Northwest Fisheries Science Center

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NWFSC Publications for James Thorson

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54 record(s) found.

Cao, J., J. T. Thorson, R. Richards, Y. Chen. 2017. Spatiotemporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine. Canadian Journal of Fisheries and Aquatic Sciences, 74(11):1781 - 1793. doi:10.1139/cjfas-2016-0137 (The next link will exit from NWFSC web site | The next link will exit from NWFSC web site)Go to metadata icon

Kai, M., J. T. Thorson, K. R. Piner, M. Maunder. 2017. Spatiotemporal variation in size-structured populations using fishery data: an application to shortfin mako (Isurus oxyrinchus) in the Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 74(11):1765-1780. doi:10.1139/cjfas-2016-0327 (The next link will exit from NWFSC web site | The next link will exit from NWFSC web site)Go to metadata icon

Monnahan, C. C., J. T. Thorson, T. A. Branch. 2017. The next link will exit from NWFSC web site Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo. Methods in Ecology and Evolution, 8(3):339-348. doi:10.1111/2041-210X.12681Go to metadata icon

Qi, L., J. T. Thorson, V. V. Gertseva, A. E. Punt. 2017. The benefits and risks of incorporating climate-driven growth variation into stock assessment models, with application to Splitnose Rockfish (Sebastes diploproa). ICES Journal of Marine Science. doi:https://doi.org/10.1093/icesjms/fsx147Go to metadata icon

Thorson, J. T., R. Fonner, M. A. Haltuch, K. Ono, H. Winker. 2017. Accounting for spatiotemporal variation and fisher targeting when estimating abundance from multispecies fishery data. Canadian Journal of Fisheries and Aquatic Sciences, 74(11):1794-1807. doi:10.1139/cjfas-2015-0598 (The next link will exit from NWFSC web site | The next link will exit from NWFSC web site)Go to metadata icon

Thorson, J. T., L. Barnett. 2017. The next link will exit from NWFSC web site Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat. ICES Journal of Marine Science, 74(5):1311-1321. doi:https://doi.org/10.1093/icesjms/fsw193Go to metadata icon

Thorson, J. T., S. Munch, D. Swain. 2017. The next link will exit from NWFSC web site Estimating partial compensation to bridge between neutral and niche theory in spatio-temporal community dynamics. Ecology, 98(5):1277-1289. doi:10.1002/ecy.1760Go to metadata icon

Thorson, J. T., K. F. Johnson, R. D. Methot, I. G. Taylor. 2017. The next link will exit from NWFSC web site Model-based estimates of effective sample size in Stock Synthesis using the Dirichlet-multinomial distribution. Fisheries Research, 192:84-93.Go to metadata icon

Thorson, J. T., J. Cope. 2017. The next link will exit from NWFSC web site Uniform, uninformed or misinformed?: The lingering challenge of minimally informative priors in data-limited Bayesian stock assessments. Fisheries Research, 194:164-172. doi:10.1016/j.fishres.2017.06.007Go to metadata icon

Thorson, J. T., K. Somers, J. E. Jannot. 2017. Using spatio-temporal models of population growth and movement to monitor overlap between human impacts and fish populations. Journal of Applied Ecology, 52(2):577587. doi:10.1111/1365-2664.12664Go to metadata icon

Zipkin, E., S. Rossman, C. B. Yackulic, J. D. Wiens, J. T. Thorson, R. J. Davis, E. C. Grant. 2017. The next link will exit from NWFSC web site Integrating count and detectionnondetection data to model population dynamics. Ecology, 98(6):1640-1650. doi:10.1002/ecy.1831Go to metadata icon

Foss-Grant, A., E. Zipkin, J. T. Thorson, O. Jensen, W. Fagan. 2016. Hierarchical analysis of phylogenetic variation in intraspecific competition across fish species. Ecology, 97(7):17241734. doi:10.1890/15-0733.1Go to metadata icon

Head, M. A., G. L. Stokes, J. T. Thorson, A. A. Keller. 2016. Techniques for improving estimates of maturity ogives in groundfish using double-reads and measurement error models. Fisheries Research.Go to metadata icon

Johnson, K. F., E. Councill, J. T. Thorson, E. Brooks, R. D. Methot, A. E. Punt. 2016. Can autocorrelated recruitment be estimated using integrated assessment models, and how does it affect population forecasts? Fisheries Research, 183:222232. doi:10.1016/j.fishres.2016.06.004Go to metadata icon

Thorson, J. T., K. Kristensen. 2016. A generic approach to bias correction in population models using random effects, with spatial and age-structured examples. Fisheries Research, 175:6674. doi:doi:10.1016/j.fishres.2015.11.016Go to metadata icon

Thorson, J. T., A. Rindorf, J. Gao, D. Hanselman, H. Winker. 2016. The next link will exit from NWFSC web site Global meta-analysis of density-dependent changes in effective area occupied for bottom-associated marine fishes. Proceedings of the National Academy of Sciences, 283(1840). doi:10.1098/rspb.2016.1853Go to metadata icon

