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A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data

Spatial capture–recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub‐models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub‐mod...

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Autores principales: Zhang, Wei, Chipperfield, Joseph D., Illian, Janine B., Dupont, Pierre, Milleret, Cyril, de Valpine, Perry, Bischof, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078592/
https://www.ncbi.nlm.nih.gov/pubmed/36217822
http://dx.doi.org/10.1002/ecy.3887
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author Zhang, Wei
Chipperfield, Joseph D.
Illian, Janine B.
Dupont, Pierre
Milleret, Cyril
de Valpine, Perry
Bischof, Richard
author_facet Zhang, Wei
Chipperfield, Joseph D.
Illian, Janine B.
Dupont, Pierre
Milleret, Cyril
de Valpine, Perry
Bischof, Richard
author_sort Zhang, Wei
collection PubMed
description Spatial capture–recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub‐models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub‐models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi‐complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages for more complicated models that account for spatial variation in either population density or detection. We present the model formulation, test it with simulations, quantify computational efficiency gains, and conclude with a real‐life example using non‐invasive genetic sampling data for an elusive large carnivore, the wolverine (Gulo gulo) in Norway.
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spelling pubmed-100785922023-04-07 A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data Zhang, Wei Chipperfield, Joseph D. Illian, Janine B. Dupont, Pierre Milleret, Cyril de Valpine, Perry Bischof, Richard Ecology Statistical Report Spatial capture–recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub‐models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub‐models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi‐complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages for more complicated models that account for spatial variation in either population density or detection. We present the model formulation, test it with simulations, quantify computational efficiency gains, and conclude with a real‐life example using non‐invasive genetic sampling data for an elusive large carnivore, the wolverine (Gulo gulo) in Norway. John Wiley & Sons, Inc. 2022-11-30 2023-01 /pmc/articles/PMC10078592/ /pubmed/36217822 http://dx.doi.org/10.1002/ecy.3887 Text en © 2022 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Statistical Report
Zhang, Wei
Chipperfield, Joseph D.
Illian, Janine B.
Dupont, Pierre
Milleret, Cyril
de Valpine, Perry
Bischof, Richard
A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title_full A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title_fullStr A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title_full_unstemmed A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title_short A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data
title_sort flexible and efficient bayesian implementation of point process models for spatial capture–recapture data
topic Statistical Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078592/
https://www.ncbi.nlm.nih.gov/pubmed/36217822
http://dx.doi.org/10.1002/ecy.3887
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