Curriculum Vitae
James T. Thorson
Program Leader
Habitat and Ecosystem Process Research
Alaska Fisheries Science Center
National Marine Fisheries Service (NMFS)
Education
Ph.D. School of Aquatic and Fisheries Sciences (SAFS), University of Washington (UW), 2009-2011.
M.Sc. Department of Fisheries and Wildlife (FiW), Virginia Tech (V.T.), 2007-2009.
B.Sc. Environmental Studies, Philosophy, Minor: Economics, Emory University 2002-2006.
Employment
Program Lead, Habitat & Ecosystem Process Research, AK Fisheries Science Center, NMFS, Aug. 2018 – present.
Operations Research Analyst, Northwest Fisheries Science Center (NWFSC), NMFS, June 2012 – Aug 2018.
Post doctoral researcher, NWFSC, NMFS, March 2012 – June 2012.
Research Scientist, Commonwealth Scientific and Industrial Research Organization, July-Aug. 2011.
Affiliations
Affiliate Faculty, Oregon State University, Department of Fisheries and Wildlife, 2016-present
Affiliate Faculty, University of Washington, School of Aquatic and Fisheries Sciences, 2015-present
Stock Assessments
Thorson, J., and Wallace, J. 2017 A catch-only update assessment for canary rockfish (Sebastes pinniger) in the California Current in 2017. Pacific Fisheries Management Council.
Thorson, J., and Wetzel, C. 2015 The status of canary rockfish (Sebastes pinniger) in the California Current in 2015. Pacific Fisheries Management Council.
Gertseva, V., and Thorson, J. 2013. Status of the darkblotched rockfish resource off the continental US Pacific Coast in 2013. Pacific Fisheries Management Council.
Stewart, I., Thorson, J., and Wetzel, C. 2011. Status of the US sablefish resource in 2011. Pacific Fisheries Management Council.
Reports and Tech Memos
Winker, H. Carvalho, F., Thorson, J., Parker, D., Kerwath, S., Booth, A., Kell, L. JABBA-Select: an alternative surplus production model to account for changes in selectivity and relative mortality from multiple fisheries. Marine Resource Assessment and Management Group, University of Cape Town, MARAM/IWS/2018/Linefish/P2
Winker, H., Thorson, J., Fairweather, Tracy, Leslie, Rob, and Durholtz, Deon. Towards improving precision in South African demersal trawl survey indices using geostatistical GLMMs. Marine Resource Assessment and Management Group, University of Cape Town, MARAM/IWS/2017/Hake/BG8.
Buhle, E., Scheuerell, M., Cooney, T., Ford, M., Zabel, R., Thorson, J. 2018. Using integrated population models to evaluate fishery and environmental impacts on pacific salmon viability. NOAA Technical Memorandum NMFS-NWFSC-140. DOI: 10.7289/V5/TM-NWFSC-140
Thorson, J. 2017. Estimating a Bayesian prior for steepness in Pacific rockfishes (Sebastes spp.) off the U.S. West Coast for the 2017 assessment cycle. Report for the Pacific Fisheries Management Council March 2017 briefing book.
Thorson, J., Punt, A., Sampson, D., Kell, L., De Oliveira, J. 2016. Development, testing, and evaluation of data-poor assessment and fisheries management methods. Fisheries Research, 171: 1-3.
Thorson, J. 2015. Summary of the geostatistical delta-GLMM tool. Report for the Pacific Fisheries Management Council March 2015 briefing book.
Thorson, J. 2015. Estimating a Bayesian prior for steepness in Pacific rockfishes (Sebastes spp.) off the U.S. West Coast for the 2015 assessment cycle. Report for the Pacific Fisheries Management Council March 2015 briefing book.
Thorson, J. 2012. Estimating a Bayesian prior for steepness in Pacific rockfishes (Sebastes spp.) off the U.S. West Coast for the 2013 assessment cycle. Report for the Pacific Fisheries Management Council briefing book.
Shared software (with ongoing maintenance)
Thorson, J. 2018. FishStatsUtils: Utility functions for spatio-temporal analysis (https://github.com/James-Thorson/FishStatsUtils)
Thorson, J. 2017. FishLife: Estimate fish traits for all marine fish species globally (https://github.com/James-Thorson/FishLife)
Thorson, J. 2017. FishData: Tools to download and harmonize publicly available fisheries data (https://github.com/James-Thorson/FishData)
Thorson, J. 2016. VAST: an R package for vector autoregressive spatio-temporal modelling of fish catch rate data (https://github.com/James-Thorson/VAST)
Thorson, J., and Cope, J. 2014. CCSRA: an R package for implementing catch-curve stock reduction analysis, a new tool for data-poor assessments (https://github.com/James-Thorson/CCSRA).
Thorson, J., Stewart, I., and Punt, A. 2011. nwfscAgeingError: an R package user interface for estimating and assessing model fit for ageing bias and imprecision (https://github.com/nwfsc-assess/nwfscAgeingError).
Shared software (deprecated)
Thorson, J. 2016. MIST: an R package for Multispecies Interactions Spatio-Temporal models (https://github.com/James-Thorson/MIST)
Thorson, J. 2015. SpatialFA: an R package for spatial factor analysis when estimating joint species distribution models (https://github.com/James-Thorson/spatial_factor_analysis)
Thorson, J. 2014. SpatialDeltaGLMM: an R package for spatial index standardization (https://github.com/nwfsc-assess/geostatistical_delta-GLMM)
Thorson, J. 2013. NegLogInt_Fn(), a tool for estimating random effects in Stock Synthesis (https://github.com/cran/r4ss).
Ward, E., and Thorson J. 2012. nwfscDeltaGLM: an R package for Bayesian index standardization of post-stratified survey data (https://github.com/nwfsc-assess/nwfscDeltaGLM).
Scholarships and Awards
Best presentation, North Pacific Marine Sciences Organization (PICES) annual meeting, Sept. 2017.
Presidential Early Career Award for Scientists and Engineers, Winter 2016.
Reviewer of the Year, Canadian Journal of Fisheries and Aquatic Sciences, 2015.
Employee of the Year, Northwest Fisheries Science Center, NMFS, NOAA, 2015.
Faculty Merit Award from SAFS, 2012.
National Research Council Fellowship, 2012.
FINS travel award, 2011
SAFS Top Scholar Fellowship, 2012-2014
Sea Grant Pop. Dy. Fellowship, 2009-2012
AFS Marine Section Travel Grant, June 2009
Skinner Memorial Award (Runner-Up), June 2009
Young’s Award for Written Excellence in Natural Resources, April 2009
NMFS-RTR Fellowship, Virginia Tech, 2007-2009.
Louis S. Gilbert Fund Grant, Mote Marine Labs, 2006.
Scholastic Inquiry and Research at Emory (SIRE), Emory University, 2005.
Dean’s Achievement Scholarship, Emory University, 2002-2006.
National Merit Scholarship, Emory University, 2002-2006.
Teaching
Instructor (2 day workshop): Spatio-temporal analysis of ecological time series, Irish Marine Institute, Galway, Ireland, March 21-22, 2019.
Instructor (20 lectures/labs): FISH 556: Spatio-temporal models for ecologists, Univ. Wash., Spring 2018
Instructor (1 day tutorial): CAPAM mini-workshop on spatio-temporal models for fishery catch-per-unit-effort data. La Jolla, CA, USA, March 2, 2018.
Instructor (2 day workshop): Mini-Symposium: Future of Statistical Fisheries Science and Ecology, Yokohama, Japan, Feb. 20-21, 2018.
Instructor (4 day workshop): Spatio-temporal modelling to derive indices of abundance from scientific surveys, Seattle, USA, Jan 29-Feb. 1, 2018.
Instructor (2 day intensive course): Spatial models using mixed effects in Template Model Builder, Institute of Marine Resources, Bergen, Norway, Aug. 23-24, 2017.
Instructor (3 day intensive course): FishStats: A spatio-temporal toolbox for fisheries, Alaska Fisheries Science Center, Seattle, Feb. 8-10, 2017.
Instructor (20 lectures/labs): FISH 509: Spatio-temporal models for ecologists, Univ. Wash., Spring 2016
Instructor (5 day intensive course): Spatio-temporal models for fisheries, National Institute of Water and Atmospheric Research, Wellington, New Zealand, March 14-18, 2016.
Instructor (5 day intensive course): Using Template Model Builder for fisheries models, Univ. Wash. Winter 2016.
Instructor (10 day intensive course): Tag-resighting models and applications, Univ. Concepcion, Jan 11-22 2016 (2 week course)
Guest lecturer (1 lecture): Applied stock assessment methods, Univ. Wash., Fall 2014
Instructor (20 lectures/labs): FISH 509: Hierarchical approach to population modelling, Univ. Wash., Spring 2014
Guest lecture (2 lectures): Decision analysis, University of Washington, Fall 2013.
Guest lecturer (3 lectures): Numerical computing, University of Washington, Fall 2012.
Guest lecturer (8 lectures): Simulation Modeling, Virginia Tech, Spring 2009
Co-instructor: Statistical Programming, Virginia Tech, Fall 2008
Teaching Assistant: population dynamics workshop, Virginia Tech, Jan. 2008, Jan. 2009.
Teaching Assistant: Meteorology, Emory University, 2006.
Peer-reviewed publications (n = 113)
(Collaborators – *undergraduate, ‡graduate, ±international at beginning of writing)
1. In press. Grüss, A., Walter, J., Babcock, E., Forrestal, F., Thorson, J., Lauretta, M, Schirripa, M. Evaluation of the impacts of different treatments of spatio-temporal variation in catch-per-unit-effort standardization models. Fisheries Research. https://doi.org/10.1016/j.fishres.2019.01.008
2. In press. Grüss, A., Thorson, J. Developing spatio-temporal models using multiple data types for evaluating population trends and habitat usage. ICES Journal of Marine Sciences.
3. In press. Perretti, C., Thorson, J. Spatio-temporal dynamics of summer flounder (Paralichthys dentatus) on the Northeast US Shelf. Fisheries Research. https://doi.org/10.1016/j.fishres.2019.03.006
4. In press. Monnahan, C.‡, Branch, T., Stewart, I, Thorson, J., Szuwalski, C. Overcoming long Bayesian run times in integrated fisheries stock assessments. ICES Journal of Marine Sciences.