Thorson, J. T., J. N. Ianelli, E. Larsen, M. D. Scheuerell, C. Szuwalski, E. Zipkin. 2016. Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. Global Ecology and Biogeography, 25(9):http://onlinelibrary.wiley.com/doi/10.1111/geb.12464/abstract. doi:10.1111/geb.12464Go to metadata icon

Thorson, J. T., M. L. Pinsky, E. Ward. 2016. Model-based inference for estimating distribution changes in marine fishes. Global Change Biology.Go to metadata icon

Thorson, J. T., C. Minte-Vera. 2016. The next link will exit from NWFSC web site Relative magnitude of cohort, age, and year effects on size at age of exploited marine fishes. Fisheries Research, 180:45-53. doi:doi:10.1016/j.fishres.2014.11.016Go to metadata icon

Webber, D. N., J. T. Thorson. 2016. The next link will exit from NWFSC web site Variation in growth among individuals and over time: A case study and simulation experiment involving tagged Antarctic toothfish. Fisheries Research, 180:6776. doi:10.1016/j.fishres.2015.08.016Go to metadata icon

Cope, J., J. T. Thorson, C. R. Wetzel, J. D. DeVore. 2015. Evaluating a prior on relative stock status using simplified age-structured models. Fisheries Research.Go to metadata icon

Ono, K., A. O. Shelton, E. J. Ward, J. T. Thorson, B. E. Feist, R. Hilborn. 2015. Space-time investigation of the effects of fishing on fish populations. Ecological Applications.Go to metadata icon

Thorson, J. T., D. B. Sampson, L. T. Kell, J. A. De Oliveirad, A. E. Punt. 2015. Development, testing, and evaluation of data-poor assessment and fisheries management methods. Fisheries Research, 171:1-3. doi:doi:10.1016/j.fishres.2015.08.008Go to metadata icon

Thorson, J. T., A. O. Shelton, E. J. Ward, H. Skaug. 2015. The next link will exit from NWFSC web site Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science, 72(5):1297-1310. doi:10.1093/icesjms/fsu213Go to metadata icon

Thorson, J. T., J. Cope, K. Kleisner, J. F. Samhouri, A. O. Shelton, E. J. Ward. 2015. Giants' shoulders 15 years later: Lessons, challenges, and guidelines in fisheries meta-analysis. Fish and Fisheries, 16(2):342361. doi:DOI: 10.1111/faf.12061Go to metadata icon

Thorson, J. T., C. Minto. 2015. The next link will exit from NWFSC web site Mixed effects: a unifying framework for statistical modelling in fisheries biology. ICES Journal of Marine Science, 72(5):1245-1256. doi:10.1093/icesjms/fsu213Go to metadata icon

Thorson, J. T., O. Jensen, R. Hilborn. 2015. Probability of stochastic depletion: an easily interpreted diagnostic for stock assessment modelling and fisheries management. International Council for the Exploration of the Sea Techniques in Marine Environmental Sciences, 72(2):428-435. doi:10.1093/icesjms/fsu127Go to metadata icon

Thorson, J. T., A. C. Hicks, R. D. Methot. 2015. Random effect estimation of time-varying factors in Stock Synthesis. ICES Journal of Marine Science, 72(1):178-185. doi:10.1093/icesjms/fst211Go to metadata icon

Thorson, J. T., J. N. Ianelli, S. Munch, K. Ono, P. Spencer. 2015. The next link will exit from NWFSC web site Spatial delay-difference models for estimating spatiotemporal variation in juvenile production and population abundance. Canadian Journal of Fisheries and Aquatic Sciences.Go to metadata icon

Thorson, J. T., M. D. Scheuerell, K. E. See, A. O. Shelton, H. Skaug, K. Kristensen. 2015. The next link will exit from NWFSC web site Spatial factor analysis: a new tool estimating multispecies spatial distributions and correlated ranges. Methods in Ecology and Evolution, 6(6):627-637. doi:10.1111/2041-210X.12359Go to metadata icon

Thorson, J. T. 2015. Spatio-temporal variation in fish condition is not consistently explained by density, temperature, or season for Northeast Pacific groundfishes. Marine Ecology Progress Series, 526:101-112. doi:10.3354/meps11204Go to metadata icon

Thorson, J. T., H. Skaug, K. Kristensen, A. O. Shelton, E. J. Ward, J. Harms, J. A. Benante. 2015. The importance of spatial models for estimating the type and strength of density dependence. Ecology, 96(5):12021212. doi:10.1890/14-0739.1Go to metadata icon

Thorson, J. T., C. C. Monnahan, J. Cope. 2015. The next link will exit from NWFSC web site The potential impact of time-variation in vital rates on fisheries management targets for marine fishes. Fisheries Research, 169:8-17.Go to metadata icon

Ward, E. J., J. E. Jannot, Y. Lee, K. Ono, A. O. Shelton, J. T. Thorson. 2015. Using spatiotemporal species distribution models to identify temporally evolving hotspots of species co-occurrence. Ecological Applications.Go to metadata icon

