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Modernising fish and shark growth curves with Bayesian length-at-age models

Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are...

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Detalles Bibliográficos
Autores principales: Smart, Jonathan J., Grammer, Gretchen L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7870076/
https://www.ncbi.nlm.nih.gov/pubmed/33556124
http://dx.doi.org/10.1371/journal.pone.0246734
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author Smart, Jonathan J.
Grammer, Gretchen L.
author_facet Smart, Jonathan J.
Grammer, Gretchen L.
author_sort Smart, Jonathan J.
collection PubMed
description Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are under-sampled. In growth models, two key parameters have a direct biological interpretation: L(0), which should correspond to length-at-birth and L(∞), which should approximate the average length of full-grown individuals. Here, we present an approach of fitting Bayesian growth models using Markov Chain Monte Carlo (MCMC), with informative priors on these parameters to improve the biological plausibility of growth estimates. A generalised framework is provided in an R package ‘BayesGrowth’, which removes the hurdle of programming an MCMC model for new users. Four case studies representing different sampling scenarios as well as three simulations with different selectivity functions were used to compare this Bayesian framework to standard frequentist growth models. The Bayesian models either outperformed or matched the results of frequentist growth models in all examples, demonstrating the broad benefits offered by this approach. This study highlights the impact that Bayesian models could provide in age and growth studies if applied more routinely rather than being limited to only complex or sophisticated applications.
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spelling pubmed-78700762021-02-11 Modernising fish and shark growth curves with Bayesian length-at-age models Smart, Jonathan J. Grammer, Gretchen L. PLoS One Research Article Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are under-sampled. In growth models, two key parameters have a direct biological interpretation: L(0), which should correspond to length-at-birth and L(∞), which should approximate the average length of full-grown individuals. Here, we present an approach of fitting Bayesian growth models using Markov Chain Monte Carlo (MCMC), with informative priors on these parameters to improve the biological plausibility of growth estimates. A generalised framework is provided in an R package ‘BayesGrowth’, which removes the hurdle of programming an MCMC model for new users. Four case studies representing different sampling scenarios as well as three simulations with different selectivity functions were used to compare this Bayesian framework to standard frequentist growth models. The Bayesian models either outperformed or matched the results of frequentist growth models in all examples, demonstrating the broad benefits offered by this approach. This study highlights the impact that Bayesian models could provide in age and growth studies if applied more routinely rather than being limited to only complex or sophisticated applications. Public Library of Science 2021-02-08 /pmc/articles/PMC7870076/ /pubmed/33556124 http://dx.doi.org/10.1371/journal.pone.0246734 Text en © 2021 Smart, Grammer http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Smart, Jonathan J.
Grammer, Gretchen L.
Modernising fish and shark growth curves with Bayesian length-at-age models
title Modernising fish and shark growth curves with Bayesian length-at-age models
title_full Modernising fish and shark growth curves with Bayesian length-at-age models
title_fullStr Modernising fish and shark growth curves with Bayesian length-at-age models
title_full_unstemmed Modernising fish and shark growth curves with Bayesian length-at-age models
title_short Modernising fish and shark growth curves with Bayesian length-at-age models
title_sort modernising fish and shark growth curves with bayesian length-at-age models
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7870076/
https://www.ncbi.nlm.nih.gov/pubmed/33556124
http://dx.doi.org/10.1371/journal.pone.0246734
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