Exploring the limits of spatiotemporal and design-based index standardization under reduced survey coverage

The shadow model: how and why small choices in spatially explicit species distribution models affect predictions

(2022) Christian J. C. Commander et al.   PeerJ

On comparing design-based estimation versus model-based prediction to assess the abundance of biological populations

(2022) Philippe Aubry et al.   ECOLOGICAL INDICATORS

Cross validation for model selection: A review with examples from ecology

(2022) Luke A. Yates et al.   ECOLOGICAL MONOGRAPHS

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

(2021) Cole C Monnahan et al.   ICES JOURNAL OF MARINE SCIENCE

Bridging the gap between commercial fisheries and survey data to model the spatiotemporal dynamics of marine species

(2021) Marie‐Christine Rufener et al.   ECOLOGICAL APPLICATIONS

Estimating fine‐scale movement rates and habitat preferences using multiple data sources

(2021) James T. Thorson et al.   FISH AND FISHERIES

Predicting abundance indices in areas without coverage with a latent spatio-temporal Gaussian model

(2021) Olav Nikolai Breivik et al.   ICES JOURNAL OF MARINE SCIENCE

Monitoring change in a dynamic environment: spatio-temporal modelling of calibrated data from different types of fisheries surveys of Pacific halibut

(2020) Raymond A. Webster et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Highly resolved spatiotemporal simulations for exploring mixed fishery dynamics

(2020) Paul J. Dolder et al.   ECOLOGICAL MODELLING

SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populations

(2020) Paul M. Regular et al.   PLoS One

Assessing spillover from marine protected areas and its drivers: A meta‐analytical approach

(2020) Manfredi Di Lorenzo et al.   FISH AND FISHERIES

The surprising sensitivity of index scale to delta-model assumptions: Recommendations for model-based index standardization

(2020) James T. Thorson et al.   FISHERIES RESEARCH

The effect of random and density‐dependent variation in sampling efficiency on variance of abundance estimates from fishery surveys

(2019) Stan Kotwicki et al.   FISH AND FISHERIES

Evaluation of the impacts of different treatments of spatio-temporal variation in catch-per-unit-effort standardization models

(2019) Arnaud Grüss et al.   FISHERIES RESEARCH

Developing spatio-temporal models using multiple data types for evaluating population trends and habitat usage

(2019) Arnaud Grüss et al.   ICES JOURNAL OF MARINE SCIENCE

Investigating the value of including depth during spatiotemporal index standardization

(2019) Kelli F. Johnson et al.   FISHERIES RESEARCH

Trade‐offs in covariate selection for species distribution models: a methodological comparison

(2019) Stephanie Brodie et al.   ECOGRAPHY

A unified framework for analysis of individual-based models in ecology and beyond

(2019) Stephen J. Cornell et al.   Nature Communications

Constructing Priors that Penalize the Complexity of Gaussian Random Fields

(2018) Geir-Arne Fuglstad et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

(2018) James T. Thorson   FISHERIES RESEARCH

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

Implementing a generic method for bias correction in statistical models using random effects, with spatial and population dynamics examples

(2016) James T. Thorson et al.   FISHERIES RESEARCH

TMB: Automatic Differentiation and Laplace Approximation

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

virtualspecies, an R package to generate virtual species distributions

(2015) Boris Leroy et al.   ECOGRAPHY

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 semiparametric models improve estimates of species abundance and distribution

(2014) Andrew Olaf Shelton et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models

(2013) Casper W. Berg et al.   FISHERIES RESEARCH

Likelihood-based and Bayesian methods for Tweedie compound Poisson linear mixed models

(2012) Yanwei Zhang   STATISTICS AND COMPUTING

Data weighting in statistical fisheries stock assessment models

(2011) R.I.C. Chris Francis   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Annual egg production estimates of cod (Gadus morhua), plaice (Pleuronectes platessa) and haddock (Melanogrammus aeglefinus) in the Irish Sea: The effects of modelling choices and assumptions

(2011) David L. Maxwell et al.   FISHERIES RESEARCH

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

Adding Spatially-Correlated Errors Can Mess Up the Fixed Effect You Love

(2010) James S. Hodges et al.   AMERICAN STATISTICIAN