Alun Thomas, Karim Khader, Andrew Redd, Molly Leecaster, Yue Zhang, Makoto Jones, Tom Greene, Matthew Samore
{"title":"医院感染的扩展模型:参数估计和模型选择。","authors":"Alun Thomas, Karim Khader, Andrew Redd, Molly Leecaster, Yue Zhang, Makoto Jones, Tom Greene, Matthew Samore","doi":"10.1093/imammb/dqx010","DOIUrl":null,"url":null,"abstract":"<p><p>We consider extensions to previous models for patient level nosocomial infection in several ways, provide a specification of the likelihoods for these new models, specify new update steps required for stochastic integration, and provide programs that implement these methods to obtain parameter estimates and model choice statistics. Previous susceptible-infected models are extended to allow for a latent period between initial exposure to the pathogen and the patient becoming themselves infectious, and the possibility of decolonization. We allow for multiple facilities, such as acute care hospitals or long-term care facilities and nursing homes, and for multiple units or wards within a facility. Patient transfers between units and facilities are tracked and accounted for in the models so that direct importation of a colonized individual from one facility or unit to another might be inferred. We allow for constant transmission rates, rates that depend on the number of colonized individuals in a unit or facility, or rates that depend on the proportion of colonized individuals. Statistical analysis is done in a Bayesian framework using Markov chain Monte Carlo methods to obtain a sample of parameter values from their joint posterior distribution. Cross validation, deviance information criterion and widely applicable information criterion approaches to model choice fit very naturally into this framework and we have implemented all three. We illustrate our methods by considering model selection issues and parameter estimation for data on methicilin-resistant Staphylococcus aureus surveillance tests over 1 year at a Veterans Administration hospital comprising seven wards.</p>","PeriodicalId":49863,"journal":{"name":"Mathematical Medicine and Biology-A Journal of the Ima","volume":"35 suppl_1","pages":"29-49"},"PeriodicalIF":0.8000,"publicationDate":"2018-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/imammb/dqx010","citationCount":"10","resultStr":"{\"title\":\"Extended models for nosocomial infection: parameter estimation and model selection.\",\"authors\":\"Alun Thomas, Karim Khader, Andrew Redd, Molly Leecaster, Yue Zhang, Makoto Jones, Tom Greene, Matthew Samore\",\"doi\":\"10.1093/imammb/dqx010\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>We consider extensions to previous models for patient level nosocomial infection in several ways, provide a specification of the likelihoods for these new models, specify new update steps required for stochastic integration, and provide programs that implement these methods to obtain parameter estimates and model choice statistics. Previous susceptible-infected models are extended to allow for a latent period between initial exposure to the pathogen and the patient becoming themselves infectious, and the possibility of decolonization. We allow for multiple facilities, such as acute care hospitals or long-term care facilities and nursing homes, and for multiple units or wards within a facility. Patient transfers between units and facilities are tracked and accounted for in the models so that direct importation of a colonized individual from one facility or unit to another might be inferred. We allow for constant transmission rates, rates that depend on the number of colonized individuals in a unit or facility, or rates that depend on the proportion of colonized individuals. Statistical analysis is done in a Bayesian framework using Markov chain Monte Carlo methods to obtain a sample of parameter values from their joint posterior distribution. 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We illustrate our methods by considering model selection issues and parameter estimation for data on methicilin-resistant Staphylococcus aureus surveillance tests over 1 year at a Veterans Administration hospital comprising seven wards.</p>\",\"PeriodicalId\":49863,\"journal\":{\"name\":\"Mathematical Medicine and Biology-A Journal of the Ima\",\"volume\":\"35 suppl_1\",\"pages\":\"29-49\"},\"PeriodicalIF\":0.8000,\"publicationDate\":\"2018-03-16\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1093/imammb/dqx010\",\"citationCount\":\"10\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Mathematical Medicine and Biology-A Journal of the Ima\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/imammb/dqx010\",\"RegionNum\":4,\"RegionCategory\":\"数学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Mathematical Medicine and Biology-A Journal of the Ima","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/imammb/dqx010","RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOLOGY","Score":null,"Total":0}
Extended models for nosocomial infection: parameter estimation and model selection.
We consider extensions to previous models for patient level nosocomial infection in several ways, provide a specification of the likelihoods for these new models, specify new update steps required for stochastic integration, and provide programs that implement these methods to obtain parameter estimates and model choice statistics. Previous susceptible-infected models are extended to allow for a latent period between initial exposure to the pathogen and the patient becoming themselves infectious, and the possibility of decolonization. We allow for multiple facilities, such as acute care hospitals or long-term care facilities and nursing homes, and for multiple units or wards within a facility. Patient transfers between units and facilities are tracked and accounted for in the models so that direct importation of a colonized individual from one facility or unit to another might be inferred. We allow for constant transmission rates, rates that depend on the number of colonized individuals in a unit or facility, or rates that depend on the proportion of colonized individuals. Statistical analysis is done in a Bayesian framework using Markov chain Monte Carlo methods to obtain a sample of parameter values from their joint posterior distribution. Cross validation, deviance information criterion and widely applicable information criterion approaches to model choice fit very naturally into this framework and we have implemented all three. We illustrate our methods by considering model selection issues and parameter estimation for data on methicilin-resistant Staphylococcus aureus surveillance tests over 1 year at a Veterans Administration hospital comprising seven wards.
期刊介绍:
Formerly the IMA Journal of Mathematics Applied in Medicine and Biology.
Mathematical Medicine and Biology publishes original articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome. The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged.
The journal welcomes contributions relevant to any area of the life sciences including:
-biomechanics-
biophysics-
cell biology-
developmental biology-
ecology and the environment-
epidemiology-
immunology-
infectious diseases-
neuroscience-
pharmacology-
physiology-
population biology