{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T11:20:48Z","timestamp":1787743248416,"version":"build-2784847793"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012032","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T00:00:00Z","timestamp":1715212800000}}],"reference-count":116,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T00:00:00Z","timestamp":1714348800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1761603"],"award-info":[{"award-number":["1761603"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1646108"],"award-info":[{"award-number":["1646108"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Public health decisions must be made about when and how to implement interventions to control an infectious disease epidemic. These decisions should be informed by data on the epidemic as well as current understanding about the transmission dynamics. Such decisions can be posed as statistical questions about scientifically motivated dynamic models. Thus, we encounter the methodological task of building credible, data-informed decisions based on stochastic, partially observed, nonlinear dynamic models. This necessitates addressing the tradeoff between biological fidelity and model simplicity, and the reality of misspecification for models at all levels of complexity. We assess current methodological approaches to these issues via a case study of the 2010-2019 cholera epidemic in Haiti. We consider three dynamic models developed by expert teams to advise on vaccination policies. We evaluate previous methods used for fitting these models, and we demonstrate modified data analysis strategies leading to improved statistical fit. Specifically, we present approaches for diagnosing model misspecification and the consequent development of improved models. Additionally, we demonstrate the utility of recent advances in likelihood maximization for high-dimensional nonlinear dynamic models, enabling likelihood-based inference for spatiotemporal incidence data using this class of models. Our workflow is reproducible and extendable, facilitating future investigations of this disease system.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012032","type":"journal-article","created":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T17:38:06Z","timestamp":1714412286000},"page":"e1012032","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Informing policy via dynamic models: Cholera in 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to either of two crossed factors with a logistic regression model","volume":"35","author":"L Li","year":"2016","journal-title":"Statistics in Medicine"},{"key":"pcbi.1012032.ref075","doi-asserted-by":"crossref","first-page":"2571","DOI":"10.1016\/j.spa.2011.07.005","article-title":"Compound Markov Counting Processes and their Applications to Modeling Infinitesimally Over-Dispersed Systems","volume":"121","author":"C Bret\u00f3","year":"2011","journal-title":"Stochastic Processes and their Applications"},{"issue":"3","key":"pcbi.1012032.ref076","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1093\/biostatistics\/kxy057","article-title":"Model Selection and Parameter Estimation for Dynamic Epidemic Models via Iterated Filtering: Application to Rotavirus in Germany","volume":"21","author":"T Stocks","year":"2020","journal-title":"Biostatistics"},{"key":"pcbi.1012032.ref077","doi-asserted-by":"crossref","first-page":"i5516","DOI":"10.1136\/bmj.i5516","article-title":"Cholera threatens Haiti after Hurricane Matthew","volume":"355","author":"S Ferreira","year":"2016","journal-title":"BMJ"},{"key":"pcbi.1012032.ref078","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":"Annals of Applied Statistics"},{"key":"pcbi.1012032.ref079","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1098\/rsif.2008.0172","article-title":"Approximate Bayesian Computation Scheme for Parameter Inference and Model Selection in Dynamical Systems","volume":"6","author":"T Toni","year":"2009","journal-title":"Journal of the Royal Society Interface"},{"key":"pcbi.1012032.ref080","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1111\/j.1467-9868.2009.00736.x","article-title":"Particle Markov chain Monte Carlo methods","volume":"72","author":"C Andrieu","year":"2010","journal-title":"Journal of the Royal Statistical 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Pons-Salort","year":"2018","journal-title":"Science"},{"key":"pcbi.1012032.ref087","doi-asserted-by":"crossref","first-page":"e1000898","DOI":"10.1371\/journal.pcbi.1000898","article-title":"Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in NW India","volume":"6","author":"K Laneri","year":"2010","journal-title":"PLoS Computational Biology"},{"issue":"772","key":"pcbi.1012032.ref088","first-page":"700","article-title":"A Contribution to the Mathematical Theory of Epidemics","volume":"115","author":"WO Kermack","year":"1927","journal-title":"Proceedings of the Royal Society of London, Series A"},{"issue":"2","key":"pcbi.1012032.ref089","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.idm.2017.02.001","article-title":"Mathematical Epidemiology: Past, Present, and Future","volume":"2","author":"F Brauer","year":"2017","journal-title":"Infectious Disease Modelling"},{"issue":"6","key":"pcbi.1012032.ref090","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1038\/s41591-020-0883-7","article-title":"Modelling the COVID-19 Epidemic and Implementation of Population-Wide Interventions in Italy","volume":"26","author":"G Giordano","year":"2020","journal-title":"Nature Medicine"},{"key":"pcbi.1012032.ref091","unstructured":"Dadlani A, Afolabi RO, Jung H, Sohraby K, Kim K. Deterministic Models in Epidemiology: From Modeling to Implementation. arXiv:200404675. 2020;."