Mixed effects: a unifying framework for statistical modelling in fisheries biology

JT Thorson, C Minto - ICES Journal of Marine Science, 2015 - academic.oup.com
Fisheries biology encompasses a tremendous diversity of research questions, methods, and
models. Many sub-fields use observational or experimental data to make inference about …

sdmTMB: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields

SC Anderson, EJ Ward, PA English, LAK Barnett - BioRxiv, 2022 - biorxiv.org
Geostatistical data—spatially referenced observations related to some continuous spatial
phenomenon—are ubiquitous in ecology and can reveal ecological processes and inform …

Guidance for decisions using the Vector Autoregressive Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate assessments

JT Thorson - Fisheries Research, 2019 - Elsevier
Fisheries scientists provide stock, ecosystem, habitat, and climate assessments to support
interdisplinary fisheries management in the US and worldwide. These assessment activities …

Defining spatial structure for fishery stock assessment

SX Cadrin - Fisheries Research, 2020 - Elsevier
In principle, the spatial extent of fishery stock assessment should reflect the biological
population, and major fishing patterns or population heterogeneity within the area should be …

Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes

JT Thorson, AO Shelton, EJ Ward… - ICES Journal of Marine …, 2015 - academic.oup.com
Indices of abundance are the bedrock for stock assessments or empirical management
procedures used to manage fishery catches for fish populations worldwide, and are …

Comparing estimates of abundance trends and distribution shifts using single-and multispecies models of fishes and biogenic habitat

JT Thorson, LAK Barnett - ICES Journal of Marine Science, 2017 - academic.oup.com
Several approaches have been developed over the last decade to simultaneously estimate
distribution or density for multiple species (eg “joint species distribution” or “multispecies …

Addressing uncertainty when projecting marine species' distributions under climate change

SC Davies, PL Thompson, C Gomez, J Nephin… - …, 2023 - Wiley Online Library
Species distribution models (SDMs) have been widely used to project terrestrial species'
responses to climate change and are increasingly being used for similar objectives in the …

Catch per unit effort modelling for stock assessment: A summary of good practices

SD Hoyle, RA Campbell, ND Ducharme-Barth… - Fisheries …, 2024 - Elsevier
Indices of abundance based on fishery catch-per-unit-effort (CPUE) are important
components of many stock assessments, particularly when fishery-independent surveys are …

Joint dynamic species distribution models: a tool for community ordination and spatio‐temporal monitoring

JT Thorson, JN Ianelli, EA Larsen… - Global Ecology and …, 2016 - Wiley Online Library
Aim Spatial analysis of the distribution and density of species is of continuing interest within
theoretical and applied ecology. Species distribution models (SDMs) are being increasingly …

Return of large fin whale feeding aggregations to historical whaling grounds in the Southern Ocean

H Herr, S Viquerat, F Devas, A Lees, L Wells… - Scientific reports, 2022 - nature.com
Fin whales (Balaenoptera physalus quoyi) of the Southern Hemisphere were brought to
near extinction by twentieth century industrial whaling. For decades, they had all but …