5. In press. Maunder, M., Thorson, J. Modeling temporal variation in recruitment in fisheries stock assessment: A review of theory and practice. Fisheries Research. https://doi.org/10.1016/j.fishres.2018.12.014
6. In press. Rudd, M., Thorson, J., Sagarese, S. Ensemble models for data-poor assessment: accounting for uncertainty in life history information. ICES Journal of Marine Sciences. https://doi.org/10.1093/icesjms/fsz012
7. In press. Lowerre-Barbieri, S., Kays, R., Thorson, J., Wikelski, M±. The ocean’s movescape: fisheries management in the bio-logging decade (2018-2028). ICES Journal of Marine Sciences. https://doi.org/10.1093/icesjms/fsy211
8. In press. Stock, B.‡, Ward, Thorson, J., Jannot, J., and Semmens, B. The utility of spatial model-based estimators of unobserved bycatch: future or folly? ICES Journal of Marine Sciences. https://doi.org/10.1093/icesjms/fsy153
9. In press. O’Leary, C.‡, Thorson, J., Nye, J., Miller, T. Understanding retrospective Summer Flounder (Paralichthys dentatus) abundance patterns through incorporation of oceanographic dependent vital rates in Bayesian state-space models. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2018-0092
10. In press. Thorson, J, Winker, H., and Rudd, M. The case for estimating recruitment variation in data-moderate and data-poor age-structured models. Fisheries Research. https://doi.org/10.1016/j.fishres.2018.07.007
11. In press. McClatchie, S., Gao, J., Drenkard, L., Thompson, A., Watson, W., Cianelli, L, Bograd, S., Thorson, J. Inter-annual and secular variability of mesopelagic and forage fishes in the southern California Current System. Journal of Geophysical Research – Oceans. https://doi.org/10.1029/2018JC014011
12. In press. Brooks, L, Thorson, J, Shertzer, K, Nash, R±, Brodziak, J., Johnson, K., Klibansky, N.±, Wells, B., White, J±. Paulik revisited: Statistical framework and estimation performance of multistage recruitment functions. Fisheries research. https://doi.org/10.1016/j.fishres.2018.06.018
13. In press. Thorson, J, Dorn, M, Hamel, O. Steepness for West Coast rockfishes: Results (so far) from a twelve-year experiment in regional meta-analysis. Fisheries Research. https://doi.org/10.1016/j.fishres.2018.03.014
14. In press. Thorson, J. Perspective: Let’s simplify stock assessment by replacing tuning algorithms with statistics. Fisheries Research. https://doi.org/10.1016/j.fishres.2018.02.005
15. In press. McGowan, D.‡, Horne, J., Thorson, J., Zimmermann, M. Influence of environmental factors on capelin distributions in the Gulf of Alaska. Deep Sea Research II. https://doi.org/10.1016/j.dsr2.2017.11.018
16. 2019. Free, C.‡,Thorson, J., Pinsky, M., Oken, K.,Wiedenmann, J., Jensen, O. Impacts of historical warming on marine fisheries production. Science. 363(6430): 979-983. https://doi.org/10.1126/science.aau1758.
17. 2019. Jacobson, N, Thorson, J., Essington, T. Detecting mortality variation to enhance forage fish population assessments. ICES Journal of Marine Sciences. 76(1): 124–135. https://doi.org/10.1093/icesjms/fsy160.
18. 2019. Thorson, J. , Haltuch, M. Spatio-temporal analysis of compositional data: increased precision and improved workflow using model-based inputs to stock assessment. Canadian Journal of Fisheries and Aquatic Sciences. 76(3): 401-414. https://doi.org/10.1139/cjfas-2018-0015.
19. 2019. Xu, H., Thorson, J., Taylor, I., and Methot, R. A new semi-parametric approach to autocorrelated age- and time-varying selectivity in age-structured assessment models. Canadian Journal of Fisheries and Aquatic Sciences. 76(2): 268-285. https://doi.org/10.1139/cjfas-2017-0446
20. 2019. Thorson, J. Evaluating skill for short-term forecasts of fish distribution shifts in the Eastern Bering Sea. Fish and Fisheries. 20(1): 159-173. https://doi.org/10.1111/faf.12330.
21. 2019. Thorson, J. Guidance for decisions using the Vector Autoregressive Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate assessments. Fisheries Research. 210: 143-161. https://doi.org/10.1016/j.fishres.2018.10.013
22. 2018. Walsh, J., Minto, C., Jardim, E., Anderson, C., Jensen O., Afflerbach, J., Dickey-Collas, M., Kleisner, K., Longo, C., Osio, G., Selig, E., Thorson, J., Rudd, M., Papacostas, K., Kittinger, J., Rosenberg, A., Cooper, A. Trade‐offs for data‐limited fisheries when using harvest strategies based on catch‐only models. Fish and Fisheries. 19(6): 1130-1146. http://dx.doi.org/10.1111/faf.12316
23. 2018. Grüss, A; Perryman, H.; Babcock, E., Sagarese, R., Thorson, J., Ainsworth, C., Anderson, E., Brennan, K., Campbell, M., Christman, M., Cross, S., Drexler, M., Drymon, J., Gardner, C., Hanisko, D., Hendon, J., Koenig, C., Love, M., Martinez-Andrade, F., Morris, J., Noble, B., Nuttall, M, Osborne, J., Pattengill-Semmens, C., Pollack, A., Sutton, T., Switzer, T. Monitoring programs of the U.S. Gulf of Mexico: inventory, development and use of a large monitoring database to map fish and invertebrates spatial distributions. Reviews in Fish Biology and Fisheries. 28(4): 667-691. https://doi.org/10.1007/s11160-018-9525-2
24. 2018. Thorson, J., Scheuerell, M., Olden, J., and Schindler, D. Spatial heterogeneity contributes more to portfolio effects than species differences in bottom-associated marine fishes. Proceedings of the Royal Society B. 285(1888). https://dx.doi.org/10.6084/m9.figshare.c.4249172.
25. 2018. Dolder, P.‡, Thorson, J, and Minto, C. Using joint-species distribution models to inform mixed fishery management. Scientific Reports. 8:13886. https://doi.org/10.1038/s41598-018-31881-w
26. 2018. Hocking, D., Thorson, J., O’Neil, K, and Letcher, B. A geostatistical state-space model of animal densities for stream networks. Ecological Applications. 28(7): 1782-1796. https://doi.org/10.1002/eap.1767
27. 2018. Thorson, J. Three problems with the conventional delta-model for biomass sampling data, and a computationally efficient alternative. Canadian Journal of Fisheries and Aquatic Sciences. 75(9): 1369-1382. https://doi.org/10.1139/cjfas-2017-0266
28. 2018. Rudd, M.‡, Thorson, J. Accounting for variable recruitment and fishing mortality in length-based stock assessments for data-limited fisheries. Canadian Journal of Fisheries and Aquatic Sciences. 75(7): 1019-1035. https://doi.org/10.1139/cjfas-2017-0143.
29. 2018. Neubauer, P.±, Thorson, J., Melnychuk, M, Methot, R., and Blackhart, K. Drivers and rates of stock assessment in the United States. PLOS one. https://doi.org/10.1371/journal.pone.0196483
30. 2018. Qi, L.‡, Thorson, J., Gertseva, V., and Punt, A. The benefits and risks of incorporating climate-driven variation in growth into the stock assessment models, with application to Splitnose Rockfish (Sebastes diploproa). ICES Journal of Marine Sciences. 75(1): 245–256. DOI: https://doi.org/10.1093/icesjms/fsx147.
31. 2018. Rosenberg, A., Kleisner, K., Afflerbach, J., Anderson, S., Dickey-Collas, M.±, Cooper, A., Fogarty, M., Fulton, E.±, Gutierrez, N.±, Hyde, K., Jardim, E., Jensen, O., Kristiansen, T, Longo, C., Minte-Vera, C., Minto, C., Mosqueira, I.±, Osio, C.±, Ovando, D., Selig, E., Thorson, J., Walsh, J., Ye, Y.±. Applying a new ensemble approach to estimating stock status of marine fisheries around the world. Conservation Letters. 11(1): 1-9. https://doi.org/10.1111/conl.12363 .
32. 2018. Grüss, A., Thorson, J, Babcock, E., Tarnecki, J. Producing distribution maps for informing ecosystem-based fisheries management using a comprehensive survey database and spatio-temporal models. ICES Journal of Marine Sciences. 75(1): 158–177. https://doi.org/10.1093/icesjms/fsx120.
33. 2017. Thorson, J., Munch, S., Cope, J., Gao, J. Predicting life history parameters for all fishes worldwide. Ecological Applications. 27(8): 2262–2276. https://doi.org//10.1002/eap.1606
34. 2017. Conn, PB, Thorson, J, and Johnson, DS. Confronting preferential sampling in count and occupancy surveys: diagnosis and triage. Methods in Ecology and Evolution. 8(11): 1535–1546. https://doi.org/10.1111/2041-210X.12803
35. 2017. Thorson, J., Kotwicki, S., and Ianelli, J. The relative influence of temperature and size-structure on fish distribution shifts: A case-study on Walleye pollock in the Bering Sea. Fish and Fisheries. 18:1073–1084. https://doi.org/10.1111/faf.12225.
36. 2017. Szuwalski, C.‡, and Thorson, J. Global fishery dynamics are poorly predicted by classical models. Fish and Fisheries. 18:1085–1095. https://doi.org/10.1111/faf.12226.
37. 2017. Cao, J‡, Thorson, J., Richards, A, and Chen, Y. Geostatistical index standardization improves the performance of stock assessment model: an application to northern shrimp in the Gulf of Maine. Canadian Journal of Fisheries and Aquatic Sciences. 74:(11), 1781-1793. https://doi.org/10.1139/cjfas-2016-0137
38. 2017. Kai, M±, Thorson, J., Piner, K, and Maunder, M. Spatio-temporal 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. https://doi.org/10.1139/cjfas-2016-0327
39. 2017. Thorson, J., Fonner, R., Haltuch, M., Ono, K., and Winker, H. 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. https://doi.org/10.1139/cjfas-2015-0598
40. 2017. Kai, M±, Thorson, J., Piner, K, and Maunder, M. Predicting the spatio-temporal distributions of oceanic pelagic sharks in the western and central North Pacific. Progress in Oceanography. 26(5): 569–582. https://doi.org/10.1111/fog.12217
41. 2017. Anderson, S., Cooper, A., Jensen, O., Minto, C., Thorson, J., Walsh, J., Afflerbach, J., Dickey-Collas, M., Kleisner, K., Longo, C., Osio, G., Ovando, D., Rosenberg, A., Selig, E. Improving estimates of population status and trajectory with superensemble models. Fish and Fisheries, 18(4): 732–741. https://doi.org/10.1111/faf.12200
42. 2017. Hovel‡, R., Thorson, J., Carter, J., and Quinn, T. Within-lake habitat heterogeneity mediates community response to warming trends. Ecology. 98(9): 2333–2342. https://doi.org/10.1002/ecy.1944.
43. 2017. Thorson, J., and Cope, J. Uniform, uninformed or misinformed?: The lingering challenge of minimally informative priors in data-limited Bayesian stock assessments. Fisheries Research. 194: 164-172. https://doi.org/10.1016/j.fishres.2017.06.007.
44. 2017. Rindorf, A, Dichmont, CM., Thorson, J., Charles, A, Clausen, LW, Degnbol, P, Garcia, D, Hintzen, NT, Kempf, A, Levin, P, Mace, P, Maravelias, C, Minto, C, Mumford, J, Pascoe, A, Prellezo, R, Punt, AE, Reid, D, Röckmann, C, Stephenson, RL, Thebaud, O, Tserpes, G, and Voss, R. Inclusion of ecological, economic, social, and institutional considerations when setting targets and limits for multispecies fisheries. ICES Journal of Marine Sciences. 74 (2): 453-463. https://doi.org/10.1093/icesjms/fsw226.
45. 2017. Grüss, A, Thorson, J., Sagarese, S., Babcock, E., Karnauskas, M., Walter III, J., Drexler, M. Ontogenetic spatial distributions of red grouper (Epinephelus morio) and gag grouper (Mycteroperca microlepis) in the U.S. Gulf of Mexico. Fisheries Research. 193: 129–142. https://doi.org/10.1016/j.fishres.2017.04.006
46. 2017. Thorson, J. and Barnett, L. Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat. ICES Journal of Marine Sciences, 74(5): 1311-1321. https://doi.org/10.1093/icesjms/fsw193.
47. 2017. Zipkin, E., Rossman, S., Yackulic, C., Wiens, J.D., Thorson, J., Davis, R.J., and Grant, E.H.C. Integrating count and detection–nondetection data to model population dynamics. Ecology, 98(6): 1640–1650. https://doi.org/10.1002/ecy.1831
48. 2017. Thorson, J., Jannot, J, Somers, K. Using spatio-temporal models of population growth and movement to monitor overlap between human impacts and fish populations. Journal of Applied Ecology, 54(2): 577–587. https://doi.org/10.1111/1365-2664.12664
49. 2017. Thorson, J., Johnson, K., Methot, R., and Taylor, I. Model-based estimates of effective sample size in Stock Synthesis using the Dirichlet-multinomial distribution. Fisheries Research. 192: 84-93. https://doi.org/10.1016/j.fishres.2016.06.005
50. 2017. Monnahan, Cole C. ‡, Thorson, J., Branch, TA. Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo. Methods in Ecology and Evolution. 8(3): 339–348. https://doi.org/10.1111/2041-210X.12681
51. 2017. Thorson, J., Munch, S, and Swain, D±. Estimating partial regulation in community dynamics using spatio-temporal models. Ecology. 98(5): 1277-1289. https://doi.org/10.1002/ecy.1760.
52. 2016. Thorson, J., Rindorf, A±, Gao, J, Hanselman, D, and Winker, H±. Density-dependent changes in effective area occupied for sea-bottom associated marine fishes. Proceedings of the Royal Society B. 283(1840). https://doi.org/10.1098/rspb.2016.1853
53. 2016. Head, M., Stokes, G.*, Thorson, J., and Keller, A. Techniques for improving estimates of maturity ogives in groundfish using double-reads and measurement error models. Fisheries Research. 179: 251–258. https://doi.org/10.1016/j.fishres.2016.03.004.
54. 2016. Thorson, J., Scheuerell, M., Szuwalski, C., Zipkin, E., Ries, L, and Ianelli, J. Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. Global Ecology and Biogeography. 25(9): 1144–1158. https://doi.org/10.1111/geb.12464
55. 2016. Foss-Grant, A.‡, Zipkin, E., Thorson, J., Jensen, O., and Fagan, W. Hierarchical analysis of phylogenetic variation in intraspecific competition across fish species. Ecology, 97(7): 1724–1734. https://doi.org/10.1890/15-0733.1.
56. 2016. Thorson, J., Pinsky, M., and Ward, E. Model-based inference for estimating shifts in species distribution, area occupied, and center of gravity. Methods in Ecology and Evolution, 7(8): 990–1002. https://doi.org/10.1111/2041-210X.12567
57. 2016. Johnson‡, K., Councill, E., Thorson, J., Brooks, L., Methot, R., and Punt, A. Can autocorrelated recruitment be estimated using integrated assessment models and how does it affect population forecasts? Fisheries Research. 183: 222-232. https://doi.org/10.1016/j.fishres.2016.06.004
58. 2016. Webber, D’Arcy‡±, and Thorson, J. Variation in growth among individuals and over time: A case study and simulation experiment involving tagged Antarctic toothfish. Fisheries Research, 180: 67-76. https://doi.org/10.1016/j.fishres.2015.08.016
59. 2016. Thorson, J., Minte-Vera, C. Relative magnitude of cohort, age, and year-effects on growth of marine fishes. Fisheries Research, 180: 45-53. https://doi.org/10.1016/j.fishres.2015.10.023
60. 2016. Fogarty, M.J., Rosenberg, A.A., Cooper, A.B., Dickey-Collas, M., Fulton, E.A., Gutiérrez, N.L., Hyde, K.J.W., Kleisner, K.M., Kristiansen, T., Longo, C., Minte-Vera, C.V., Minto, C., Mosqueira, I., Osio, G.C., Ovando, D., Selig, E.R., Thorson, J. & Ye, Y. Fishery production potential of large marine ecosystems: A prototype analysis. Environmental Development, 17, Supplement 1, 211–219. https://doi.org/10.1016/j.envdev.2016.02.001
61. 2016. Ono, K.‡, Shelton, A.O., Ward, E.J., Thorson, J., Feist, B.E., Hilborn, R. Space-time investigation of the effects of fishing on fish populations. Ecological Applications, 26(2): 392–406, https://doi.org/10.1890/14-1874
62. 2016. Thorson, J., and Kristensen, K±. Implementing a generic method for bias correction in statistical models using random effects, with spatial and population dynamics examples. Fisheries Research, 175: 66–74. https://doi.org/10.1016/j.fishres.2015.11.016.
63. 2015. Ward, E., Shelton, O., Thorson, J., Ono, K., and Lee, Y. Using spatiotemporal species distribution models to identify temporally evolving hotspots of species co-occurrence. Ecological Applications, 25(8): 2198–2209, https://doi.org/10.1890/15-0051.1
64. 2015. Thorson, J., Ianelli, J., Munch, S., Ono, K.‡, and Spencer, P. Spatial delay-difference models for estimating spatiotemporal variation in juvenile production and population abundance. Canadian Journal of Fisheries and Aquatic Sciences, 72(12): 1897-1915, https://doi.org/10.1139/cjfas-2014-0543.
65. 2015. Cope, J., Thorson, J., Wetzel, C., and DeVore, J. Evaluating a prior on relative stock status using simplified age-structured models. Fisheries Research. 171: 101-109. https://doi.org/10.1016/j.fishres.2014.07.018
66. 2015. Thorson, J., and Cope, J. Catch curve stock-reduction analysis: an alternative solution to the catch equation. Fisheries Research. 171: 33-41. https://doi.org/10.1016/j.fishres.2014.03.024
67. 2015. Thorson, J. Skaug, H.±, Shelton, A.O., Kristensen, K.±, and Scheuerell, M. Spatial factor analysis: a new tool estimating multispecies spatial distributions and correlated distributions among species. Methods in Ecology and Evolution. 6(6): 627-637. https://doi.org/10.1111/2041-210X.12359
68. 2015. Thorson, J., and Minto, C±. Mixed effects: a unifying framework for statistical modelling in fisheries biology. ICES Journal of Marine Sciences. 72 (5): 1245-1256. https://doi.org/10.1093/icesjms/fsu213
69. 2015. Thorson, J., Shelton, O., Ward, E., and Skaug, H±. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Sciences. 72 (5): 1297-1310. https://doi.org/10.1093/icesjms/fsu243
70. 2015. Thorson, J., Monnahan, C.‡, and Cope, J. The potential impact of time-variation in vital rates on fisheries management targets for marine fishes. Fisheries Research. 169: 8-17. https://doi.org/10.1016/j.fishres.2015.04.007
71. 2015. Thorson, J., Skaug, H. ±, Kristensen, K. ±, Ward, E., Shelton, O., Harms, J., Benante, J. The importance of spatial models for estimating the strength of density dependence. Ecology. 96(5): 1202–1212. https://doi.org/10.1890/14-0739.1
72. 2015. Thorson, J. Spatio-temporal variation in fish condition is not consistently explained by density, temperature, or season for Northeast Pacific groundfishes. Mar. Ecol. Progress Series. 526: 101-112. https://doi.org/10.3354/meps11204
73. 2015. Thorson, J., Kleisner, K., Samhouri, J., Ward, E., Shelton, A. and Cope, J. Giants’ shoulders 15 years later: Lessons, challenges, and guidelines in fisheries meta-analysis. Fish and Fisheries. 16, 342–361. https://doi.org/10.1111/faf.12061
74. 2015. Thorson, J., Jensen, O., and Hilborn, R. Probability of stochastic depletion: an easily interpreted diagnostic for stock assessment modelling and fisheries management. ICES Journal of Marine Sciences, 72(2): 428-435. https://doi.org/10.1093/icesjms/fsu127
75. 2015. Berkson, J., and Thorson, J. The determination of data-poor catch limits in the United States: Is there a better way? ICES Journal of Marine Sciences, 72(1): 237-242. https://doi.org/10.1093/icesjms/fsu085
76. 2015. Thorson, J., Hicks, A., and Methot, R. Jr. Random effect estimation of time-varying parameters in Stock Synthesis. ICES Journal of Marine Sciences, 72(1): 178-185. https://doi.org/10.1093/icesjms/fst211
77. 2014. Thorson, J., Scheuerell, M, Ward, E., Semmens, B., and Semmens, C. Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes. Ecology, 95(12): 3251-3258. https://doi.org/10.1890/13-2223.1
78. 2014. Lynch, H., Thorson, J., and Shelton, A. Dealing with under- and over-dispersed count data in life history, spatial, and community ecology. Ecology, 95(11):3173–3180. https://doi.org/10.1890/13-1912.1
79. 2014. Zipkin, E., Thorson, J., Lynch, H., Royle, A., Grant, E., Kanno, Y., See, K, and Chandler, D. Modeling structured population dynamics using data from unmarked individuals. Ecology 95:22–29. https://doi.org/10.1890/13-1131.1
80. 2014. Thorson, J., Jensen, O., and Zipkin, E. How variable is recruitment in marine fishes? A hierarchical model for testing life history theory. Canadian Journal of Fisheries and Aquatic Sciences 71(7): 973-983, https://doi.org/10.1139/cjfas-2013-0645.
81. 2014. Thorson, J. Standardizing compositional data for stock assessment. ICES Journal of Marine Sciences. 71(5):1117-1128. https://doi.org/10.1093/icesjms/fst224
82. 2014. Shelton, A.O., Thorson, J., Ward, E.J., and Feist, B.E. Spatial semiparametric models improve estimates of species abundance and distribution. Canadian Journal of Fisheries and Aquatic Sciences 71: 1655–1666. https://doi.org/10.1139/cjfas-2013-0508.
83. 2014. Ward, E.J., Holmes, E.E., Thorson, J., Collen, B. Complexity is costly: a meta-analysis of parametric and non-parametric methods for short-term population forecasting. Oikos 123 (6): 652–661. https://doi.org/10.1111/j.1600-0706.2014.00916.x
84. 2014. Thorson, J., and Ward, E. Accounting for vessel effects when standardizing catch rates from cooperative surveys. Fisheries Research. 155: 168-176. https://doi.org/10.1016/j.fishres.2014.02.036
85. 2014. Thorson, J., and Taylor, I.G. A comparison of parametric, semi-parametric, and non-parametric approaches to selectivity in age-structured assessment models. Fisheries Research 158: 74–83. https://doi.org/10.1016/j.fishres.2013.10.002
86. 2014. Patrick, W., Cope, J.M., and Thorson, J. Validating and improving life history data in FishBase. Fisheries. 39(4): 173-176. https://doi.org/10.1080/03632415.2014.891504
87. 2014. Thorson, J., Munch, S., and Ono, K‡. A Bayesian approach to identifying and compensating for model misspecification in population models. Ecology 95: 329-341. https://doi.org/10.1890/13-0187.1
88. 2014. Froese, R.±, Thorson, J., and Reyes, R.B. Jr.± A Bayesian approach to estimation of length-weight relationships in fishes. Journal of Applied Ichthyology 30(1): 78-85. https://doi.org/10.1111/jai.12299.
