A variational Bayes approach to the analysis of occupancy models

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dc.contributor.authorClark, Allan Een_ZA
dc.contributor.authorAltwegg, Resen_ZA
dc.contributor.authorOrmerod, John Ten_ZA
dc.date.accessioned2016-03-08T10:55:11Z
dc.date.available2016-03-08T10:55:11Z
dc.date.issued2016en_ZA
dc.description.abstractDetection-nondetection data are often used to investigate species range dynamics using Bayesian occupancy models which rely on the use of Markov chain Monte Carlo (MCMC) methods to sample from the posterior distribution of the parameters of the model. In this article we develop two Variational Bayes (VB) approximations to the posterior distribution of the parameters of a single-season site occupancy model which uses logistic link functions to model the probability of species occurrence at sites and of species detection probabilities. This task is accomplished through the development of iterative algorithms that do not use MCMC methods. Simulations and small practical examples demonstrate the effectiveness of the proposed technique. We specifically show that (under certain circumstances) the variational distributions can provide accurate approximations to the true posterior distributions of the parameters of the model when the number of visits per site ( K ) are as low as three and that the accuracy of the approximations improves as K increases. We also show that the methodology can be used to obtain the posterior distribution of the predictive distribution of the proportion of sites occupied (PAO).en_ZA
dc.identifier.apacitationClark, A. E., Altwegg, R., & Ormerod, J. T. (2016). A variational Bayes approach to the analysis of occupancy models. <i>PLoS One</i>, http://hdl.handle.net/11427/17574en_ZA
dc.identifier.chicagocitationClark, Allan E, Res Altwegg, and John T Ormerod "A variational Bayes approach to the analysis of occupancy models." <i>PLoS One</i> (2016) http://hdl.handle.net/11427/17574en_ZA
dc.identifier.citationClark, A. E., Altwegg, R., & Ormerod, J. T. (2016). A variational Bayes approach to the analysis of occupancy models. PloS one, 11(2), e0148966. doi:10.1371/journal.pone.0148966en_ZA
dc.identifier.ris TY - Journal Article AU - Clark, Allan E AU - Altwegg, Res AU - Ormerod, John T AB - Detection-nondetection data are often used to investigate species range dynamics using Bayesian occupancy models which rely on the use of Markov chain Monte Carlo (MCMC) methods to sample from the posterior distribution of the parameters of the model. In this article we develop two Variational Bayes (VB) approximations to the posterior distribution of the parameters of a single-season site occupancy model which uses logistic link functions to model the probability of species occurrence at sites and of species detection probabilities. This task is accomplished through the development of iterative algorithms that do not use MCMC methods. Simulations and small practical examples demonstrate the effectiveness of the proposed technique. We specifically show that (under certain circumstances) the variational distributions can provide accurate approximations to the true posterior distributions of the parameters of the model when the number of visits per site ( K ) are as low as three and that the accuracy of the approximations improves as K increases. We also show that the methodology can be used to obtain the posterior distribution of the predictive distribution of the proportion of sites occupied (PAO). DA - 2016 DB - OpenUCT DO - 10.1371/journal.pone.0148966 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2016 T1 - A variational Bayes approach to the analysis of occupancy models TI - A variational Bayes approach to the analysis of occupancy models UR - http://hdl.handle.net/11427/17574 ER - en_ZA
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0148966en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/17574
dc.identifier.vancouvercitationClark AE, Altwegg R, Ormerod JT. A variational Bayes approach to the analysis of occupancy models. PLoS One. 2016; http://hdl.handle.net/11427/17574.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentDepartment of Statistical Sciencesen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2016 Clark et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherTangentsen_ZA
dc.subject.otherStatistical distributionsen_ZA
dc.subject.otherApproximation methodsen_ZA
dc.subject.otherSimulation and modelingen_ZA
dc.subject.otherBayesian methoden_ZA
dc.subject.otherBirdsen_ZA
dc.subject.otherProbability distributionen_ZA
dc.subject.otherAlgorithmsen_ZA
dc.titleA variational Bayes approach to the analysis of occupancy modelsen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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