Infectious Disease Outbreaks Using Constrained P-spline Smoothing.","volume":"30","author":"J Van De Kassteele","year":"2019","journal-title":"Epidemiology."},{"key":"pcbi.1012520.ref094","doi-asserted-by":"crossref","first-page":"4363","DOI":"10.1002\/sim.8303","article-title":"A modelling approach for correcting reporting delays in disease surveillance data.","volume":"38","author":"LS Bastos","year":"2019","journal-title":"Stat Med"},{"key":"pcbi.1012520.ref095","doi-asserted-by":"crossref","first-page":"e50972","DOI":"10.1371\/journal.pone.0050972","article-title":"The Incubation Periods of Dengue Viruses.","volume":"7","author":"M Chan","year":"2012","journal-title":"PLoS ONE"},{"key":"pcbi.1012520.ref096","doi-asserted-by":"crossref","first-page":"841","DOI":"10.2471\/BLT.16.174540","article-title":"Times to key events in Zika virus infection and implications for blood donation: a systematic review","volume":"94","author":"J Lessler","year":"2016","journal-title":"Bull World Health Organ"},{"key":"pcbi.1012520.ref097","doi-asserted-by":"crossref","first-page":"538","DOI":"10.3390\/jcm9020538","article-title":"Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data.","volume":"9","author":"N Linton","year":"2020","journal-title":"J Clin Med."},{"key":"pcbi.1012520.ref098","doi-asserted-by":"crossref","first-page":"577","DOI":"10.7326\/M20-0504","article-title":"The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application.","volume":"172","author":"SA Lauer","year":"2020","journal-title":"Ann Intern Med"},{"key":"pcbi.1012520.ref099","first-page":"7","article-title":"CODA: Convergence Diagnosis and Output Analysis for MCMC.","volume":"6","author":"M Plummer","year":"2006","journal-title":"R News"},{"key":"pcbi.1012520.ref100","doi-asserted-by":"crossref","article-title":"bayesplot: Plotting for Bayesian Models.","author":"J Gabry","DOI":"10.32614\/CRAN.package.bayesplot"},{"key":"pcbi.1012520.ref101","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.3201\/eid2810.221126","article-title":"Early Estimates of Monkeypox Incubation Period, Generation Time, and Reproduction Number, Italy, May\u2013June 2022","volume":"28","author":"G Guzzetta","year":"2022","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1012520.ref102","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1056\/NEJMoa1306742","article-title":"Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus","volume":"369","author":"A Assiri","year":"2013","journal-title":"N Engl J Med"},{"key":"pcbi.1012520.ref103","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2023.28.27.2200806","article-title":"Estimated incubation period distributions of mpox using cases from two international European festivals and outbreaks in a club in Berlin, May to June 2022.","volume":"28","author":"SE McFarland","year":"2023","journal-title":"Eurosurveillance."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012520","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T17:22:22Z","timestamp":1730136142000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012520"}},"subtitle":[],"editor":[{"given":"Samuel V.","family":"Scarpino","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,10,28]]},"references-count":103,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012520","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,28]]}}}