Froese, R., J. T. Thorson, R. Reyes. 2014. Bayesian approach to the estimation of length-weight relationships in fishes. Journal of Applied Ichthyology, 30(1):78-85. doi:10.1111/jai.12299Go to metadata icon

Gertseva, V. V., J. T. Thorson. 2014. Status of the Darkblotched Rockfish Resource off the Continental U.S. Pacific Coast in 2013. In Status of the Pacific Coast Groundfish Fishery through 2013, Stock Assessment and Fishery Evaluation: Stock Assessments, STAR Panel Reports, and Rebuilding Analyses. Pacific Fishery Management Council, Portland, Oregon, 351 pp.Go to metadata icon

Lynch, H., J. T. Thorson, A. O. Shelton. 2014. Dealing with under- and over-dispersed count data in life history, spatial, and community ecology. Ecology, 95(11):31733180. doi:http://dx.doi.org/10.1890/13-1912.1Go to metadata icon

Shelton, A. O., J. T. Thorson, E. J. Ward, B. E. Feist. 2014. Spatial, semi-parametric models improve estimates of species abundance and distribution. Canadian Journal of Fisheries and Aquatic Sciences, 71(11):1655-1666. doi:10.1139/cjfas-2013-0508Go to metadata icon

Thorson, J. T., K. Ono, S. Munch. 2014. A Bayesian approach to identifying and compensating for model misspecification in population models Read More: http://www.esajournals.org/doi/abs/10.1890/13-0187.1. Ecology, 95:329-341.Go to metadata icon

Thorson, J. T., I. G. Taylor. 2014. A comparison of parametric, semi-parametric, and non-parametric approaches to selectivity in age-structured assessment models. Fisheries Research, 158:7483. doi:10.1016/j.fishres.2013.10.002Go to metadata icon

Thorson, J. T., E. J. Ward. 2014. Accounting for vessel effects when standardizing catch rates from cooperative surveys. Fisheries Research.Go to metadata icon

Thorson, J. T., J. Cope, W. S. Patrick. 2014. Assessing the quality of life history information in publicly available databases. Ecological Applications.Go to metadata icon

Thorson, J. T., M. D. Scheuerell, B. X. Semmens, C. Pattengill-Semmens. 2014. Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes. Ecology, 95(12):3251-3258.Go to metadata icon

Thorson, J. T., O. Jensen, E. Zipkin. 2014. How variable is recruitment for marine fishes? A hierarchical model for testing life history theory. Canadian Journal of Fisheries and Aquatic Sciences.Go to metadata icon

Thorson, J. T., I. G. Taylor, I. J. Stewart, A. E. Punt. 2014. Rigorous meta-analysis of life history correlations by simultaneously analyzing multiple population dynamics models. Ecological Applications, 24(2):215-326. doi:10.1890/12-1803.1Go to metadata icon

Thorson, J. T., M. D. Scheuerell, E. Buhle, T. Copeland. 2014. The next link will exit from NWFSC web site Spatial variability buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon. Journal of Animal Ecology, 83(1):157-167.Go to metadata icon

Thorson, J. T. 2014. Standardizing compositional data for stock assessment. ICES Journal of Marine Science, 71(5):1117-1128. doi:10.1093/icesjms/fst224Go to metadata icon

Ward, E. J., E. E. Holmes, J. T. Thorson. 2014. Complexity is costly: comparing parametric and non-parametric methods for short-term population forecasting. Oikos, 123(6):652-661.Go to metadata icon

Zipkin, E., J. T. Thorson, K. E. See, H. Lynch, E. Grant, Y. Kanno, R. Chandler, B. H. Letcher, J. A. Royle. 2014. Modeling structured population dynamics using data from unmarked individuals. Ecology, 95(1):2229. doi:http://dx.doi.org/10.1890/13-1131.1Go to metadata icon

Stewart, I. J., A. C. Hicks, I. G. Taylor, J. T. Thorson, C. R. Wetzel, S. Kupschas. 2013. The next link will exit from NWFSC web site A comparison of stock assessment uncertainty estimates using maximum likelihood and Bayesian methods implemented with the same model framework. Fisheries Research, 142(May 2013):37-46. doi:10.1016/j.fishres.2012.07.003Go to metadata icon

Thorson, J. T., C. Minto, C. Minte-Vera, K. Kleisner, K. Longo. 2013. A new role for effort dynamics in the theory of harvested populations and data-poor stock assessment. Canadian Journal of Fisheries and Aquatic Sciences, 70(12):1829-1844. doi:10.1139/cjfas-2013-0280Go to metadata icon

Thorson, J. T., E. J. Ward. 2013. Accounting for space-time interactions in index standardization models. Fisheries Research.Go to metadata icon

Thorson, J. T., E. J. Ward. 2013. Accounting for space-time interactions in index standardization models. Fisheries Research, 147:426-433.Go to metadata icon

Thorson, J. T., I. J. Stewart, I. G. Taylor, A. E. Punt. 2013. Using a recruitment-linked multispecies stock assessment model to estimate common trends in recruitment for US West Coast groundfishes. Marine Ecology Progress Series.Go to metadata icon