},{"key":"pcbi.1012032.ref092","first-page":"6185","article-title":"Stochastic Mathematical Models in Epidemiology","volume":"20","author":"MZ Ndii","year":"2017","journal-title":"Information"},{"key":"pcbi.1012032.ref093","unstructured":"Asfaw K, Park J, King AA, Ionides EL. Partially Observed Markov Processes with Spatial Structure via the R Package spatPomp. arXiv:210101157v3. 2023;."},{"key":"pcbi.1012032.ref094","unstructured":"King AA, Rowan T. subplex: Unconstrained Optimization using the Subplex Algorithm. R package, available at https:\/\/cranr-projectorg\/web\/packages\/subplex. 2020;."},{"issue":"1806","key":"pcbi.1012032.ref095","doi-asserted-by":"crossref","first-page":"20150347","DOI":"10.1098\/rspb.2015.0347","article-title":"Avoidable Errors in the Modelling of Outbreaks of Emerging Pathogens, with Special Reference to Ebola","volume":"282","author":"AA King","year":"2015","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"8","key":"pcbi.1012032.ref096","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1016\/j.jbusres.2015.03.026","article-title":"Simple Versus Complex Forecasting: The Evidence","volume":"68","author":"KC Green","year":"2015","journal-title":"Journal of Business Research"},{"key":"pcbi.1012032.ref097","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1109\/MCS.2009.932223","article-title":"The Ensemble Kalman Filter for Combined State and Parameter Estimation","volume":"29","author":"G Evensen","year":"2009","journal-title":"IEEE Transactions on Control Systems"},{"key":"pcbi.1012032.ref098","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-030-96709-3","volume-title":"Data assimilation fundamentals: A unified formulation of the state and parameter estimation problem","author":"G Evensen","year":"2022"},{"key":"pcbi.1012032.ref099","article-title":"Bagged filters for partially observed interacting systems","author":"EL Ionides","year":"2021","journal-title":"Journal of the American Statistical Association"},{"key":"pcbi.1012032.ref100","first-page":"1","article-title":"Iterated block particle filter for high-dimensional parameter learning: Beating the curse of dimensionality","volume":"24","author":"N Ning","year":"2023","journal-title":"Journal of Machine Learning Research"},{"key":"pcbi.1012032.ref101","article-title":"An Iterated Block Particle Filter for Inference on Coupled Dynamic Systems with Shared and Unit-Specific Parameters","author":"EL Ionides","year":"2022","journal-title":"Statistica Sinica"},{"issue":"5","key":"pcbi.1012032.ref102","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1214\/14-AAP1061","article-title":"Can Local Particle Filters Beat the Curse of Dimensionality?","volume":"25","author":"P Rebeschini","year":"2015","journal-title":"The Annals of Applied Probability"},{"key":"pcbi.1012032.ref103","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1007\/s11222-020-09957-3","article-title":"Inference on High-Dimensional Implicit Dynamic Models using a Guided Intermediate Resampling Filter","volume":"30","author":"J Park","year":"2020","journal-title":"Statistics & Computing"},{"key":"pcbi.1012032.ref104","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/B978-0-12-438150-6.50018-2","volume-title":"Robustness in Statistics","author":"GE Box","year":"1979"},{"key":"pcbi.1012032.ref105","doi-asserted-by":"crossref","DOI":"10.1017\/9781107286184","volume-title":"Statistical Inference as Severe Testing","author":"DG Mayo","year":"2018"},{"issue":"6","key":"pcbi.1012032.ref106","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A New Look at the Statistical Model Identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Transactions on Automatic Control"},{"issue":"4","key":"pcbi.1012032.ref107","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1080\/10618600.2017.1384734","article-title":"50 Years of Data Science","volume":"26","author":"D Donoho","year":"2017","journal-title":"Journal of Computational and Graphical Statistics"},{"key":"pcbi.1012032.ref108","volume-title":"Monte Carlo Strategies in Scientific Computing","author":"JS Liu","year":"2001"},{"key":"pcbi.1012032.ref109","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1038\/nature09319","article-title":"Statistical Inference for Noisy Nonlinear Ecological Dynamic Systems","volume":"466","author":"SN Wood","year":"2010","journal-title":"Nature"},{"key":"pcbi.1012032.ref110","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.3389\/fmicb.2016.01131","article-title":"Strong Inference in Mathematical Modeling: a Method for Robust Science in the Twenty-First Century","volume":"7","author":"VV Ganusov","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"4","key":"pcbi.1012032.ref111","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1097\/EDE.0b013e3182572581","article-title":"Cholera Modeling: Challenges to Quantitative Analysis and Predicting the Impact of Interventions","volume":"23","author":"YH Grad","year":"2012","journal-title":"Epidemiology"},{"key":"pcbi.1012032.ref112","article-title":"The Power of Forecasts to Advance Ecological Theory","author":"ASL Lewis","year":"2022","journal-title":"Methods in Ecology and Evolution"},{"issue":"9","key":"pcbi.1012032.ref113","doi-asserted-by":"crossref","first-page":"e1011515","DOI":"10.1371\/journal.pcbi.1011515","article-title":"Profile-wise analysis: a profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models","volume":"19","author":"MJ Simpson","year":"2023","journal-title":"PLoS Computational Biology"},{"key":"pcbi.1012032.ref114","article-title":"Forecasting for COVID-19 has Failed","author":"JP Ioannidis","year":"2020","journal-title":"International Journal of Forecasting"},{"issue":"1","key":"pcbi.1012032.ref115","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1198\/106186007X178663","article-title":"Statistical Analyses and Reproducible Research","volume":"16","author":"R Gentleman","year":"2007","journal-title":"Journal of Computational and Graphical Statistics"},{"key":"pcbi.1012032.ref116","unstructured":"R Core Team. 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