Applying Bayesian model selection to determine ecological covariates for recruitment and natural mortality in stock assessment

• Published in: ICES Journal of Marine Science
• Main Authors: Trochta, John T, Branch, Trevor A
• Other Authors: Zhou, Shijie
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2021
• Subjects: Pacific; Pink salmon; Alaska
• Online Access: http://dx.doi.org/10.1093/icesjms/fsab165; https://academic.oup.com/icesjms/article-pdf/78/8/2875/41764686/fsab165.pdf

Abstract Incorporating ecological covariates into fishery stock assessments may improve estimates, but most covariates are estimated with error. Model selection criteria are often used to identify support for covariates, have some limitations and rely on assumptions that are often violated. For a more rigorous evaluation of ecological covariates, we used four popular selection criteria to identify covariates influencing natural mortality or recruitment in a Bayesian stock assessment of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska. Within this framework, covariates were incorporated either as fixed effects or as latent variables (i.e. covariates have associated error). We found most support for pink salmon increasing natural mortality, which was selected by three of four criteria. There was ambiguous support for other fixed effects on natural mortality (walleye pollock and the North Pacific Gyre Oscillation) and recruitment (hatchery-released juvenile pink salmon and a 1989 regime shift). Generally, similar criteria values among covariates suggest no clear evidence for a consistent effect of any covariate. Models with covariates as latent variables were sensitive to prior specification and may provide potentially very different results. We recommend using multiple criteria and exploring different statistical assumptions about covariates for their use in stock assessment.