89. 2014. Plagányi, E.E. ±, Punt, A.E., Hillary, R. ±, Morello, E.B. ±, Thebaud, O. ±, Hutton, T. ±, Pillans, R. ±, Thorson, J., Fulton, E.A. ±, Smith, A.D.M. ±, Bayliss, P. ±, Haywood, M. ±, Lyne, V. ±, and Rothlisberg, P.C±. Multispecies fisheries management and conservation: tactical applications using models of intermediate complexity. Fish and Fisheries. 15(1): 1-20. https://doi.org/10.1111/j.1467-2979.2012.00488.x
90. 2014. Thorson, J., Taylor, I., Stewart, I.J., and Punt, A.E. Rigorous meta-analysis of life history correlations by simultaneously analyzing multiple population dynamics models. Ecological Applications. 24(2): 315–326. https://doi.org/10.1890/12-1803.1
91. 2014. Thorson, J., Cope, J., and Patrick, W.S. Assessing the quality of life history information in publicly available databases. Ecological Applications 24(1): 217–226. https://doi.org/10.1890/12-1855.1
92. 2014. Thorson, J., Scheuerell, M., Buhle, E., and Copeland, T. Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon. Journal of Animal Ecology 83(1): 157-167. https://doi.org/10.1111/1365-2656.12117
93. 2013. Thorson, J., Minto, Coilin, Minte-Vera, C. ±, Kleisner, K., and Longo, C. A new role for effort dynamics in the theory of harvest populations and data-poor stock assessment. Canadian Journal of Fisheries and Aquatic Sciences 70(12): 1829-1844. https://doi.org/10.1139/cjfas-2013-0280
94. 2013. Thorson, J., Ward, E. Accounting for space-time interactions in index standardization models. Fisheries Research. 147: 426-433. https://doi.org/10.1016/j.fishres.2013.03.012
95. 2013. Thorson, J., Stewart, I. J., Taylor, I., and Punt, A.E. Using a recruitment-linked multispecies stock assessment model to estimate common trends in recruitment for U.S. West Coast groundfishes. Marine Ecology Progress Series 483: 245-256. https://doi.org/10.3354/meps10295
96. 2013. Thorson, J., Clarke, M.E., Stewart, I. J., and Punt, A.E. The implications of spatially varying catchability on bottom trawl surveys of fish abundance, and a proposed solution involving underwater vehicles. Canadian Journal of Fisheries and Aquatic Sciences 70(2): 294-306. https://doi.org/10.1139/cjfas-2012-0330
97. 2013. Thorson, J., Zhou, S. ±, Punt, A.E., and Smith, A.D.M±. A stepwise-selected spline approximation to time-varying parameters, with application to occupancy modelling. Methods in Ecology and Evolution. 4(2): 123-132. https://doi.org/10.1111/j.2041-210x.2012.00260.x
98. 2013. Stewart, I. J., Hicks, A., Taylor, I., Thorson, J., Wetzel, C. and Kupschas, S. A comparison of stock assessment uncertainty estimates using maximum likelihood and Bayesian methods implemented with the same model framework. Fisheries Research. 142: 37-46. https://doi.org/10.1016/j.fishres.2012.07.003
99. 2012. Lapointe, N.W.R., Thorson, J., and Angermeier, P.L. Relative roles of natural and anthropogenic drivers of watershed invasibility in riverine ecosystems. Biological Invasions 14(9): 1931-1945. https://doi.org/10.1007/s10530-012-0204-2
100. 2012. Gutierrez, N.L., Valencia, S.R.‡, Branch, T.A., Agnew, D.J. ±, Baum, J.K. ±, Bianchi, P.L., Cornejo-Donoso, J. ±, Costello, C., Defeo, O., Essington, T.E., Hoggarth, D., Larsen, A., Ninnes, C., Selden, R.L., Sistla, S., Smith, A.D.M., Stern-Pirlot, A. ±, Teck, S.J., Thorson, J., Williams, N.E. Eco-Label Conveys Reliable Information on Fish Stock Health to Seafood Consumers. PLoS One 7(8) e43765. https://doi.org/10.1371/journal.pone.0043765
101. 2012. Thorson, J., Cope, J., Branch, T., and Jensen, O. Spawning biomass reference points for exploited marine fishes, incorporating taxonomic and body size information. Canadian Journal of Fisheries and Aquatic Sciences 69(9): 1556-1568. https://doi.org/10.1139/f2012-077
102. 2012. Zhou, S.±, Yin, S., Thorson, J., Smith, A.D.M. ±, and Fuller, M±. Linking fishing mortality biological reference points to life history traits: an empirical study. Canadian Journal of Fisheries and Aquatic Sciences 69 (8), 1292-1301. https://doi.org/10.1139/f2012-060
103. 2012. Thorson, J., Stewart, I., and Punt, A. Development and application of an agent-based model to evaluate methods for estimating stock abundance for shoaling fishes such as Pacific rockfish (Sebastes spp.). ICES Journal of Marine Sciences 69 (4):635-647. https://doi.org/10.1093/icesjms/fss003
104. 2012. Thorson, J., Punt, A.E, and Nel, R±. Evaluating population recovery for sea turtles under nesting beach protection while accounting for nesting behaviors and changes in availability. Journal of Applied Ecology 49: 601-610. https://doi.org/10.1111/j.1365-2664.2012.02143.x
105. 2012. Thorson, J., Branch, T., and Jensen, O. Using model-based inference to evaluate global fisheries status from landings, location and life history data. Canadian Journal of Fisheries and Aquatic Sciences 69: 645–655. https://doi.org/10.1139/f2012-016
106. 2011. Thorson, J. Focal and auxiliary assessment models: A proof-of-concept involving time-varying catchability and stock status estimation. ICES Journal of Marine Sciences, 68: 2264-2276. https://doi.org/10.1093/icesjms/fsr160
107. 2011. Thorson, J., Stewart, Ian, and Punt, A.E. Accounting for fish shoals in single- and multi-species survey data using mixture distribution models. Canadian Journal of Fisheries and Aquatic Sciences, 68(9): 1681-1693. https://doi.org/10.1139/f2011-086
108. 2011. Thorson, J., and Prager, M.H. Better catch curves: Incorporating age-specific natural mortality and logistic selectivity. Transactions of the American Fisheries Society. 140:2, 356-366. https://doi.org/10.1080/00028487.2011.557016
109. 2010. Lapointe, N‡, Thorson, J., Angermeier, P. Seasonal meso- and microhabitat selection by the northern snakehead (Channa argus) in the Potomac river system. Ecology of Freshwater Fishes. 9:566-577. https://doi.org/10.1111/j.1600-0633.2010.00437.x
110. 2010. Thorson, J. and Berkson, J. Multispecies estimation of Bayesian priors for catchability trends and density dependence in the US Gulf of Mexico. Canadian Journal of Fisheries and Aquatic Sciences 67:936-954. https://doi.org/10.1139/F10-040
111. 2010. Wilberg, M., Thorson, J., Linton, B., and Berkson, J. Incorporating time-varying catchability into population dynamics stock assessment models. Reviews in Fisheries Science, 18(1):7-24. https://doi.org/10.1080/10641260903294647
112. 2009. Thorson, J., and Berkson, J. Evaluating single- and multi-species procedures to estimate time-varying catchability functional parameters. Fisheries Research 101:38-49. https://doi.org/10.1016/j.fishres.2009.09.005
113. 2009. Thorson, J. and Simpfendorfer, C±. Gear selectivity and sample size effects on growth curve selection in shark age and growth studies. Fisheries Research 98:75-84. https://doi.org/10.1016/j.fishres.2009.03.016
Manuscripts in review or revisions
1. In review. Thorson, J., Litzow, M., Cianelli, L. The Bering Sea Oscillation: Defining oceanographic indices using biological samples of fish communities.
2. In review. Stock, B.‡, Ward, E., Eguchi, T., Jannot, J., Thorson, J., Feist, B., and Semmens, B. Random forests outperform other species distribution models for spatiotemporal fisheries bycatch prediction
3. In review. Gao, J., Thorson, J. Szuwalski, C., and Wang, H-Y. Historical dynamics of the demersal fish community in the East and South China Seas.
4. In review. Thorson, J. Predicting density dependence in recruitment for all fishes worldwide using a data-integrated life-history model.
5. In review. Barnett, L., Jacobson, N., Thorson, J., Cope, J. Long live the trait-based revolution.
6. In review. Carroll, G., Holsman, K., Brodie, K., Thorson, J., Hazen, E., Bograd, S., Haltuch, M., Kotwicki, S., Samhouri, S., Spencer, P., Willis-Norton, E., Selden, B. A review of methods for quantifying spatial predator-prey overlap.
7. In review. Johnson, K.‡, Thorson, J., Punt, A.E. Justification for the inclusion of habitat covariates in spatiotemporal index standardization.
8. In review. Currie, J.‡, Winker, H., Thorson, J. Distribution changes in the demersal fish community of the Agulhas Bank, 1986-2016.
9. In review. Selden, B., Thorson, J., and Samhouri, J. Adapting to change? Availability of fish to West Coast communities
10. In review. Karp, M., Peterson, J, Lynch, P, Griffis, R, Adams, C, Arnold, B, Barnett, L, deReynier, Y, DiCosimo, J., Fenske, K, Gaichas, S, Hollowed, A, Holsman, K, Karnauskas, M, Kobayashi, D., Leising, A., Manderson, J., McClure, M., Morrison, W., Schnettler, E., Thompson, A., Thorson, J, Walter, J, Yau, A., Methot, R., Link, J. Accounting for shifting distributions and changing productivity in the development of scientific advice for fishery management
11. In review. Godefroid, M., Boldt, J., Thorson, J, Forrest, R., Gauthier, S. Spatio-temporal models provide new insights on the biotic and abiotic drivers shaping Pacific Herring distribution
12. In review. Winker, H, Carvalho, F., Thorson, J, Kell, L, Parker, D, Kerwath, S, Kapur, M, Sharma, R, Booth, A. JABBA-Select: an alternative surplus production model to account for changes in selectivity and relative mortality from multiple fisheries.
13. In review. Brodie, S, Thorson, J., Carroll, G, Hazen, E., Bograd, S, Haltuch, M, Holsman, K., Kotwicki, S, Samhouri, J, Willis-Norton, E., Selden, R. Pattern or Process: considering space, time, and the environment in species distribution models.
Manuscripts in preparation
1. In preparation. Chasco, B., Thorson, J., Kinzer, R., Ward, E. Spatio-temporal model of salmon spawner abundance in a tributary network.
2. In preparation. Thorson, J., Kristensen, K.±, Skaug, H.±, Maunder, M., Aires-Da-Silva, A. Spatial predator-prey dynamics: a model of fishery development for Western Pacific tuna
3. In preparation. Xu, H.‡, Miller, T., Thorson, J., and Nye, J. Consequences of implementing a 2D survival smoother into a state-space assessment model for Southern New England-Mid Atlantic yellowtail flounder.
4. In preparation. Chasco, B., Heppell, S., Thorson, J., Avens, L., Braun-McNeill, J., and Ward, E. Estimating length-at-age models when the true age of the first observation is unknown: a case study for using an integrated mixed-effect model to estimate loggerhead (Caretta caretta) sea turtle age and growth.
5. In preparation. Xu, H., Thorson, J., Methot, R. Best practices for weighting age-composition data under age- and time-varying selectivity
6. In preparation. O’Leary, C., Thorson, J., Nye, J. Effects of Climate-Dependencies and Estimation Methods on Biological Reference Points.
7. In preparation. Hamel, O., Taylor, G, Cope, J., Gertseva, V., Haltuch, M., Keller, K., Stephens, A., Thorson, J., Wallace, J., Wetzel, C. The effect of survey frequency and intensity on US West Coast stock assessment estimates
8. In preparation. Cao, J., Thorson, J., Punt, A., and Szuwalsky, A. A simulation comparison of spatio-temporal and spatially-implicit size-structured models for northern shrimp and snow crab.
9. In preparation. Thorson, J., Holsman, K., Adams, G. Spatio-temporal models of intermediate complexity: a new tool for spatial ecosystem-based fisheries management.
10. In preparation. Thorson, J. Forecasting distribution shifts using oceanographic indices: the spatially-varying impact of cold-pool extent in the Eastern Bering Sea
11. In preparation. Golding, N., Thorson, J., Guillera-Arroita, G., Gardner, B., O’Hara, R, Warton, D. The complementary log-log: a link function you can count on.
Student committees
Paige, Johnny. Ph.D., Statistics Department, Univ. Wash. Title TBD. Expected graduation: 2020.
Thurner, Stephanie. M.S., School of Aquatic and Fisheries Sciences, Univ. Wash. Title TBD. Expected graduation: 2020.
Best, John. Ph.D., Quantitative Ecology and Resource Management (QERM), Univ. Wash. Title TBD. Expected graduation: 2021.
Vert Pre, Katyana, Ph.D. University Pierre and Marie CURIE. “Bioindicators of marine fishes: the case of the eastern Mediterranean Sea.” Expected graduation: 2019.
2019. Chasco, Brandon, Ph.D., Dept. Fish. and Wildlife, OSU. “Combining disparate data sources with ecosystem and integrated models: case studies for improving management of protected species.” Graduated: March 2019.
2018. O’Leary, Cecilia, Ph.D., School of Marine and Atmospheric Sciences, Stony Brook University.
“Statistical Approaches to Determine the Influence of Climate and Fishing on Flatfish Abundances.” Graduated: December 2018.
2017. Monnahan, Cole. Ph.D., Quantitative Ecology and Resource Management (QERM), Univ. Wash., “Optimizing Bayesian integration in data-rich stock assessments.” Graduated: June 2017.
2017. Rudd, Merrill. Ph.D., School of Aquatic and Fisheries Sciences, Univ. Wash., “Data limited assessment options and application for global coral reef fisheries.” Graduated June 2017.
2017. Qi, Lee, M.S., School of Aquatic and Fisheries Sciences, Univ. Wash. “Incorporating an otolith-derived environmental index into growth for stock assessment models.” Graduated: June 2017.
Supervision of post-doctoral researchers
O’Leary, Cecilia. “Integrating data from multiple surveys designs with different data availabilities to estimate basin-scale trends in abundance and distribution.” Co-supervised with J. Ianelli, S. Kotwicki, and A. Punt, 2019-2021 (24 months).
Monnahan, Cole. “Combining acoustic and bottom trawl data using a vertically integrated, multivariate spatio-temporal model”. Co-supervised with J. Ianelli, S. Kotwicki, and A. Punt, 2018-2019 (12 months).
Grüss, Arnaud. “Spatio-temporal analysis for stock and ecosystem assessment applications”. Co-supervised with T. Essington, 2018-2020 (18 months).
Ovando, Dan. “Economic information for data-poor stock assessment worldwide”. Co-supervised with R. Hilborn, 2018-ongoing.
Rudd, Merrill, “Accounting for variable fishing mortality and recruitment in length-based data-limited stock assessments”. Co-supervised with T. Branch, 2017-2019 (2 years at half time)
Cao, Jie, “Development and application of a size-structured spatiotemporal model for invertebrates: individual growth, size-transitions, and natural and fishing mortality”. Co-supervised with A. Punt. 2017-2018 (1 year)
Xu, Haikun. “Statistical integration of environmental indices in an integrated assessment model, Stock Synthesis”. Co-supervised with T. Essington and R. Methot, 2016-2017 (1 year).
Gao, Jin. “New geostatistical index standardization and habitat modeling tool for stock assessments and essential fish habitat designation”. Co-supervised with T. Essington. 2015-2017 (2 years)
Councill, Elizabeth. “Simulation Study to Improve Forecasts of Stock Rebuilding” Co-supervised with A. Punt, L. Brooks, and R. Methot. 2014-2015 (1 year).
Supervision of interns
Denson, LaTreese. “Environmental influences on indices of abundance for King Mackerel in the Gulf of Mexico examined through spatiotemporal geostatistical models.” Co-supervised with B. Babcock, June-Sept 2018 (3 months).
Committees, Working Groups, and Service
“Spatio-temporal modelling mini-workshop” Center for the Advancement of Population Modelling (CAPAM) plan team, March 2017-Feb 2018.
“Incorporating Climate and Environmental Information into Fisheries Management” (ICE-FM) NOAA plan team, May 2017-present day.
Fisheries and the Environment (FATE) scientific and statistical committee, Nov. 2016–present day.
Associate editor, Canadian Journal of Fisheries and Aquatic Sciences, Nov. 2015–present day.
“Regional stock status”, Conservation International, DC, Oct. 2014-Oct. 2016.
Handling editor, Fisheries Research special issue on data-poor stock assessment, Jan. 2014-July 2015.
“National Habitat Assessment Working Group,” NOAA working group, San Francisco, July 22-24, 2014.
“ICES working group on forecasting recruitment,” ICES working group, Copenhagen, June 16-20, 2014.
“'Improving the Accuracy of Fishery-Independent Survey Indices by Accounting for Dynamic Habitats,” Virginia Institute of Marine Sciences, May 2, 2014.
“Ocean Modelling Forum,” Moore Foundation working group, Seattle, Mar. 26-27, 2014.
“Data-poor assessment methods,” NRDC working group, Miami, Jan. 15-17, 2014.
“Future directions for Stock Synthesis,” NMFS working group, Seattle, Dec. 10-12, 2013.
“Stock Assessment Model Database (SAMDB)”, Multi-agency collaboration, Seattle, July-present day.
“Northwest Regional Habitat Assessment Prioritization Working Group,” NMFS, Seattle, June-Dec. 2013.
"Combining occupancy and tag-resighting models," Powell Center, Fort Collins, CO, ongoing.
"Global stock status," FAO and Conservation International, DC, June 18, 2012.
"Non-parametric forecasting methods," SWFSC, La Jolla, CA, April 17, 2012.
"Evaluating success of marine stewardship council," NCEAS, Santa Barbara, June 22, 2011.
Positions and Internships
Co-organizer, session on Marine Ecosystem Modelling at International Statistical Ecology Conference (ISEC), Seattle, WA, 2016.
Co-organizer, MyFish symposium on maximum sustainable yield targets, Athens, Greece, 2015.
Co-organizer, Monster Jam seminar (visiting speaker series), NWFSC, Seattle, 2014.
Co-organizer, Symposium on Time-Varying Effects in Stock Assessment, AFS national meeting, 2011.
Representative for ESAC, Climate Action Plan Land Use Policy Committee, 2011.
Liaison to undergraduates, University of Washington chapter of AFS, 2011.
Organizer, Think Tank seminar series, School of Aquatic and Fisheries Sciences, 2010-2011.
Grad. student representative. School of Aquatic and Fisheries Science Curriculum Committee, 2010-2011.
Grad. student senate representative, Environmental Stewardship Advisory Committee (ESAC), 2010-2011.
Intern, Environmental Management Certificate program, working with WA Restaurant Association, 2010.
Communications chair, Virginia Tech chapter of American Fisheries Society, 2007-2009.
Website designer, Virginia Tech chapter of Habitat for Humanity, 2007-2008.
Intern, NMFS-RTR research for Marine Protected Areas in Florida and the U.S. Virgin Islands, 2006.
Intern, Shark research laboratory, MOTE Marine Labs, Sarasota, FL, 2006.
Pending proposals
2019. Best, J., Punt, A., and Thorson, J. Title TBD. Sea Grant Pop. Dy. Fellowship, 2019 RFP.
2019. Iwicki, C., Jensen, O., and Thorson, J. The role of climate in fisheries productivity. Sea Grant Pop. Dy. Fellowship, 2019 RFP.
Funded Grant Proposals
2019. Pirtle, J., and Thorson, J. Refine Nearshore EFH Models and Maps to Improve Non-fishing Effects Consultation for Alaska. Office of Habitat Conservation 2019 RFP. $120,000 awarded.
2019. Thorson, J., Aydin, K., and Pirtle, J. Dynamic designation of Essential Fish Habitat under changing environment: skill test involving spatially downscaled models for habitat, population, and ecosystem dynamics. Magnuson-Stevens Implementation 2018 RFP. $229,306 awarded.
2019. McGilliard, C., Thorson, J., and Essington, T. Inferring effects of loss of sea ice on movement phenology of yellowfin and flathead sole in the Bering Sea and Aleutian Islands from fishery-dependent data using spatio-temporal modeling. National Cooperative Research Program, 2019 RFP. Feb. 2019. $101,00 awarded.
2018. Omori, K., Thorson, J., and Hoenig, J. Dealing with the most species: improving the methodology to appropriately form and assess species complexes. Sea Grant Pop. Dy. Fellowship, 2018 FRP. Jan. 2018. $115,000 awarded.
2018. Hoff, G., Thorson, J., and Punt, A. Spatio-temporal dynamics of groundfish availability to EBS bottom trawl surveys and abundance estimate uncertainties. North Pacific Research Board (NPRB) 2018 RFP. Dec. 2017. $251,304 awarded.
2017. Ianelli, J., Thorson, J., Kotwicki, S. Combining acoustic and bottom-trawl data in a spatio-temporal index standardization model for Eastern Bering Sea pollock. Improve a Stock Assessment 2018 RFP. June 2017. $109,785 awarded.
2017. Boldt, J., Thorson, J. Gauthier, S., Forrest, R. Evaluating the effects of environmental conditions on pelagic fish distributions in marine waters of British Columbia. SPERA proposal for 2017 DFO. 324,000 CAD awarded.
2017. Haynie, A., and Thorson, J. The integration of spatiotemporal fishery and biological survey data. Economics 2016 RFP. $95,000 awarded.
2017. Rooper, C., Thorson, J., and Boldt, J. Detecting changes in life history traits and distribution shifts in eastern Bering Sea fishes in response to climate change. Habitat Information for Stock Assessments 2016 RFP. $110,919 awarded.
2017. Thorson, J., Bryan, M., and Nadon, M. Accounting for variable fishing mortality and recruitment in length-based data-limited stock assessments. Improve a Stock Assessment 2016 RFP. $93,093 awarded.
2016. Forsman, J., Thorson, J. Diversity of species interactions: a missing key for understanding biodiversity in a changing world. Kone Foundation 2016 RFP. 300,000€ ($320,000 value) awarded.
2016. Chasco, B., Heppell, S., Thorson, J., Thompson, G., and Dalziel, B. Integrated spatial, temporal mixed-effects models: leveraging stock assessment techniques for threatened and protected species. Sea Grant Pop. Dy. Fellowship, 2016 RFP. $104,000 awarded.
2016. Thorson, J., Szuwalski, C., and Punt, A. Development and application of a size-structured spatiotemporal model for invertebrates: individual growth, size-transitions, and natural and fishing mortality. Stock Assessment Analytical Methods 2015 RFP. $181,587 awarded.
2015. Scheuerell, M., and Thorson, J. Improving salmon population forecasts by combining environmental drivers, variable age composition and spatial structure into hierarchical models. Fisheries and the Environment 2014 RFP. $149,050 awarded.
2015. Thorson, J., Ianelli, J., and O’Brien, L. Distribution and application of a new geostatistical index standardization and habitat modeling tool for stock assessments and essential fish habitat designation in Alaska and Northwest Atlantic regions. Habitat Assessment Improvement Plan 2014 RFP. $205,000 awarded.
2014. Stock, B., Semmens, B., and Thorson, J. Improving assessment models of aggregating fish species: a case study of Nassau grouper (Epinephelus striatus). Sea Grant Pop. Dy. Fellowship 2014 RFP. $130,000 awarded (award declined by B. Stock)
2014. Thorson, J., Brooks, E.M., and Methot, R.D. Simulation Study to Improve Forecasts of Stock Rebuilding and Estimated Probability of Exceeding Target/Limit Reference Points in the Presence of Autocorrelation and Environmentally Driven Recruitment. Stock Assessment Improvement Plan, 2013 RFP. $123,000 awarded.
2013. Monnahan, C., Branch, T., and Thorson, J. Optimizing Bayesian integration in data-rich stock assessments. Sea Grant Pop. Dy. Fellowship, 2013 RFP. $130,200 awarded.
2013. Thorson, J., Punt, A., and Gertseva, A. Incorporating climate driven growth variability into stock assessment models: a simulation-based decision table approach. Fisheries and the environment (FATE), 2012 RFP. $112,600 awarded.
2013. Shelton, O., Ward, E., Thorson, J., Bellman, M., and Feist, B. Integrating spatial habitat and fisheries effort data to improve abundance estimates of West Coast groundfish. Habitat assessment improvement, 2012 RFP. $60,000 awarded
2012. Thorson, J. Developing generic meta-analysis tools for estimating ecological processes and anthropogenic effects in marine and anadromous fishes. National Research Council Fellowship program. $56,000 awarded.
2009. Thorson, J., Punt, A., and Stewart, I. Evaluating Pacific groundfish schooling behavior and untrawlable refuges using multi-species mixture models and data from autonomous underwater vehicles. Sea Grant Population Dynamics Fellowship. $96,250 awarded.
Unfunded proposals (starting 2016)
Declined for funding. Barbeaux, S., Thorson, J., Hollowed, Anne, Hazen, E. Projecting climate impacts on shifts in distribution and abundance of groundfish using a coast-wide 3 km Regional Ocean Model with biogeochemistry: a cross-funding proposal. Stock Assessment Analytical Methods 2018 RFP. June 2017. $199,614 requested.
Declined for funding. Thorson, J., Essington, T. Causal Statistical Modelling to Improve Forecast of Species Response to Environmental Change. Fisheries and the Environment 2018 RFP. June 2017. $145,541 requested
Declined for funding. Wakefield, W., Thorson, J., Keller, A., Cianelli, L. General guidance and decision support tool for including habitat information during index standardization for stock assessments. Habitat Information for Stock Assessment 2018 RFP. June 2017. $112,870 requested.
Declined for funding. Cianelli, L., Spitz, Y., Watson, J., Fonner, R., Thorson, J., McClatchie, S., Hunsicker, M., Keller, A. Adaptability of fish and fisheries to climate change in the California Current System under biological and socio-economic constraints. COCA Competition I (Understanding Climate Impacts on Fish Stocks and Fisheries in the California Current Large Marine Ecosystem), 2017 RFP.
Declined for funding. Wiedenmann, J., Pinsky, M. Seagraves, R. Miller, T., Thorson, J. Adapting to Climate Variability and Change in the Assessment and Management of Northeast Fisheries. COCA Competition II (Competition II: Understanding Climate Impacts on Fish Stocks and Fisheries in the Northeast U.S. Continental Shelf Large Marine Ecosystem), 2017 RFP. $1,328,677 requested.
Declined for funding. Hauser, L., Canino, M., Spies, I., Thorson, J. Seasonal movement of Pacific cod in the Aleutian Islands, and its effect on stock assessment. North Pacific Research Board (NPRB) 2017 RFP. $264,250 requested.
Declined for funding. Crone, P., Piner, K., Lee, H., Thorson, J., Maunder, M. Does variability in juvenile M matter? Model structure to minimize impact or predator data to estimate the variability in juvenile M. Stock Assessment Analytical Methods 2016 RFP. Sept. 2016. $54,794 requested.
Declined for funding. Thorson, J., Kotwicki, S., Hanselman, D. A data-integrated spatio-temporal model for index standardization, demonstrated using acoustic/bottom trawl and fishery/survey case studies. Stock Assessment Analytical Methods 2016 RFP. Sept. 2016. $229,797 requested.
Declined for funding. Hollowed, A., Keller, A., King, J., Rooper, C., Shelton, O., Thorson, J., and Li, L. Multi-model spatial comparison of fish responses to anomalous climate conditions along the US and Canadian west coast. Fisheries and the Environment 2016 RFP. Sept. 2016. $97,908 requested.
Declined for funding. Thorson, J. Using a global database of fish catch rates and interactive online tools to analyse spatial distribution in support of ecosystem-based ocean management. Pew Marine Fellows Program, June 2016. $150,000 requested.
Review and editorial service
Handling editor for 29 papers in total (through May 2018): Canadian Journal of Fisheries and Aquatic Sciences (23), Fisheries Research (6),
Reviewer for 2 stock assessments for tactical fisheries management (through Oct. 2017): Canada Dept. of Fisheries and Oceans (2)
Reviewer for 20 internal reviews for NOAA (through Oct. 2017)
Reviewer for 14 grant proposals (through Oct. 2017): Sea Grant population dynamics fellowship (8), NOAA Habitat Assessment Improvement Plan (6)
Reviewed 108 papers in total (through Oct 2017): for Fisheries Research (19), Ecological Applications (9), Canadian Journal of Aquatic and Fisheries Sciences (10), ICES Journal of Marine Sciences (12), Conservation Biology (1), Journal of Aquatic and Living Resources (2), Journal of Applied Ecology (4), Fish and Fisheries (2), North American Journal of Fisheries Management (2), Transactions of the American Fisheries Society (1), Population Ecology (2), Convention on Living and Marine Resources of Antarctica (1), Conservation Letters (1), Chinese Journal of Oceanography and Limnology (1), Marine Policy (2), Methods in Ecology and Evolution (5), Nature (2), Nature climate (1), Nature Communications (2) Ecology (3), Environmental and Ecological Statistics (1), PloS (2), Ecology Letters (1), African Journal of Marine Science (1), Ecology and Evolution (1), Proceedings of the Royal Society B (1), Fisheries Bulletin (1), Global Ecology and Biogeography (1), Marine Ecology Progress Series (1), Spatial Statistics (1), and Ecography (1).
For partial list of reviews, see: https://publons.com/author/1213978/james-t-thorson#profile
Invited presentations (excluding region-specific NMFS presentations)
2019. Thorson, J. The world through a fish-eye lens: Multivariate approaches to big data. Irish Marine Institute, Galway, Ireland, March 30, 2019.
2018. Thorson, J. Two talks: Model-based inference for distribution; and Spatio-temporal models: Ecosystem dynamics, attribution, and skill-testing. Workshop in changes in productivity and distribution. Aberdeen, Scotland, Nov. 24, 2018.
2018. Thorson, J. Three uncertainties for ecosystem-based management: Life-history, spatial heterogeneity, and forecast skill. FAO-IMR joint workshop regarding the Nansen program for bioregionalization in Western Africa, Rome, Aug. 23, 2018.
2018. Thorson, J., Conn, P., Johnson, D., and Best, J. Using Joint Models of Fisher Targeting and Resource Abundance to Account for Preferential Sampling in Fisheries. Joint Statistics Meeting, Vancouver, Canada, July 30, 2018.
2018. Thorson, J. Spatio-temporal models for fishery catch and effort data: Solving old problems and creating new ones. CAPAM mini-workshop on spatio-temporal models for fishery catch-per-unit-effort data. La Jolla, CA, USA, Feb 26, 2018.
2018. Thorson, J. Know Thy Stochastic Process: The key to generality in statistical ecology. Invited seminar, University of Tokyo Biodiversity laboratory, Yokohama, Japan, Feb. 23, 2018.
2017. Thorson, J. Measuring density dependence, portfolio effects, and climate-drivers in the North Pacific using spatio-temporal models and causal statistics. PICES annual science meeting, Vladivostok, Russia, Sept. 26, 2017.
2017. Thorson, J. The importance of causal inference in assessing management and attributing climate-impacts for fisheries. Invited speaker at weekly seminar, Institute of Marine Resources, Bergen, Norway, Aug 25, 2017.
2017. Thorson, J. Oceans through a fisheye lens: Estimating community regulation and synchrony due to spatial and multispecies biocomplexity for fishes worldwide. Invited speaker at organized session “Dynamic Approaches to Changing Communities” at ESA annual meeting, Portland, OR, Aug 8, 2017.
2017. Thorson, J. Know Thy Stochastic Process: The key to generality in statistical ecology. Invited speaker at Quantitative Scientist interview, University of Washington, Seattle, WA, March 27, 2016.
2017. Thorson, J. A marriage of models and maps: Community theory and species distribution models. Invited speaker at organized session, American Academy for the Advancement of Sciences annual meeting, Boston, MA, Feb. 20, 2017.
2016. Thorson, J. FishStats: A toolbox for combining stock assessment, habitat, ecosystem, and climate research. NOAA QUEST seminar, Washington, DC (speaking remotely), Dec. 15, 2016.
2016. Thorson, J. Fish community dynamics and interactions: An illustration of multivariate spatio-temporal models. Invited seminar, North Atlantic Regional Team NOAA workshop, Fall River, MA, Aug. 19, 2016.
2016. Thorson, J. Estimating dynamics, stability, and distribution shifts for fish communities using multispecies spatio-temporal models. Invited speaker at International Biometric Society, Victoria, BC, July 13, 2016
2016. Thorson, J. Advancements in spatio-temporal models in TMB. ADMB/TMB developers workshop, Seattle, WA, June 20, 2016
2016. Thorson, J. Fish community dynamics and interactions: An illustration of multivariate spatio-temporal models. Invited statistics seminar, University of British Columbia Statistics Department, Vancouver, BC, June 16, 2016
2016. Thorson, J., Rindorf, A., Gao, J., Hanselman, D., Winker, H., Fonner, R., Haltuch, M., Ono, K. A framework for estimating abundance from multispecies fishery data incorporating spatiotemporal variation and fisher targeting. World Fish Congress, Busan, Korea, May 23, 2016
2016. Thorson, J. Spatio-temporal models for fisheries: the case for a global bottom trawl database. National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand, March 14, 2016.
2016. Thorson, J. The potential for a global database of bottom trawl data to estimate abundance and range shifts for marine fishes. Invited speaker at Pacific Biological Station, Nanaimo, BC, Feb. 3, 2016.
2015. Thorson, J. A marriage of models and maps: understanding community dynamics, climate impacts, and fisher behaviors using multivariate spatiotemporal models. IGB Departmental Seminar, Berlin, Germany, Nov. 3, 2015.
2015. Thorson, J., Johnson, K., Methot, R., Taylor, I. What is the likelihood that your model is wrong? Generalized tests and corrections for overdispersion during model fitting and exploration. Center for the Advancement of Population Modelling, La Jolla, CA, Oct. 19, 2015.
2015. Thorson, J., Skaug, H., Kristensen, K. New developments in spatial modeling. United States-New Zealand JCM, Sustainable Fisheries theme. Portland, OR, Aug. 21, 2015.
2015. Thorson, J., Hovel, R., Munch, S., Skaug, H., Kristensen, K., Maunder, M., Aires-da-Silva, A. State-space models for addressing pressing fisheries problems: climate, movement, and spatial overfishing limits. Advancements to State-Space Models for Fisheries Science, Halifax, Canada, June 17, 2015.
2015. Thorson, J. Introduction to template model builder, an improved tool for maximum likelihood and mixed-effects models in R. Marine Mammal Roundtable. Vancouver, BC, May 6, 2015.
2015. Thorson, J. and Cope, J. Progress and roadblocks in the estimation of stock status and catch limits for global fisheries. National Scientific and Statistical Committee annual meeting, Honolulu, Hawaii, Feb. 23, 2015.
2015. Thorson, J. A Marriage of Models and Maps: New Directions for Estimating Density Dependence, Species Distributions, and Coupled Natural and Human Systems. University of Idaho, graduate student invited speaker. Moscow, Idaho, Jan. 27, 2015.
2014. Thorson, J. Tutorial on Template Model Builder. Center for the Advancement of Population Assessment Methods, La Jolla, CA, Nov. 4, 2014.
2014. Kanno, Y., Letcher, B., Thorson, J., and Zipkin, E. Modeling species response to environmental change: development of integrated, scalable Bayesian models of population persistence. Fort Collins USGS invited seminar, Fort Collins, CO, Sept. 18, 2014.
2014. Thorson, J., and Ward, E. Analysis of survey data: the delta-GLMM approach. VIMS working group on dynamic habitat, Seattle, WA (attending remotely), May 2.
2013. Thorson, J. Links between theory and practice: developing new tools for population ecology and management. Vancouver, BC, Feb. 28, 2013.
Contributed presentations
2019. Thorson, J., Ciannelli, L., Ianelli, J., Kotwicki, S., Litzow, M. Learning ecological and evolutionary dynamics from multivariate data: life-history theory and oceanographic drivers of Bering Sea groundfishes. University of Alaska Fairbanks weekly seminar, Juneau, April 12, 2019.
2019. Thorson, J. New uses for vector autoregressive spatio-temporal (VAST) models: MICE-in-space, oceanographic indices, and expanding composition data from multiple surveys. Quantitative Seminar, Seattle, WA, Feb. 20, 2019.
2019. Thorson, J. How to simultaneously fit presence-absence and presence-only data, and why we should never throw out absence data. Deep-Sea Coral Initiative modelling workshop, Seattle, WA, Feb. 19, 2019.
2018. Thorson, J. The world through a fish-eye lens: Multivariate approaches to big data, CalCOFI annual conference, La Jolla, Dec. 4, 2018.
2018. Thorson, J. The world through a fish-eye lens: Multivariate approaches to big data, Departmental seminar, Stoney Brook University, Nov. 9, 2018.
2018. Thorson, J. From vessels to models: Steps to measure the value of age/length/diet sampling in data collection and model-based management advice. Groundfish Seminar, Seattle, WA, Oct. 7, 2018.
2018. Thorson, J. Spatial downscaling of adult fish dynamics: skill testing and species interactions. Site-visit to Auke Bay Laboratory, Juneau, AK, Sept. 31, 2018.
2018. Thorson, J. Mesopelagic dynamics in California Current, 1951-2016, from larval samples. Pacific Fisheries Management Council Ecosystem Subcommittee technical review, Seattle, WA, Sept. 5, 2018.
2018. Thorson, J. Catch-up workshop for VAST users. VAST users workshop, Seattle, WA, July 25, 2018.
2018. Thorson, J. Spatio-temporal approaches to estimating species interactions. AFSC workshop on predation, Seattle, WA, July 23, 2018.
2018. Thorson, J. Forecast skill for predicting distribution shifts: A retrospective experiment for the Eastern Bering Sea, Washington, DC, June 7, 2018.
2018. Thorson, J. Data-integrated model for life-history and recruitment. National Stock Assessment Workshop, Irvine, CA, May 24, 2018
2018. Thorson, J. Variability + Uncertainty = Steepness. Quantitative Seminar, Seattle, WA, March 9, 2018.
2018. Thorson, J., and Haltuch, M. New features for FishStats: An improved model for biomass sampling data, spatial expansion of age/length compositions, and short-term forecasts for distribution shift. Think Tank seminar, Seattle, WA, Jan. 9, 2018.
2017. Thorson, J. and Gao, J. A biological PDO: Dominant spatio-temporal patterns for fish communities. BioOcean Brown Bag lunch seminar, Seattle, WA, Nov. 13, 2017.
2017. Thorson, J. Replacing tuning algorithms with parameter estimation, and a regional meta-analysis for steepness. CAPAM meeting on recruitment, La Jolla, CA, USA, Oct. 29, 2017.
2017. Thorson, J. Time-varying processes in stock assessment: A bridge to ecosystem-based reference points. PICES annual science meeting, Vladivostok, Russia, Sept. 26, 2017.
2017. Thorson, J., Ianelli, J., and Kotwicki, S. Using the FishStats spatio-temporal toolbox to attribute and communicate uncertain drivers of distribution shifts for assessed stocks. ICES Annual Science Conference, Fort Lauderdale, FL, Sept. 19, 2017.
2017. Thorson, J., and Barnett, L. Does incorporating spatio-temporal correlations among fishes and biogenic habitat improve estimates of abundance trends and distribution shifts? NOAA Protected Species Workshop, Seattle, WA, Jan. 18, 2017.
2016. Thorson, J. Autocorrelation in recruitment and its effect on estimation of stock recruit parameters. Pacific Fisheries Management Council Productivity Workshop, Seattle, WA, Dec. 5, 2016.
2016. Thorson, J, Munch, S., Cope, J, and Gao, J. A multivariate life-history analysis of global fisheries data to generate priors on length, weight, growth, mortality, and maturity parameters for all 32,000 marine fishes. Pacific Fisheries Management Council Productivity Workshop, Seattle, WA, Dec. 6, 2016.
2016. Thorson, J. Autocorrelation in recruitment and its effect on estimation of stock recruit parameters. Pacific Fisheries Management Council Productivity Workshop, Seattle, WA, Dec. 5, 2016.
2016. Thorson, J. FishStats: A fisheries spatio-temporal toolbox. SAFS Think Tank seminar, Seattle, WA, Nov. 29, 2016.
2016. Thorson, J. Spatio-temporal index tools for 2017 assessments. Pacific Fisheries Management Council Methodology Review for 2017 assessments, Seattle, WA, Oct. 15, 2016.
2016. Thorson, J. Fisher targeting and standardizing fishery catch-rate data. Half-baked seminar for economics research, Seattle, WA, July 27, 2016.
2016. Thorson, J. Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. International Statistical Ecology Conference, Seattle, WA, June 29, 2016.
2016. Thorson, J., Fonner, R., Haltuch, M., Ianelli, J., Larsen, E., Ries, L., Ono, K., Winker, H., Scheuerell, M., Szuwalski, C., Zipkin, E. Joint dynamic species distribution models: a statistical tool for monitoring community dynamics, World Fish Congress, Busan, Korea, May 24, 2016
2016. Thorson, J. Developments in geostatistical modeling of survey data for pollock. Center for Independent Experts (CIE) review for walleye pollock assessment, Seattle, WA, May 16, 2016.
2016. Thorson, J. Recent and future developments in geostatistical index standardization: the case for a global bottom trawl database. Quantitative Seminar, Seattle, WA, March 4, 2016.
2016. Thorson, J. The potential for a global database of bottom trawl data to estimate abundance and range shifts for marine fishes. Fish and Chips seminar, UBC, Vancouver, BC, Feb. 2, 2016.
2016. Thorson, J., Hovel, R., Scheuerell, M., Quinn, T. What can we learn about community dynamics and climate impacts from spatiotemporal models? A case study of freshwater fishes. American Mathematical Association Annual Meeting, Seattle, WA, Jan. 8, 2016.
2015. Thorson, J. Spatial models for population ecology. MyFish meeting on MSY targets and limits. Athens, Greece, Oct. 27, 2015.
2015. Thorson, J., Jannot, J., Somers, K. New methodology for estimating OFL for using data from Fmsy/M methods. Pacific Fisheries Management Council Scientific and Statistical Committee Methodology Review. Seattle, WA, Sept. 29, 2015.
2015. Thorson, J., Scheuerell, M., Semmens, B., and Pattengill-Semmens, C. Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes. American Fisheries Society Annual Meeting, Portland, OR, Aug. 20, 2015.
2015. Thorson, J., Maunder, M., Skaug, H., Munch, S., Aires-Da-Silva, A., Kristensen, K. Spatial Predator-Prey Dynamics: A Model of Tuna Longline Fishery Development in the Pacific Ocean. American Fisheries Society Annual Meeting, Portland, OR, Aug. 18, 2015.
2015. Thorson, J. New tools and techniques for understanding spatial dynamics of populations and communities. Southwest Fisheries Science Center seminar series, Santa Cruz, CA, July 14, 2015.
2015. Thorson, J. and Wetzel, C. Status of the canary rockfish (Sebastes pinniger) population in U.S. waters. SSC defense, Spokane, WA, June 10, 2015.
2015. Thorson, J., Hovel, R., Munch, S., Skaug, H., Kristensen, K., Maunder, M., Aires-da-Silva, A. Combining climate and fisheries sciences using reaction-advection-diffusion and spatial dynamic factor analysis models. UW Quant. Sem. Seattle, WA, May 14, 2015.
2015. Thorson, J. A marriage of models and maps. Marine Mammal Roundtable. Vancouver, BC, May 5, 2015.
2015. Thorson, J. and Wetzel, C. Draft Status of the canary rockfish (Sebastes pinniger) population in U.S. waters. STAR panel, Seattle, WA, April 27, 2015.
2015. Thorson, J., Scheuerell, M., Semmens, B., and Pattengill-Semmens, C. Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes. American Academy for the Advancement of Science Symposium on Citizen Science. San Jose, CA, Feb. 16, 2014.
2015. Lee Qi, Thorson, J., Vlada Gertseva, and André Punt. Incorporating climate driven growth variability into stock assessment models: a simulation-based decision table approach. Fisheries and the Environment (FATE) annual meeting. La Jolla, CA, Jan. 12, 2015.
2014. Thorson, J. Improvements in habitat-based methods in stock assessments. Habitat Advisory Committee of the Pacific Fisheries Management Council (PFMC) meeting. Costa Mesa, CA, Nov. 13, 2014.
2014. Thorson, J., Shelton, A.O., Ward, E., and Skaug, H. Geostatistical index standardization. Science and Statistical Committee (SSC) of the Pacific Fisheries Management Council (PFMC) meeting. Costa Mesa, CA, Nov. 12, 2014.
2014. Thorson, J., Minte-Vera, C., and Webber, D. How much does growth vary over time, space, and among individuals? Three case studies and their implications on biological reference points. Center for the Advancement of Population Assessment Methods, La Jolla, CA, Nov. 6, 2014.
2014. Thorson, J., and Cope, J. New data-poor assessment methods in 2014. Conservation International, Washington, DC., Oct. 27, 2014.
2014. Thorson, J. Summary of recent “integrated, scalable” research for populations. Powell Center Working Group, Fort Collins, CO, Sept. 15, 2014.
2014. Thorson, J., Skaug, H., and Kristensen, K. New spatial modelling tools for stock assessments. American Fisheries Society Annual Meeting, Quebec City, Canada, Aug. 19, 2014.
2014. Thorson, J. Estimating recruitment variability including autocorrelated, synchronous, and spatial components. ICES Working group on recruitment forecasting, Copenhagen, June 18, 2014.
2014. Thorson, J., Skaug, H., Kristensen, K., Shelton, O., Ward, E., Ono, K., Scheuerell, M., Benante, J., Harms, J. Random Fields: A Marriage of Models and Maps. UW Quant. Sem. Seattle, WA, May 24, 2014.
2014. Thorson, J. Alternatives to design-based estimators when analyzing survey data. AFSC team meeting, Seattle WA, May 12, 2014.
2014. Thorson, J. Spatial modelling: An important direction for quantitative ecology and environmental management. Univ. British Columbia Fish. Centre seminar, Vancouver, Canada, April 4, 2014.
2014. Thorson, J., Kristensen, K., Skaug, H. Introduction to template model builder, an improved tool for maximum likelihood and mixed-effects models in R. UW Seminar on advanced R programming. Seattle, WA, Mar. 7.
2014. Thorson, J., and Cope, J. Catch curve stock-reduction analysis: A new solution to the catch equations. Data-poor working group, Miami, FL, Jan. 14.
2013. Thorson, J., Hicks, A., and Methot R. Using the Laplace approximation to estimate random effects in ADMB and Stock Synthesis. Stock Synthesis working group, Dec. 12.
2013. Cope, J., and Thorson, J. Alternative solutions to the catch equations. Think Tank Seminar, University of Washington, Seattle, WA, Nov. 13.
2013. Thorson, J., Hicks, A., and Methot, R. Random effect estimation in Stock Synthesis. Think Tank Seminar, University of Washington, Seattle, WA, Oct. 30.
2013. Thorson, J., See, K., Scheuerell, K., Ward, E., Semmens, B, and Semmens, C. Two case-studies showing the broad applicability of state-space models for count data. Quantitative Seminar, Seattle, WA, Oct. 25, 2013.
2013. Gertseva, Vlada, and Thorson, James. Stock assessment for darkblotched rockfish in 2013. STAR panel, Seattle, WA, May 13, 2013.
2013. Thorson, J. Surplus production: new directions for one of the oldest models in fisheries. Quantitative Seminar, Seattle, WA, April 19, 2013.
2013. Thorson, J. A proposal for penalized-likelihood estimation of semi-parametric selectivity in age-structured stock assessment models. La Jolla, CA, Mar. 12, 2013.
2013. Thorson, J. Priors for rockfish steepness. PFMC SSC meeting. Tacoma, WA, Mar. 5, 2013.
2013. Thorson, J. 2013 update to delta-GLMM software. PFMC SSC meeting. Tacoma, WA, Mar. 5, 2013.
2013. Monnahan, Cole, Thorson, J., and Taylor, Ian. Next-generation MCMC: theory, options, and practice for Bayesian inference in ADMB. Univ. Wash. Think Tank. Seattle, WA, Feb. 27, 2013.
2013. Punt, A. E., and Thorson, J. Estimating steepness for U.S. West Coast groundfishes. Univ. Wash. Think Tank. Seattle, WA, Jan. 28, 2013.
2013. Thorson, J. Effort dynamics and assessing fishery status using catch data. FAO/CI working group, Seattle, WA, Jan. 1, 2013.
2012. Thorson, J., and Ward, Eric. Accounting for space-time interactions in index standardization models. Think Tank Seminar, Seattle, WA, Nov. 28, 2012.
2012. Thorson, J., Cope, Jason, and Patrick, Wes. Assessing the quality of life history information in FishBase, a publicly available database. Quantitative Seminar, Seattle, WA, Oct. 25, 2012.
2012. Thorson, J., Clarke, M. Elizabeth, Stewart, Ian J., and Punt, A. The implications of untrawlable habitats on bottom trawl surveys for West Coast groundfishes. National Habitat Assessment Workshop, Seattle, WA, Sept. 6, 2012.
2012. Thorson, J., Nel, Ronel, and Punt, A. Is nesting beach protection successful for South African sea turtles? ESA Annual Meeting, Portland, OR, Aug. 7, 2012.
2012. Thorson, J. Meta-analysis in support of data-poor stock assessment methods. Pacific Science and Statistical Committee, Seattle, WA, June 6, 2012.
2012. Thorson, J. Improved biological realism in the design and analysis of surveys. USGS weekly seminar series, Olympia, WA, June 19, 2012.
2012. Thorson, J. Summary and next-steps for Using model-based inference to evaluate global fisheries status from landings, location and life history data. FAO/CI meeting on data-poor stocks, Washington, DC, June 4, 2012.
2012. Thorson, J. Meta-analysis in support of data-poor stock assessment methods. Think Tank Seminar, Seattle, WA. May 2, 2012.
2012. Thorson, J. Generalized fisheries meta‐analysis, with application to natural mortality and cohort strength. ICES/PICES Young Investigators Meeting, Mallorca, Spain, April 26, 2012.
2012. Thorson, J. Preliminary results for developing Bayesian priors for relative cohort strength of groundfishes off the U.S. West Coast using multi-species Stock Synthesis models. PFMC Science and Statistical Committee Meeting, Seattle, WA, April 4, 2012.
2012. Thorson, J., Clarke, E., and Stewart, I. Bias in survey results arising from spatially varying bottom trawl gear efficiency, and a proposed solution involving in situ underwater vehicles. Presentation at Western Groundfish Conference, Seattle, WA, Feb. 8, 2012.
2012. Thorson, J. Ichs, herps, and splines: How approximating time-varying parameters can improve model accuracy and interpretability. Presentation at University of British Columbia Quantitative Seminar, Vancouver, BC, Feb. 2, 2012.
2012. Thorson, J. "Rationale, preliminary development, and simulation testing of meta-analysis capabilities using stock synthesis." Presentation at Think Tank seminar, Seattle, WA, Jan. 10, 2012.
2011. Thorson, J. "A general approximation to time-varying parameters in ecological models." Presentation at University of Washington Quantitative Seminar, Seattle, WA, Oct. 28, 2011.
2011. Thorson, J. "Comparing accuracy of stock status estimates among integrated models using functional-form and random-walk catchability." Presentation at American Fisheries Society National Meeting, Seattle, WA, Sept. 6, 2011.
2011. Thorson, J., Clarke, Elizabeth, Stewart, Ian, and Punt, André E., "Simulation comparison of simple and stratified sampling designs for Pacific coast rockfish involving bottom trawl and submersible gears." Presentation at American Fisheries Society National Meeting, Seattle, WA, Sept. 5, 2011.
2011. Thorson, J. "Optimization in R: algorithms, sequencing, and automatic differentiation." Presentation at Hobart R User Group, Hobart, Tasmania. Aug. 26, 2011.
2011. Thorson, J. "Multi-species occupancy modeling and species range maps." Presentation at Data-Poor Fisheries Workshop, Hobart, Tasmania, July 20, 2011.
2011. Thorson, J. "Meta-analysis in support of data-poor stock assessment and time-varying effects." Presentation at Lab Meeting, Hobart, Tasmania, July 7, 2011.
2011. Thorson, J. "Propensity score matching: identifying control fisheries for comparison with MSC data." Invited presentation at NCEAS working-group regarding Marine Stewardship Council (MSC) certification, Santa Barbara, CA, June 22, 2011.
2011. Thorson, J., Stewart, I, and Punt, A. "Agent-based model evaluation of methods to estimate annual abundance for shoaling fishes such as Pacific rockfish (Sebastes spp.)." Presentation at Annual Sea Grant Fellows Meeting, Southeast Fisheries Science Center, Miami, FL, May 23, 2011.
2011. Ono, K., Cunningham, C., and Thorson, J. "Fishing vessel search patterns, evolutionary ecology of salmons, and groundfish sampling designs: three examples of agent-based modeling." Presentation at Think Tank seminar, Seattle, WA, May 5, 2011.
2011. Thorson, J., Stewart, I., and Punt, A.E. "Accounting for fish shoals in single- and multi-species survey data." Presentation at University of British Columbia Quantitative Seminar, Vancouver, WA, April 14, 2011.
2010. Thorson, J. and Branch, T. "Global status and predictive models for fishery collapse from the NCEAS database and landings data." Presentation at University of Washington Think Tank seminar, Seattle, WA, Oct. 13, 2010.
2010. Thorson, J., and Prager, M. “Better catch curves: Incorporating age-specific natural mortality and logistic selectivity.” AFS Symposium on Data-Poor Methods, Pittsburg, PA, Sept. 14, 2010
2010. Thorson, J., and Stewart, I. “Learning about Schools: Mixture distributions and Pacific rockfish.” National Stock Assessment Workshop, St. Petersberg, FL, May 17, 2010.
2010. Thorson, J. “Learning About Schools: Mixture Distributions and Pacific rockfish.” Western Groundfish Conference, Juneau, AK, April 28, 2010.
2010. Thorson, J. “Learning About Schools: Mixture Distributions and Pacific rockfish.” Sea Grant Fellows Meeting, Seattle, WA, April 15-16, 2010.
2010. Thorson, J. and Lapointe, N. “Improving Predictive Models for Ecosystem Invasibility.” AFS/TWS Joint Symposium on Invasive Species, Starkville, MI, April 8, 2010.
2009. Thorson, J. “Evaluating management benchmark estimates from single- and multi-species state-space models for time-varying catchability.” Presentation at University of Washington Mini-Workshop, Seattle, WA, November 10, 2009.
2009. Thorson, J. and Berkson, J. “Multi-species estimation of Bayesian priors for catchability functional parameters.” Quantitative Seminar, Seattle, WA, Oct. 9, 2009.
2009. Thorson, J. and Berkson, J. “Time-varying catchability in the Gulf of Mexico.” AFS National Meeting, St. Louis, MO, 2009.
2009. Thorson, J. “Time-varying catchability in the Gulf of Mexico.” Southeast Stock Assessment Workshop (SESAW), Miami, FL, May 5, 2009.
2009. Thorson, J. “Estimating and evaluating multi-species catchabilility models in the Gulf of Mexico.” Southeast Data, Assessment, and Review (SEDAR) procedural workshop II: Catchability, Atlanta, GA, Feb. 10, 2009.
2009. Thorson, J. “Mechanisms and models for time-varying catchability.” Southeast Data, Assessment, and Review (SEDAR) procedural workshop II: Catchability, Atlanta, GA, Feb. 9, 2009.
2008. Thorson, J. and Simpfendorfer, C. “Improvements from Multi-Model Estimation: A Shark Length-Growth Case Study.” AFS National Meeting, Ottawa, Ontario, Aug. 20, 2008.
2008. Thorson, J. “Nonstationarity and nonlinearity in Gulf of Mexico catchability” Southeast Fisheries Science Center technical meeting, Miami, FL, July 16, 2008.
2007. Thorson, J. and Simpfendorfer, C. “Gear selectivity and sample size effects on growth curve selection in shark age and growth studies” Joint Meeting of Ichthyologists and Herpatologists, St. Louis, MO. July 16, 2007.