Incorporating vertical distribution in index standardization accounts for spatiotemporal availability to acoustic and bottom trawl gear for semi-pelagic species

Adapting to climate‐driven distribution shifts using model‐based indices and age composition from multiple surveys in the walleye pollock ( Gadus chalcogrammus ) stock assessment

(2020) Cecilia A. O’Leary et al.   FISHERIES OCEANOGRAPHY

Don’t work too hard: Subsampling leads to efficient analysis of large acoustic datasets

(2019) Mike Levine et al.   FISHERIES RESEARCH

Combining data from bottom-trawl and acoustic-trawl surveys to estimate an index of abundance for semipelagic species

(2018) Stan Kotwicki et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

A guide to Bayesian model checking for ecologists

(2018) Paul B. Conn et al.   ECOLOGICAL MONOGRAPHS

The effect of hook spacing on longline catch rates: Implications for catch rate standardization

(2018) Cole C. Monnahan et al.   FISHERIES RESEARCH

No-U-turn sampling for fast Bayesian inference in ADMB and TMB: Introducing the adnuts and tmbstan R packages

(2018) Cole C. Monnahan et al.   PLoS One

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

(2018) James T. Thorson   FISHERIES RESEARCH

The relative influence of temperature and size-structure on fish distribution shifts: A case-study on Walleye pollock in the Bering Sea

(2017) James T Thorson et al.   FISH AND FISHERIES

Predicting the spatio-temporal distributions of pelagic sharks in the western and central North Pacific

(2017) Mikihiko Kai et al.   FISHERIES OCEANOGRAPHY

Multispecies acoustic dead-zone correction and bias ratio estimates between acoustic and bottom-trawl data

(2017) Kotaro Ono et al.   ICES JOURNAL OF MARINE SCIENCE

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

(2017) James T. Thorson et al.   ICES JOURNAL OF MARINE SCIENCE

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Three problems with the conventional delta-model for biomass sampling data, and a computationally efficient alternative

(2017) James T. Thorson   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

TMB: Automatic Differentiation and Laplace Approximation

(2016) Kasper Kristensen et al.   Journal of Statistical Software

Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

(2016) Aki Vehtari et al.   STATISTICS AND COMPUTING

Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo

(2016) Cole C. Monnahan et al.   Methods in Ecology and Evolution

Factors affecting the availability of walleye pollock to acoustic and bottom trawl survey gear

(2015) Stan Kotwicki et al.   ICES JOURNAL OF MARINE SCIENCE

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

(2015) James T. Thorson et al.   ICES JOURNAL OF MARINE SCIENCE

Spatial factor analysis: a new tool for estimating joint species distributions and correlations in species range

(2015) James T. Thorson et al.   Methods in Ecology and Evolution

Daylight vertical segregation of young-of-the-year Argentine hake Merluccius hubbsi: Advances in assessment of juvenile abundance with acoustic methods

(2014) G.L. Álvarez-Colombo et al.   FISHERIES RESEARCH

A toolbox for fitting complex spatial point process models using integrated nested Laplace approximation (INLA)

(2012) Janine B. Illian et al.   Annals of Applied Statistics

Combining bottom trawl and acoustic data to model acoustic dead zone correction and bottom trawl efficiency parameters for semipelagic species

(2012) Stan Kotwicki et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Using acoustic data from fishing vessels to estimate walleye pollock (Theragra chalcogramma) abundance in the eastern Bering Sea

(2011) Taina Honkalehto et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach

(2011) Finn Lindgren et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY