All Stories

  1. The Benefits of Hierarchical Ecosystem Models: Demonstration Using EcoState, a New State‐Space Mass‐Balance Model

    Article • Fish and Fisheries, December 2024, Wiley

    Dr. James T Thorson

  2. Measuring complexity for hierarchical models using effective degrees of freedom

    Article • Ecology, June 2024, Wiley

    Dr. James T Thorson

  3. Cross-scale environmental impacts across persistent and dynamic aggregations within a complex population: implications for fisheries management

    Article • Canadian Journal of Fisheries and Aquatic Sciences, March 2024, Canadian Science Publishing

    Dr. James T Thorson

  4. Coupling state‐of‐the‐art modelling tools for better informed Red List assessments of marine fishes

    Article • Journal of Applied Ecology, February 2024, Wiley

    Dr. James T Thorson

  5. Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms

    Article • Methods in Ecology and Evolution, February 2024, Wiley

    Dr. James T Thorson

  6. An ensemble approach to species distribution modelling reconciles systematic differences in estimates of habitat utilization and range area

    Article • Journal of Applied Ecology, December 2023, Wiley

    Dr. James T Thorson

  7. Simulating benefits, costs and trade‐offs of spatial management in marine social‐ecological systems

    Article • Fish and Fisheries, November 2023, Wiley

    Dr. James T Thorson

  8. Trees for fishes: The neglected role for phylogenetic comparative methods in fisheries science

    Article • Fish and Fisheries, November 2023, Wiley

    Dr. James T Thorson

  9. Assessing small pelagic fish trends in space and time using piscivore stomach contents

    Article • Canadian Journal of Fisheries and Aquatic Sciences, October 2023, Canadian Science Publishing

    Dr. James T Thorson

  10. phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models

    Article • Journal of Evolutionary Biology, October 2023, Oxford University Press (OUP)

    Dr. James T Thorson

  11. Marine heatwaves are not a dominant driver of change in demersal fishes

    Article • Nature, August 2023, Springer Science + Business Media

    Dr. James T Thorson

  12. Modelling time-varying growth in state-space stock assessments

    Article • ICES Journal of Marine Science, August 2023, Oxford University Press (OUP)

    Dr. James T Thorson

  13. Integrating survey and observer data improves the predictions of New Zealand spatio-temporal models

    Article • ICES Journal of Marine Science, August 2023, Oxford University Press (OUP)

    Dr. James T Thorson

  14. Spatio-temporal species distribution models reveal dynamic indicators for ecosystem-based fisheries management

    Article • ICES Journal of Marine Science, August 2023, Oxford University Press (OUP)

    Dr. James T Thorson

  15. Spatially varying catchability for integrating research survey data with other data sources: case studies involving observer samples, industry-cooperative surveys, and predators as samplers

    Article • Canadian Journal of Fisheries and Aquatic Sciences, June 2023, Canadian Science Publishing

    Dr. James T Thorson

  16. Spatially varying coefficients can improve parsimony and descriptive power for species distribution models

    Article • Ecography, April 2023, Wiley

    Dr. James T Thorson

  17. Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models

    Article • Methods in Ecology and Evolution, March 2023, Wiley

    Dr. James T Thorson

  18. Incorporating distribution shifts and spatio-temporal variation when estimating weight-at-age for stock assessments: a case study involving the Bering Sea pollock (Gadus chalcogrammus)

    Article • ICES Journal of Marine Science, January 2023, Oxford University Press (OUP)

    Dr. James T Thorson

  19. Do large‐scale associations in birds imply biotic interactions or environmental filtering?

    Article • Journal of Biogeography, November 2022, Wiley

    Dr. James T Thorson

  20. The multivariate-Tweedie: a self-weighting likelihood for age and length composition data arising from hierarchical sampling designs

    Article • ICES Journal of Marine Science, September 2022, Oxford University Press (OUP)

    Dr. James T Thorson

  21. The estimated impact of changes to otolith field-sampling and ageing effort on stock assessment inputs, outputs, and catch advice

    Article • Canadian Journal of Fisheries and Aquatic Sciences, September 2022, Canadian Science Publishing

    Dr. James T Thorson

  22. Climate‐informed models benefit hindcasting but present challenges when forecasting species–habitat associations

    Article • Ecography, July 2022, Wiley

    Dr. James T Thorson

  23. The influence of age and cohort on the distribution of walleye pollock (Gadus chalcogrammus) in the eastern Bering Sea

    Article • Canadian Journal of Fisheries and Aquatic Sciences, June 2022, Canadian Science Publishing

    Dr. James T Thorson

  24. Shifting fish distributions impact predation intensity in a sub‐Arctic ecosystem

    Article • Ecography, June 2022, Wiley

    Dr. James T Thorson

  25. Understanding transboundary stocks’ availability by combining multiple fisheries-independent surveys and oceanographic conditions in spatiotemporal models

    Article • ICES Journal of Marine Science, March 2022, Oxford University Press (OUP)

    Dr. James T Thorson

  26. sdmTMB: An R Package for Fast, Flexible, and User-Friendly Generalized Linear Mixed Effects Models with Spatial and Spatiotemporal Random Fields

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Dr. James T Thorson

  27. Combining scientific survey and commercial catch data to map fish distribution

    Article • ICES Journal of Marine Science, March 2022, Oxford University Press (OUP)

    Dr. James T Thorson

  28. Identifying species complexes based on spatial and temporal clustering from joint dynamic species distribution models

    Article • ICES Journal of Marine Science, February 2022, Oxford University Press (OUP)

    Dr. James T Thorson

  29. A spatial statistical approach for identifying population structuring of marine fish species: European sprat as a case study

    Article • ICES Journal of Marine Science, February 2022, Oxford University Press (OUP)

    Dr. James T Thorson

  30. Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

    Article • Ecology, January 2022, Wiley

    Dr. James T Thorson

  31. Development and simulation testing for a new approach to density dependence in species distribution models

    Article • ICES Journal of Marine Science, December 2021, Oxford University Press (OUP)

    Dr. James T Thorson

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

    Article • Fish and Fisheries, August 2021, Wiley

    Dr. James T Thorson

  33. Estimating spatiotemporal availability of transboundary fishes to fishery‐independent surveys

    Article • Journal of Applied Ecology, July 2021, Wiley

    Dr. James T Thorson

  34. Improving estimates of the state of global fisheries depends on better data

    Article • Fish and Fisheries, July 2021, Wiley

    Dr. James T Thorson

  35. Grand challenge for habitat science: stage-structured responses, nonlocal drivers, and mechanistic associations among habitat variables affecting fishery productivity

    Article • ICES Journal of Marine Science, June 2021, Oxford University Press (OUP)

    Dr. James T Thorson

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

    Article • ICES Journal of Marine Science, May 2021, Oxford University Press (OUP)

    Dr. James T Thorson

  37. Implementing two-dimensional autocorrelation in either survival or natural mortality improves a state-space assessment model for Southern New England-Mid Atlantic yellowtail flounder

    Article • Fisheries Research, May 2021, Elsevier

    Dr. James T Thorson

  38. Range edges of North American marine species are tracking temperature over decades

    Article • Global Change Biology, April 2021, Wiley

    Dr. James T Thorson

  39. Predator stomach contents can provide accurate indices of prey biomass

    Article • ICES Journal of Marine Science, February 2021, Oxford University Press (OUP)

    Dr. James T Thorson

  40. Forecasting community reassembly using climate‐linked spatio‐temporal ecosystem models

    Article • Ecography, January 2021, Wiley

    Dr. James T Thorson

  41. The need for spatio-temporal modeling to determine catch-per-unit effort based indices of abundance and associated composition data for inclusion in stock assessment models

    Article • Fisheries Research, September 2020, Elsevier

    Dr. James T Thorson

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

    Article • Fisheries Oceanography, August 2020, Wiley

    Dr. James T Thorson

  43. Empirical orthogonal function regression: Linking population biology to spatial varying environmental conditions using climate projections

    Article • Global Change Biology, May 2020, Wiley

    Dr. James T Thorson

  44. Seasonal and interannual variation in spatio-temporal models for index standardization and phenology studies

    Article • ICES Journal of Marine Science, May 2020, Oxford University Press (OUP)

    Dr. James T Thorson, Dr Ellen Martinson Yasumiishi

  45. Simulation testing a new multi-stage process to measure the effect of increased sampling effort on effective sample size for age and length data

    Article • ICES Journal of Marine Science, April 2020, Oxford University Press (OUP)

    Dr. James T Thorson

  46. Spatio‐temporal analyses of marine predator diets from data‐rich and data‐limited systems

    Article • Fish and Fisheries, March 2020, Wiley

    Dr. James T Thorson

  47. Author Correction: Spatial separation of catches in highly mixed fisheries

    Article • Scientific Reports, March 2020, Springer Science + Business Media

    Dr. James T Thorson

  48. JABBA-Select: Incorporating life history and fisheries’ selectivity into surplus production models

    Article • Fisheries Research, February 2020, Elsevier

    Dr. James T Thorson

  49. A novel spatiotemporal stock assessment framework to better address fine‐scale species distributions: Development and simulation testing

    Article • Fish and Fisheries, December 2019, Wiley

    Dr. James T Thorson

  50. Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data‐integrated life‐history model

    Article • Fish and Fisheries, November 2019, Wiley

    Dr. James T Thorson

  51. Spatio‐temporal models of intermediate complexity for ecosystem assessments: A new tool for spatial fisheries management

    Article • Fish and Fisheries, September 2019, Wiley

    Dr. James T Thorson

  52. Investigating the value of including depth during spatiotemporal index standardization

    Article • Fisheries Research, August 2019, Elsevier

    Dr. James T Thorson

  53. Realizing the potential of trait‐based approaches to advance fisheries science

    Article • Fish and Fisheries, July 2019, Wiley

    Dr. James T Thorson

  54. Spatio-temporal dynamics of summer flounder (Paralichthys dentatus) on the Northeast US shelf

    Article • Fisheries Research, July 2019, Elsevier

    Dr. James T Thorson

  55. Measuring the impact of oceanographic indices on species distribution shifts: The spatially varying effect of cold-pool extent in the eastern Bering Sea

    Article • Limnology and Oceanography, June 2019, Wiley

    Dr. James T Thorson

  56. A novel approach to assess distribution trends from fisheries survey data

    Article • Fisheries Research, June 2019, Elsevier

    Dr. James T Thorson

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

    Article • Fisheries Research, February 2019, Elsevier

    Dr. James T Thorson

  58. Modeling temporal variation in recruitment in fisheries stock assessment: A review of theory and practice

    Article • Fisheries Research, December 2018, Elsevier

    Dr. James T Thorson

  59. Forecast skill for predicting distribution shifts: A retrospective experiment for marine fishes in the Eastern Bering Sea

    Article • Fish and Fisheries, November 2018, Wiley

    Dr. James T Thorson

  60. Spatial heterogeneity contributes more to portfolio effects than species variability in bottom-associated marine fishes

    Article • Proceedings of the Royal Society B Biological Sciences, October 2018, Royal Society Publishing

    Dr. James T Thorson, Dr Mark D Scheuerell

  61. Spatial separation of catches in highly mixed fisheries

    Article • Scientific Reports, September 2018, Springer Science + Business Media

    Dr. James T Thorson

  62. Inter-annual and secular variability of larvae of mesopelagic and forage fishes in the southern California Current System

    Article • Journal of Geophysical Research Oceans, July 2018, American Geophysical Union (AGU)

    Dr. James T Thorson

  63. Paulik revisited: Statistical framework and estimation performance of multistage recruitment functions

    Article • Fisheries Research, July 2018, Elsevier

    Dr. James T Thorson

  64. The case for estimating recruitment variation in data-moderate and data-poor age-structured models

    Article • Fisheries Research, July 2018, Elsevier

    Dr. James T Thorson

  65. Steepness for West Coast rockfishes: Results from a twelve-year experiment in iterative regional meta-analysis

    Article • Fisheries Research, March 2018, Elsevier

    Dr. James T Thorson

  66. Spatiotemporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine

    Article • Canadian Journal of Fisheries and Aquatic Sciences, November 2017, Canadian Science Publishing

    Dr. James T Thorson

  67. Global fishery dynamics are poorly predicted by classical models

    Article • Fish and Fisheries, May 2017, Wiley

    Dr. James T Thorson

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

    Article • Fish and Fisheries, May 2017, Wiley

    Dr. James T Thorson

  69. Estimating partial regulation in spatiotemporal models of community dynamics

    Article • Ecology, March 2017, Wiley

    Dr. James T Thorson

  70. Improving estimates of population status and trend with superensemble models

    Article • Fish and Fisheries, January 2017, Wiley

    Dr. James T Thorson, Miss Jessica Claire Walsh

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

    Article • ICES Journal of Marine Science, January 2017, Oxford University Press (OUP)

    Dr. James T Thorson

  72. Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo

    Article • Methods in Ecology and Evolution, November 2016, Wiley

    Dr. James T Thorson

  73. Can autocorrelated recruitment be estimated using integrated assessment models and how does it affect population forecasts?

    Article • Fisheries Research, November 2016, Elsevier

    Dr. James T Thorson

  74. Density-dependent changes in effective area occupied for sea-bottom-associated marine fishes

    Article • Proceedings of the Royal Society B Biological Sciences, October 2016, Royal Society Publishing

    Dr. James T Thorson

  75. Relative magnitude of cohort, age, and year effects on size at age of exploited marine fishes

    Article • Fisheries Research, August 2016, Elsevier

    Dr. James T Thorson

  76. Variation in growth among individuals and over time: A case study and simulation experiment involving tagged Antarctic toothfish

    Article • Fisheries Research, August 2016, Elsevier

    Dr. James T Thorson

  77. Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution

    Article • Fisheries Research, July 2016, Elsevier

    Dr. James T Thorson

  78. Hierarchical analysis of taxonomic variation in intraspecific competition across fish species

    Article • Ecology, July 2016, Wiley

    Dr. James T Thorson

  79. Techniques for improving estimates of maturity ogives in groundfish using double-reads and measurement error models

    Article • Fisheries Research, July 2016, Elsevier

    Dr. James T Thorson

  80. Corrigendum: How variable is recruitment for exploited marine fishes? A hierarchical model for testing life history theory

    Article • Canadian Journal of Fisheries and Aquatic Sciences, June 2016, Canadian Science Publishing

    Dr. James T Thorson

  81. Joint dynamic species distribution models: a tool for community ordination and spatio-temporal monitoring

    Article • Global Ecology and Biogeography, May 2016, Wiley

    Dr Mark D Scheuerell, Dr. James T Thorson

  82. Model‐based inference for estimating shifts in species distribution, area occupied and centre of gravity

    Article • Methods in Ecology and Evolution, April 2016, Wiley

    Dr. James T Thorson

  83. Using spatio-temporal models of population growth and movement to monitor overlap between human impacts and fish populations

    Article • Journal of Applied Ecology, April 2016, Wiley

    Dr. James T Thorson

  84. Accounting for spatiotemporal variation and fisher targeting when estimating abundance from multispecies fishery data1

    Article • Canadian Journal of Fisheries and Aquatic Sciences, April 2016, Canadian Science Publishing

    Dr. James T Thorson

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

    Article • Fisheries Research, March 2016, Elsevier

    Dr. James T Thorson

  86. Spatial delay-difference models for estimating spatiotemporal variation in juvenile production and population abundance

    Article • Canadian Journal of Fisheries and Aquatic Sciences, December 2015, Canadian Science Publishing

    Dr. James T Thorson

  87. Catch curve stock-reduction analysis: An alternative solution to the catch equations

    Article • Fisheries Research, November 2015, Elsevier

    Dr. James T Thorson

  88. Introduction

    Article • Fisheries Research, November 2015, Elsevier

    Dr. James T Thorson

  89. Evaluating a prior on relative stock status using simplified age-structured models

    Article • Fisheries Research, November 2015, Elsevier

    Dr. James T Thorson

  90. The potential impact of time-variation in vital rates on fisheries management targets for marine fishes

    Article • Fisheries Research, September 2015, Elsevier

    Dr. James T Thorson

  91. The importance of spatial models for estimating the strength of density dependence

    Article • Ecology, May 2015, Wiley

    Dr. James T Thorson

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

    Article • Methods in Ecology and Evolution, March 2015, Wiley

    Dr Mark D Scheuerell, Dr. James T Thorson

  93. Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes

    Article • Ecology, December 2014, Wiley

    Dr Mark D Scheuerell, Dr. James T Thorson

  94. Spatial semiparametric models improve estimates of species abundance and distribution

    Article • Canadian Journal of Fisheries and Aquatic Sciences, November 2014, Canadian Science Publishing

    Dr. James T Thorson, Blake E Feist

  95. Dealing with under- and over-dispersed count data in life history, spatial, and community ecology

    Article • Ecology, November 2014, Wiley

    Dr. James T Thorson

  96. A comparison of parametric, semi-parametric, and non-parametric approaches to selectivity in age-structured assessment models

    Article • Fisheries Research, October 2014, Elsevier

    Dr. James T Thorson

  97. How variable is recruitment for exploited marine fishes? A hierarchical model for testing life history theory

    Article • Canadian Journal of Fisheries and Aquatic Sciences, July 2014, Canadian Science Publishing

    Dr. James T Thorson

  98. Accounting for vessel effects when standardizing catch rates from cooperative surveys

    Article • Fisheries Research, July 2014, Elsevier

    Dr. James T Thorson

  99. Validating and Improving Life History Data in FishBase

    Article • Fisheries, April 2014, Wiley

    Dr. James T Thorson

  100. Complexity is costly: a meta-analysis of parametric and non-parametric methods for short-term population forecasting

    Article • Oikos, February 2014, Wiley

    Dr. James T Thorson

  101. A Bayesian approach to identifying and compensating for model misspecification in population models

    Article • Ecology, February 2014, Wiley

    Dr. James T Thorson

  102. Modeling structured population dynamics using data from unmarked individuals

    Article • Ecology, January 2014, Wiley

    Dr. James T Thorson

  103. A new role for effort dynamics in the theory of harvested populations and data-poor stock assessment

    Article • Canadian Journal of Fisheries and Aquatic Sciences, December 2013, Canadian Science Publishing

    Dr. James T Thorson

  104. Giants' shoulders 15 years later: lessons, challenges and guidelines in fisheries meta-analysis

    Article • Fish and Fisheries, October 2013, Wiley

    Dr. James T Thorson

  105. Accounting for space–time interactions in index standardization models

    Article • Fisheries Research, October 2013, Elsevier

    Dr. James T Thorson

  106. Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon

    Article • Journal of Animal Ecology, August 2013, Wiley

    Dr Mark D Scheuerell, Dr. James T Thorson

  107. A comparison of stock assessment uncertainty estimates using maximum likelihood and Bayesian methods implemented with the same model framework

    Article • Fisheries Research, May 2013, Elsevier

    Dr. James T Thorson

  108. The implications of spatially varying catchability on bottom trawl surveys of fish abundance: a proposed solution involving underwater vehicles

    Article • Canadian Journal of Fisheries and Aquatic Sciences, February 2013, Canadian Science Publishing

    Dr. James T Thorson

  109. A stepwise-selected spline approximation to time-varying parameters, with application to occupancy modelling

    Article • Methods in Ecology and Evolution, November 2012, Wiley

    Dr. James T Thorson

  110. Spawning biomass reference points for exploited marine fishes, incorporating taxonomic and body size information

    Article • Canadian Journal of Fisheries and Aquatic Sciences, September 2012, Canadian Science Publishing

    Dr. James T Thorson

  111. Linking fishing mortality reference points to life history traits: an empirical study

    Article • Canadian Journal of Fisheries and Aquatic Sciences, August 2012, Canadian Science Publishing

    Dr. James T Thorson

  112. Multispecies fisheries management and conservation: tactical applications using models of intermediate complexity

    Article • Fish and Fisheries, June 2012, Wiley

    Dr. James T Thorson

  113. Using model-based inference to evaluate global fisheries status from landings, location, and life history data

    Article • Canadian Journal of Fisheries and Aquatic Sciences, April 2012, Canadian Science Publishing

    Dr. James T Thorson

  114. Evaluating population recovery for sea turtles under nesting beach protection while accounting for nesting behaviours and changes in availability

    Article • Journal of Applied Ecology, April 2012, Wiley

    Dr. James T Thorson

  115. Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.)

    Article • ICES Journal of Marine Science, February 2012, Oxford University Press (OUP)

    Dr. James T Thorson

  116. Accounting for fish shoals in single- and multi-species survey data using mixture distribution models

    Article • Canadian Journal of Fisheries and Aquatic Sciences, September 2011, Canadian Science Publishing

    Dr. James T Thorson

  117. Better Catch Curves: Incorporating Age-Specific Natural Mortality and Logistic Selectivity

    Article • Transactions of the American Fisheries Society, May 2011, Taylor & Francis

    Dr. James T Thorson

  118. Multispecies estimation of Bayesian priors for catchability trends and density dependence in the US Gulf of Mexico

    Article • Canadian Journal of Fisheries and Aquatic Sciences, June 2010, Canadian Science Publishing

    Dr. James T Thorson

  119. Evaluating single- and multi-species procedures to estimate time-varying catchability functional parameters

    Article • Fisheries Research, January 2010, Elsevier

    Dr. James T Thorson

  120. Competing Interests, Economics, and Marine Fisheries Management: An Educational Case Study

    Article • Journal of Natural Resources and Life Sciences Education, January 2010, American Society of Agronomy

    Dr. James T Thorson

  121. Incorporating Time-Varying Catchability into Population Dynamic Stock Assessment Models

    Article • Reviews in Fisheries Science, November 2009, Taylor & Francis

    Dr. James T Thorson

  122. Gear selectivity and sample size effects on growth curve selection in shark age and growth studies

    Article • Fisheries Research, June 2009, Elsevier

    Dr. James T Thorson