Efficient Bayesian analysis of occupancy models with logit link functions
dc.contributor.author | Clark, Allan E | |
dc.contributor.author | Altwegg, Res | |
dc.date.accessioned | 2019-04-01T12:09:09Z | |
dc.date.available | 2019-04-01T12:09:09Z | |
dc.date.issued | 2018 | |
dc.description.abstract | Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coef‐ ficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We de‐ velop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub (https://github.com/AllanClark/Rcppocc). | en_US |
dc.identifier.apacitation | Clark, A. E., & Altwegg, R. (2018). Efficient Bayesian analysis of occupancy models with logit link functions. <i>Ecology and Evolution</i>, 9(2), 756-768. http://hdl.handle.net/11427/29960 | en_ZA |
dc.identifier.chicagocitation | Clark, Allan E, and Res Altwegg "Efficient Bayesian analysis of occupancy models with logit link functions." <i>Ecology and Evolution</i> 9, 2. (2018): 756-768. http://hdl.handle.net/11427/29960 | en_ZA |
dc.identifier.citation | Clark, A., Altwegg, R. 2018. Efficient Bayesian analysis of occupancy models with logit link functions. Ecology and Evolution. 9; 2; 756-768. | en_ZA |
dc.identifier.ris | TY - Journal Article AU - Clark, Allan E AU - Altwegg, Res AB - Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coef‐ ficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We de‐ velop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub (https://github.com/AllanClark/Rcppocc). DA - 2018 DB - OpenUCT DP - University of Cape Town IS - 2 J1 - Ecology and Evolution KW - Bayesian spatial occupancy model LK - https://open.uct.ac.za PY - 2018 T1 - Efficient Bayesian analysis of occupancy models with logit link functions TI - Efficient Bayesian analysis of occupancy models with logit link functions UR - http://hdl.handle.net/11427/29960 ER - | en_ZA |
dc.identifier.uri | http://hdl.handle.net/11427/29960 | |
dc.identifier.vancouvercitation | Clark AE, Altwegg R. Efficient Bayesian analysis of occupancy models with logit link functions. Ecology and Evolution. 2018;9(2):756-768. http://hdl.handle.net/11427/29960. | en_ZA |
dc.language.iso | en | en_US |
dc.publisher.department | Department of Statistical Sciences | en_US |
dc.publisher.faculty | Faculty of Science | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_US |
dc.source | Ecology and Evolution | en_US |
dc.source.journalissue | 2 | en_US |
dc.source.journalvolume | 9 | en_US |
dc.source.pagination | 756-768 | en_US |
dc.source.uri | https://onlinelibrary.wiley.com/journal/20457758 | |
dc.subject | Bayesian spatial occupancy model | en_US |
dc.subject.other | imperfect detection | |
dc.subject.other | occupancy model | |
dc.subject.other | Rcppocc | |
dc.subject.other | restricted spatial regression | |
dc.title | Efficient Bayesian analysis of occupancy models with logit link functions | en_US |
dc.type | Journal Article | en_US |
Files
Original bundle
1 - 1 of 1
Loading...
- Name:
- Clark_et_al-2019-Ecology_and_Evolution.pdf
- Size:
- 1.49 MB
- Format:
- Adobe Portable Document Format
- Description:
- Research article
License bundle
1 - 1 of 1
Loading...
- Name:
- license.txt
- Size:
- 1.72 KB
- Format:
- Item-specific license agreed upon to submission
- Description: