scratch/citations/README.md

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Publications that use sdmTMB

Table of contents

• Preprints
• Journal articles
• Theses
• Reports

Preprints

Lindmark, M., Griffiths, C. A., Bartolino, V., Thunell, V., Maioli, F., Anderson, S. C., Belgrano, A., Casini, M., Nadolna-Ałtyn, K., Pawlak, J., Pachur, M., Rakowski, M., Wikström, K., Thompson, M. S. A., Gogina, M., Ustups, D., & Jacobsen, N. S. (2025). Weak effects of local prey density and spatial overlap on predation intensity in a temperate marine ecosystem (p. 2025.03.27.645454). https://doi.org/10.1101/2025.03.27.645454

Lindmark, M., Maioli, F., Anderson, S. C., Gogina, M., Bartolino, V., Sköld, M., Ohlsson, M., Eklöf, A., & Casini, M. (2025). Quantifying competition between two demersal fish species from spatiotemporal stomach content data (p. 2024.04.22.590538). https://doi.org/10.1101/2024.04.22.590538

Ward, E. J., & Tolimieri, N. (2025). Advancing spatially explicit fisheries management with age-structured species distribution models (p. 2025.02.27.640560). https://doi.org/10.1101/2025.02.27.640560

Widlake, E., Wilson, R., Pilgrim, J., Vaux, A. G. C., Tanianis-Hughes, J., Haziqah-Rashid, A., Sherlock, K., Delnicka, A., Simpson, A., Abbott, A. J., Johnston, C. J., Martin, J., Barlow, K., Aliski, E., Shiels, S., Gandy, S., Biddlecombe, S. M., Sedda, L., Medlock, J. M., … Blagrove, M. S. C. (2025). Spatial distribution of Culex mosquitoes across England and Wales, July 2023 (p. 2025.02.28.25322982). https://doi.org/10.1101/2025.02.28.25322982

Mason, E. T. J., Watson, W., Ward, E. J., Thompson, A. R., & Semmens, B. X. (2024). Environment-driven trends in fish larval abundance predict fishery recruitment in two temperate reef congeners: Mechanisms and implications for fishery recovery under a changing ocean (p. 2023.10.11.561723). https://doi.org/10.1101/2023.10.11.561723

Kemei, B., Ochomo, E., Ombok, M., Midega, J., Lucas, E. R., Donnelly, M. J., Sedda, L., & McDermott, D. P. (2023). Spatially explicit sampling frameworks to identify regions of increased mosquito abundance (p. 2023.11.21.568008). https://doi.org/10.1101/2023.11.21.568008

Journal articles

Baker, K. D., Le Corre, N., Bourret, A., Parent, G., Fulton, S., Duprey, N. M. T., & Cox, S. (2025). Spatial stock structure of northern shrimp Pandalus Borealis Krøyer, 1838 (Decapoda: Caridea: Pandalidae) in Canada’s Northwest Atlantic. Journal of Crustacean Biology, 45(2), ruaf021. https://doi.org/10.1093/jcbiol/ruaf021

Dunic, J. C., Conner, J., Anderson, S. C., & Thorson, J. T. (2025). The generalized gamma is a flexible distribution that outperforms alternatives when modelling catch rate data. ICES Journal of Marine Science, 82(4), fsaf040. https://doi.org/10.1093/icesjms/fsaf040

Indivero, J., Anderson, S. C., Barnett, L. A. K., Essington, T. E., & Ward, E. J. (2025). Estimating a physiological threshold to oxygen and temperature from marine monitoring data reveals challenges and opportunities for forecasting distribution shifts. Ecography, 2025(e07413). https://doi.org/10.1111/ecog.07413

Jarvis Mason, E. T., Watson, W., Ward, E. J., Thompson, A. R., & Semmens, B. X. (2025). Environment-driven trends in larval abundance predict fishery recruitment in two saltwater basses. ICES Journal of Marine Science, 82(2), fsae196. https://doi.org/10.1093/icesjms/fsae196

Jonas, L., Brommer, J. E., Jung, M., Baláž, M., Borg, J. J., Božič, L., Clausen, P., Deroux, A., Devos, K., Domsa, C., Faragó, S., Fitzgerald, N., Georgiev, V., Haas, F., Hornman, M., Ieronymidou, C., Langendoen, T., Lehikoinen, A. S., Lindner, K., … Gaget, E. (2025). Interactions between climate warming and management actions determining bird community change in protected areas. Biological Conservation, 308, 111213. https://doi.org/10.1016/j.biocon.2025.111213

Lei, W., Masero, J. A., Chai, Z., Zhu, B.-R., Mu, T., Peng, H.-B., Zhang, Z., & Piersma, T. (2025). Maintaining shallow waters to maximize the potential of saltpans as foraging habitat for migratory shorebirds along an endangered flyway. Biological Conservation, 306, 111100. https://doi.org/10.1016/j.biocon.2025.111100

Lindmark, M., Ohlberger, J., & Gårdmark, A. (2025). Stronger effect of temperature on body growth in cool than in warm populations suggests lack of local adaptation. Ecography, e07518. https://doi.org/10.1002/ecog.07518

Rovellini, A., Punt, A. E., Bryan, M. D., Kaplan, I. C., Dorn, M. W., Aydin, K., Fulton, E. A., Alglave, B., Baker, M. R., Carroll, G., Ferriss, B. E., Haltuch, M. A., Hayes, A. L., Hermann, A. J., Hernvann, P.-Y., Holsman, K. K., Liu, O. R., McHuron, E., Morzaria-Luna, H. N., … Weise, M. T. (2025). Linking climate stressors to ecological processes in ecosystem models, with a case study from the Gulf of Alaska. ICES Journal of Marine Science, 82(1), fsae002. https://doi.org/10.1093/icesjms/fsae002

Wan, F., Lin, H., & Zhang, F. (2025). CPUE standardisation in the Atlantic swordfish longline fishery based on sdmTMB. Shhydxxb, 34(2), 422–433. https://doi.org/10.12024/jsou.20241104705

Anderson, S. C., English, P. A., Gale, K. S. P., Haggarty, D. R., Robb, C. K., Rubidge, E. M., & Thompson, P. L. (2024). Impacts on population indices if scientific surveys are excluded from marine protected areas. ICES Journal of Marine Science, fsae009. https://doi.org/10.1093/icesjms/fsae009

Asciutto, E., Maioli, F., Manfredi, C., Anibaldi, A., Cimini, J., Isailović, I., Marčeta, B., & Casini, M. (2024). Spatio-temporal patterns of whiting (Merlangius merlangus) in the Adriatic Sea under environmental forcing. PLOS ONE, 19(3), e0289999. https://doi.org/10.1371/journal.pone.0289999

Baker, K. D., Anderson, S. C., Mullowney, D. R. J., Walkusz, W., & Skanes, K. R. (2024). Moving away from a scale mismatch: Spatiotemporal modelling of striped shrimp (Pandalus montagui) density in Canada’s subarctic. Fisheries Research, 270, 106898. https://doi.org/10.1016/j.fishres.2023.106898

Bass, A. L., Anderson, S. C., Bateman, A. W., Connors, B. M., Peña, M. A., Li, S., Kaukinen, K. H., Patterson, D. A., Hinch, S. G., & Miller, K. M. (2024). Intrinsic and extrinsic factors associated with the spatio-temporal distribution of infectious agents in early marine Chinook and coho salmon. Marine Ecology Progress Series, 736, 107–127. https://doi.org/10.3354/meps14581

Blake, K., Anderson, S., Gleave, A., & Veríssimo, D. (2024). Impact on species’ online attention when named after celebrities. Conservation Biology, 38, e14184. https://doi.org/10.1111/cobi.14184

Carlsen, A. A., Casini, M., Masnadi, F., Olsson, O., Hejdström, A., & Hentati-Sundberg, J. (2024). Autonomous data sampling for high-resolution spatiotemporal fish biomass estimates. Ecological Informatics, 84, 102852. https://doi.org/10.1016/j.ecoinf.2024.102852

Correa, G. M., Kaplan, D., Grande, M., Uranga, J., Ramos Alonso, M., Alyón, P., Rojo, V., Merino, G., & Santiago, J. (2024). Standardized catch per unit effort of yellowfin tuna in the Atlantic Ocean for the European purse seine fleet operating on floating objects. Collective Volume of Scientific Papers ICCAT, 81(2), 1–26.

Cristiani, J., Rubidge, E. M., Thompson, P. L., Robb, C. K., Hessing-Lewis, M., & O’Connor, M. I. (2024). Quantifying marine larval dispersal to assess MPA network connectivity and inform future national and transboundary planning efforts. Can. J. Fish. Aquat. Sci., 81(6), 670–686. https://doi.org/10.1139/cjfas-2023-0188

Fordham, D. A., Brown, S. C., Canteri, E., Austin, J. J., Lomolino, M. V., Haythorne, S., Armstrong, E., Bocherens, H., Manica, A., Rey-Iglesia, A., Rahbek, C., Nogués-Bravo, D., & Lorenzen, E. D. (2024). 52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms. Proc. Natl. Acad. Sci. U.S.A., 121(24), e2316419121. https://doi.org/10.1073/pnas.2316419121

Freshwater, C., Anderson, S. C., & King, J. (2024). Model-based indices of juvenile Pacific salmon abundance highlight species-specific seasonal distributions and impacts of changes to survey design. Fisheries Research, 277, 107063. https://doi.org/10.1016/j.fishres.2024.107063

Freshwater, C., & King, J. (2024). Seasonal variability in condition and spatial distribution of Chinook Salmon: Implications for ecosystem-based management. Transactions of the American Fisheries Society, 153(6), 859–877. https://doi.org/10.1002/tafs.10495

Gilman, E., & Chaloupka, M. (2024). Evidence from interpretable machine learning to inform spatial management of Palau’s tuna fisheries. Ecosphere, 15(2), e4751. https://doi.org/10.1002/ecs2.4751

Hart, J. D., Pandolfi, A., Jones, T., & Jenkins, D. G. (2024). Ground-Based Pyrethroid Adulticides Reduce Mosquitoes But Not Nontarget Insects in Central Florida. Journal of the American Mosquito Control Association, 40(3), 125–136. https://doi.org/10.2987/24-7177

Hebert, N. E., Sameoto, J. A., Keith, D. M., Barrett, M. A., Brown, C. J., & Mills Flemming, J. (2024). Comparing spatiotemporal species distribution models: A case study of a Scotian Shelf sea cucumber (Cucumaria Frondosa). Ecosphere, 15(4), e4822. https://doi.org/10.1002/ecs2.4822

Jirinec, V., Bresnan, A. M., Clément, M. A., Colón, M. R., Long, A. M., Rhyne, G. S., Rodrigues, P. F., Stein, E. D., Pérez-Umphrey, A. A., Varian, C. P., Williams, S. T., & Taylor, S. S. (2024). Home ranges, habitat selection, and energy expenditure of Strix Varia (Barred Owls): Understanding the full diel cycle matters for enhancing urban landscapes. Ornithological Applications, 126(4), duae038. https://doi.org/10.1093/ornithapp/duae038

Knief, U., Müller, I. A., Stryjewski, K. F., Metzler, D., Sorenson, M. D., & Wolf, J. B. W. (2024). Evolution of Chromosomal Inversions across an Avian Radiation. Molecular Biology and Evolution, 41(6), msae092. https://doi.org/10.1093/molbev/msae092

Maioli, F., Weigel, B., Lindmark, M., Manfredi, C., Zupa, W., Bitetto, I., Russo, T., & Casini, M. (2024). Assessing the overlap between fishing and chondrichthyans exposes high-risk areas for bycatch of threatened species. Ecosphere, 15(11), e70050. https://doi.org/10.1002/ecs2.70050

McGill, L., Sleugh, T., Petrik, C., Schiff, K., McLaughlin, K., Aluwihare, L., & Semmens, B. (2024). The persistent DDT footprint of ocean disposal, and ecological controls on bioaccumulation in fishes. Proc. Natl. Acad. Sci. U.S.A., 121(45), e2401500121. https://doi.org/10.1073/pnas.2401500121

Monteiro, G. M., Djogbénou, L. S., Donnelly, M. J., & Sedda, L. (2024). Development and deployment of an improved Anopheles gambiae s.l. Field surveillance by adaptive spatial sampling design. Front. Ecol. Evol., 11. https://doi.org/10.3389/fevo.2023.1241617

Morant, J., Arrondo, E., Sánchez-Zapata, J. A., Donázar, J. A., Margalida, A., Carrete, M., Blanco, G., Guil, F., Serrano, D., & Pérez-García, J. M. (2024). Fine-scale collision risk mapping and validation with long-term mortality data reveal current and future wind energy development impact on sensitive species. Environmental Impact Assessment Review, 104, 107339. https://doi.org/10.1016/j.eiar.2023.107339

Mullowney, D., Baker, K., Pantin, J., Coffey, W., Lefort, K., & Morrissey, K. (2024). Merits of multi-indicator precautionary approach management in a male-only crab fishery. Fishes, 9(5), 187. https://doi.org/10.3390/fishes9050187

O’Brien, K. A., Cortés, E., Driggers III, W. B., Frazier, B. S., & Latour, R. J. (2024). Niche structure and habitat shifts for coastal sharks of the US Southeast Atlantic and Gulf of Mexico. Fisheries Oceanography, n/a(n/a), e12676. https://doi.org/10.1111/fog.12676

Olin, A. B., Bergström, U., Bodin, Ö., Sundblad, G., Eriksson, B. K., Erlandsson, M., Fredriksson, R., & Eklöf, J. S. (2024). Predation and spatial connectivity interact to shape ecosystem resilience to an ongoing regime shift. Nat Commun, 15(1), 1304. https://doi.org/10.1038/s41467-024-45713-1

Pan, K., Marshall, L., de Snoo, G. R., & Biesmeijer, J. C. (2024). Dutch landscapes have lost insect-pollinated plants over the past 87 years. Journal of Applied Ecology, 61(6), 1323–1333. https://doi.org/10.1111/1365-2664.14649

Panzeri, D., Reale, M., Cossarini, G., Salon, S., Carlucci, R., Spedicato, M. T., Zupa, W., Vrgoč, N., & Libralato, S. (2024). Future distribution of demersal species in a warming Mediterranean sub-basin. Front. Mar. Sci., 11. https://doi.org/10.3389/fmars.2024.1308325

Panzeri, D., Russo, T., Arneri, E., Carlucci, R., Cossarini, G., Isajlović, I., Krstulović Šifner, S., Manfredi, C., Masnadi, F., Reale, M., Scarcella, G., Solidoro, C., Spedicato, M. T., Vrgoč, N., Zupa, W., & Libralato, S. (2024). Identifying priority areas for spatial management of mixed fisheries using ensemble of multi-species distribution models. Fish and Fisheries, 25(2), 187–204. https://doi.org/10.1111/faf.12802

Riekkola, L., Liu, O. R., Ward, E. J., Holland, D. S., Feist, B. E., & Samhouri, J. F. (2024). Modeling the spatiotemporal patterns and drivers of Dungeness crab fishing effort to inform whale entanglement risk mitigation on the U.S. West Coast. Journal of Environmental Management, 351, 119735. https://doi.org/10.1016/j.jenvman.2023.119735

Rosa, J. O., Soares, J. R. S., & Fernandes, O. A. (2024). Harvest load transfer sites influence sugarcane billbug (Coleoptera: Curculionidae) spatiotemporal injury in sugarcane. Pest Management Science, 80(4), 1771–1778. https://doi.org/10.1002/ps.7912

Rubidge, E. M., Robb, C. K., Thompson, P. L., McDougall, C., Bodtker, K. M., Gale, K. S. P., Ban, S., Tayler Brown, K. H., Sahanatien, V., Ouchi, S., Friesen, S. K., Ban, N. C., Hunter, K. L., Pena, A., Holdsworth, A., & Martone, R. (2024). Evaluating the design of the first marine protected area network in Pacific Canada under a changing climate. FACETS, 9, 1–18. https://doi.org/10.1139/facets-2023-0126

Ruiz-Diaz, R., Pennino, M. G., Fisher, J. A. D., & Eddy, T. D. (2024). Decadal changes in biomass and distribution of key fisheries species on Newfoundland’s Grand Banks. PLOS ONE, 19(4), e0300311. https://doi.org/10.1371/journal.pone.0300311

Schooler, S. L., Svoboda, N. J., Kellner, K. F., Pu, G., Finnegan, S. P., & Belant, J. L. (2024). Variable spatiotemporal ungulate behavioral response to predation risk. Ecosphere, 15(10), e70041. https://doi.org/10.1002/ecs2.70041

Song, X., Hu, F., Xu, M., Zhang, Y., Jin, Y., Gao, X., Liu, Z., Ling, J., Li, S., & Cheng, J. (2024). Spatiotemporal Distribution and Dispersal Pattern of Early Life Stages of the Small Yellow Croaker (Larimichthys Polyactis) in the Southern Yellow Sea. Diversity, 16(9), 521. https://doi.org/10.3390/d16090521

Sutton, J. T., McDermid, J. L., Landry, L., & Turcotte, F. (2024). Spatiotemporal analysis provides solutions to mitigate bycatch of southern Gulf of St. Lawrence Atlantic Cod in an expanding Redfish fishery. Fisheries Research, 276, 107038. https://doi.org/10.1016/j.fishres.2024.107038

Tengvall, J., Søvik, G., Enberg, K., Lindstrøm, U., Strand, M., Pedersen, T., Strand, H. K., & Zimmermann, F. (2024). Fine-scale diet data reveal spatial variation in predator–prey interactions in Norwegian fjords. Journal of Applied Ecology, 1365–2664.14603. https://doi.org/10.1111/1365-2664.14603

Thompson, P. L., & Neville, C. M. (2024). Spatial estimates of juvenile Pacific salmon (Oncorhynchus spp.) abundance in the Strait of Georgia. Canadian Technical Report of Fisheries and Aquatic Sciences, 3597.

Wan, Y., Zhang, C., Xu, B., Xue, Y., Ren, Y., & Ji, Y. (2024). Which aspect of functional diversity shapes ecosystem functioning in exploited marine demersal fish community? Ecological Indicators, 163, 112083. https://doi.org/10.1016/j.ecolind.2024.112083

Ward, E. J., Anderson, S. C., Barnett, L. A. K., English, P. A., Berger, H. M., Commander, C. J. C., Essington, T. E., Harvey, C. J., Hunsicker, M. E., Jacox, M. G., Johnson, K. F., Large, S., Liu, O. R., Richerson, K. E., Samhouri, J. F., Siedlecki, S. A., Shelton, A. O., Somers, K. A., & Watson, J. T. (2024). Win, lose, or draw: Evaluating dynamic thermal niches of northeast Pacific groundfish. PLOS Climate, 3(11), e0000454. https://doi.org/10.1371/journal.pclm.0000454

Ward, E. J., Hunsicker, M. E., Marshall, K. N., Oken, K. L., Semmens, B. X., Field, J. C., Haltuch, M. A., Johnson, K. F., Taylor, I. G., Thompson, A. R., & Tolimieri, N. (2024). Leveraging ecological indicators to improve short term forecasts of fish recruitment. Fish and Fisheries, 25(6), 895–909. https://doi.org/10.1111/faf.12850

Xia, H., Liu, R., Zhou, W., & Luo, W. (2024). Modeling the Causes of Urban Traffic Crashes: Accounting for Spatiotemporal Instability in Cities. Sustainability, 16(20), 9102. https://doi.org/10.3390/su16209102

Barbato, M., Zampieri, C., D’Acunto, S., Pennino, M. G., Barausse, A., & Mazzoldi, C. (2023). Too young to die: Mapping nursery areas for early juveniles of the endangered sandbar shark ( Carcharhinus Plumbeus ) to inform conservation in the Mediterranean Sea. Journal of Applied Ecology, 1365–2664.14494. https://doi.org/10.1111/1365-2664.14494

Cardinale, M., Zimmermann, F., Søvik, G., Griffiths, C. A., Bergenius Nord, M., & Winker, H. (2023). Spatially explicit stock assessment uncovers sequential depletion of northern shrimp stock components in the North Sea. ICES Journal of Marine Science, 80(7), 1868–1880. https://doi.org/10.1093/icesjms/fsad111

English, P. A., Picco, C. M., Edwards, J. C., Haggarty, D. R., Forrest, R. E., & Anderson, S. C. (2023). Spatial restrictions hinder avoidance of choke species in an Indigenous rights-based fishery. People and Nature, 6, 75–90. https://doi.org/10.1002/pan3.10554

Evans, R., English, P. A., Gauthier, S., & Robinson, C. L. K. (2023). Quantifying the effects of extreme events and oceanographic variability on the spatiotemporal biomass and distribution of two key euphausiid prey species. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1031485

Freshwater, C., Duguid, W., Juanes, F., & McKinnell, S. (2023). A century-long time series reveals large declines and greater synchrony in Nass River sockeye salmon size-at-age. Can. J. Fish. Aquat. Sci., 80(7), 1098–1109. https://doi.org/10.1139/cjfas-2022-0259

Kochprapa, P., Savini, C., Ngoprasert, D., Savini, T., & Gale, G. A. (2023). Spatio-temporal dynamics of human-elephant conflict in a valley of pineapple plantations. Integrative Conservation, 2(2), 95–107. https://doi.org/10.1002/inc3.23

Lindmark, M., Anderson, S. C., Gogina, M., & Casini, M. (2023). Evaluating drivers of spatiotemporal variability in individual condition of a bottom-associated marine fish, Atlantic cod (Gadus Morhua). ICES Journal of Marine Science, 80(5), 1539–1550. https://doi.org/10.1093/icesjms/fsad084

Liu, O. R., Ward, E. J., Anderson, S. C., Andrews, K. S., Barnett, L. A. K., Brodie, S., Carroll, G., Fiechter, J., Haltuch, M. A., Harvey, C. J., Hazen, E. L., Hernvann, P.-Y., Jacox, M., Kaplan, I. C., Matson, S., Norman, K., Pozo Buil, M., Selden, R. L., Shelton, A., & Samhouri, J. F. (2023). Species redistribution creates unequal outcomes for multispecies fisheries under projected climate change. Science Advances, 9(33), eadg5468. https://doi.org/10.1126/sciadv.adg5468

Nephin, J., Thompson, P. L., Anderson, S. C., Park, A. E., Rooper, C. N., Aulthouse, B., & Watson, J. (2023). Integrating disparate survey data in species distribution models demonstrate the need for robust model evaluation. Can. J. Fish. Aquat. Sci., 80(12), 1869–1889. https://doi.org/10.1139/cjfas-2022-0279

Ohyama, L., Booher, D. B., & King, J. R. (2023). Ecological traits of social insects: Colony, queen and worker size relationships reveal a nexus trait with broad ecological relevance. Functional Ecology, 37(8), 2194–2206. https://doi.org/10.1111/1365-2435.14355

Stompe, D. K., Moyle, P. B., Oken, K. L., Hobbs, J. A., & Durand, J. R. (2023). A spatiotemporal history of key pelagic fish species in the San Francisco Estuary, CA. Estuaries and Coasts. https://doi.org/10.1007/s12237-023-01189-8

Thompson, P. L., Anderson, S. C., Nephin, J., Robb, C. K., Proudfoot, B., Park, A. E., Haggarty, D. R., & Rubidge, E. M. (2023). Integrating trawl and longline surveys across British Columbia improves groundfish distribution predictions. Can. J. Fish. Aquat. Sci., 80(1), 195–210. https://doi.org/10.1139/cjfas-2022-0108

Thompson, P. L., Nephin, J., Davies, S. C., Park, A. E., Lyons, D. A., Rooper, C. N., Angelica Peña, M., Christian, J. R., Hunter, K. L., Rubidge, E., & Holdsworth, A. M. (2023). Groundfish biodiversity change in northeastern Pacific waters under projected warming and deoxygenation. Philosophical Transactions of the Royal Society B: Biological Sciences, 378(1881), 20220191. https://doi.org/10.1098/rstb.2022.0191

Thompson, P. L., Rooper, C. N., Nephin, J., Park, A. E., Christian, J. R., Davies, S. C., Hunter, K., Lyons, D. A., Peña, M. A., Proudfoot, B., Rubidge, E. M., & Holdsworth, A. M. (2023). Response of Pacific halibut (Hippoglossus Stenolepis) to future climate scenarios in the Northeast Pacific Ocean. Fisheries Research, 258, 106540. https://doi.org/10.1016/j.fishres.2022.106540

van der Heever, G. M., Yemane, D., Leslie, R. W., van der Lingen, C. D., & Gibbons, M. J. (2023). Modeling and comparing the distributions and associations of two co-occurring catshark species off South Africa. Journal of Fish Biology, 103(5), 1095–1105. https://doi.org/10.1111/jfb.15497

Vogel, E. F., Skalmerud, S., Biuw, M., Blanchet, M.-A., Kleivane, L., Skaret, G., Øien, N., & Rikardsen, A. (2023). Foraging movements of humpback whales relate to the lateral and vertical distribution of capelin in the Barents Sea. Front. Mar. Sci., 10, 1254761. https://doi.org/10.3389/fmars.2023.1254761

Watson, J., Edwards, A. M., & Auger-Méthé, M. (2023). A statistical censoring approach accounts for hook competition in abundance indices from longline surveys. Can. J. Fish. Aquat. Sci., 80(3), 468–486. https://doi.org/10.1139/cjfas-2022-0159

Yalcin, S., Anderson, S. C., Regular, P. M., & English, P. A. (2023). Exploring the limits of spatiotemporal and design-based index standardization under reduced survey coverage. ICES Journal of Marine Science, 80(9), 2368–2379. https://doi.org/10.1093/icesjms/fsad155

Zimmermann, F., Tengvall, J., Strand, H. K., Nedreaas, K., Thangstad, T. H., Husson, B., & Søvik, G. (2023). Fine-scale spatial variation of northern shrimp and Atlantic cod across three Norwegian fjord systems and implications for management. Estuarine, Coastal and Shelf Science, 292, 108435. https://doi.org/10.1016/j.ecss.2023.108435

Anderson, S. C., Ward, E. J., English, P. A., & Barnett, L. A. K. (2022). sdmTMB: An R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields. bioRxiv, 2022.03.24.485545. https://doi.org/10.1101/2022.03.24.485545

Commander, C. J. C., Barnett, L. A. K., Ward, E. J., Anderson, S. C., & Essington, T. E. (2022). The shadow model: How and why small choices in spatially explicit species distribution models affect predictions. PeerJ, 10, e12783. https://doi.org/10.7717/peerj.12783

DFO. (2022). A data synopsis for British Columbia groundfish: 2021 data update. Canadian Science Advisory Secretariat Science Response, 2022/020.

Essington, T. E., Anderson, S. C., Barnett, L. A. K., Berger, H. M., Siedlecki, S. A., & Ward, E. J. (2022). Advancing statistical models to reveal the effect of dissolved oxygen on the spatial distribution of marine taxa using thresholds and a physiologically based index. Ecography, 2022, e06249. https://doi.org/10.1111/ecog.06249

Latour, R. J., Gartland, J., & Peterson, C. D. (2022). Ontogenetic niche structure and partitioning of immature sandbar sharks within the Chesapeake Bay nursery. Mar Biol, 169(6), 76. https://doi.org/10.1007/s00227-022-04066-3

Matsubayashi, J., Kimura, K., Ohkouchi, N., Ogawa, N. O., Ishikawa, N. F., Chikaraishi, Y., Tsuda, Y., & Minami, H. (2022). Using geostatistical analysis for simultaneous estimation of isoscapes and ontogenetic shifts in isotope ratios of highly migratory marine fish. Front. Mar. Sci., 9. https://doi.org/10.3389/fmars.2022.1049056

Ward, E. J., Barnett, L. A. K., Anderson, S. C., Commander, C. J. C., & Essington, T. E. (2022). Incorporating non-stationary spatial variability into dynamic species distribution models. ICES Journal of Marine Science, 79(9), 2422–2429. https://doi.org/10.1093/icesjms/fsac179

Barnett, L. A. K., Ward, E. J., & Anderson, S. C. (2021). Improving estimates of species distribution change by incorporating local trends. Ecography, 44(3), 427–439. https://doi.org/10.1111/ecog.05176

English, P. A., Ward, E. J., Rooper, C. N., Forrest, R. E., Rogers, L. A., Hunter, K. L., Edwards, A. M., Connors, B. M., & Anderson, S. C. (2021). Contrasting climate velocity impacts in warm and cool locations show that effects of marine warming are worse in already warmer temperate waters. Fish and Fisheries, 23(1), 239–255. https://doi.org/10.1111/faf.12613

Evans, R., English, P. A., Anderson, S. C., Gauthier, S., & Robinson, C. L. K. (2021). Factors affecting the seasonal distribution and biomass of E. Pacifica and T. Spinifera along the Pacific coast of Canada: A spatiotemporal modelling approach. PLOS ONE, 16(5), e0249818. https://doi.org/10.1371/journal.pone.0249818

Anderson, S. C., Keppel, E. A., & Edwards, A. M. (2020). Reproducible visualization of raw fisheries data for 113 species improves transparency, assessment efficiency, and monitoring. Fisheries, 45, 535–543. https://doi.org/10.1002/fsh.10441

Katzenberger, J. (2019). Modelling distribution and habitat suitability for the Red Kite Milvus Milvus in Germany. Vogelwelt, 139, 117–128.

Thesis chapters

Carlsen, A. (2025). Understanding predators through their prey. PhD Thesis. Swedish University of Agricultural Sciences. https://res.slu.se/id/publ/132972

Fritch, K. (2025). Understanding the habitat associations of nearshore rockfishes inside and outside of marine protected areas using hook-and-line data. MSc Thesis. California Polytechnic State University. https://digitalcommons.calpoly.edu/theses/2986

Hagaman, M. (2024). Building better homes for pollinators: How native plants benefit pollinator communities in suburban landscapes. MSc Thesis. University of Central Florida. https://stars.library.ucf.edu/etd2023/305

Soluri, K. S. (2024). Forecasting Bycatch Hotspots Using Random Forest Machine Learning, Geostatistical Linear Mixed Modeling, and Gradient Boosted Machine Learning {MSc Thesis}, University of Miami. https://www.proquest.com/openview/aaada454646679fb9cab2d6e9df59a87/1?cbl=18750&diss=y&pq-origsite=gscholar

Van Elslander, J. (2024). Spatial variation in grizzly bear diet across British Columbia. MSc Thesis. University of British Columbia. https://doi.org/10.14288/1.0441988

Frare, L. (2023). How is the queuing time for rent controlled apartments affected by the entry of a private housing agency. MSc Thesis. University of Gothenburg. https://gupea.ub.gu.se/handle/2077/77483

Hebert, N. (2023). A comparison of spatio-temporal species distribution modelling frameworks using cucumaria frondosa as a case study. MSc Thesis. Dalhousie University.

McDermott, D. (2023). Addressing sources of variation in entomological endpoints in the field evaluation of malaria vector control tools.. PhD Thesis. Liverpool School of Tropical Medicine. https://doi.org/10.57978/4qcc-yd52

Stokkeland, M. M. (2023). Improved stock estimation for Iceland scallops (Chlamys islandica) in the Svalbard area. MSc Thesis. University of Bergen.

Bugaj, M. (2022). Species distribution and abundance of bering sea tunicates with implications for coastal food security. MSc Thesis. Western Washington University.

Stompe, D. K. (2022). The distribution and abundance of striped bass and other estuarine fishes in the San Francisco and Umpqua River estuaries PhD thesis. University of California, Davis.

Woodman, S. G. (2022). From land to water: The impacts of forest disturbances on carbon cycling in northern catchments. PhD Thesis. University of Cambridge. https://doi.org/10.17863/CAM.96997

Katzenberger, J. K. (2021). Habitat use and population viability of the Red Kite (Milvus milvus) in Germany. PhD Thesis. Georg-August-University Göttingen. https://doi.org/10.53846/goediss-8583

Reports

Yeh, Z.-W., Hsu, J., & Chang, Y.-J. (2025). Spatiotemporal modelling for size-specific CPUE standardization of albacore tuna in the north Pacific Ocean caught by Taiwanese longline fisheries. ISC Albacore Working Group Intercessional Workshop, ISC/25/ALBWG-01/04. https://isc.fra.go.jp/pdf/ALB/ISC25_ALB_1/ISC25-ALBWG-01_04.pdf

DFO. (2024). Assessment of the Orange-Footed Sea Cucumber (Cucumaria Frondosa) Resource on the St. Pierre Bank (NAFO Subdivision 3Ps) in 2022. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep., 2024/018.

Hjelset, A. M., Danielsen, H. E. H., Jenssen, M., Humborstad, O. B., Anders, N., Saltskår, J., Berg, E., & Zimmermann, F. (2024). Snøkrabbe på norsk sokkel i Barentshavet-Status og rådgivning for 2025.

Perelman, J. N., Tanaka, K. R., Suca, J. J., Oliver, T. A., & Gajdzik, L. (2024). Modeling tools to help assess the distribution of priority reef fish species for jurisdictional coral reef fishery management plans in Guam. https://doi.org/10.25923/v50k-pc85

Proudfoot, B., Thompson, P. L., Vaidyanathan, T., & Robb, C. K. (2024). Spatial estimates of Blue Shark, Salmon Shark, Pacific Sleeper Shark and Bluntnose Sixgill Shark presence in British Columbia. Can. Tech. Rep. Fish. Aquat. Sci., 3600, vi + 27 p. https://publications.gc.ca/site/eng/9.935543/publication.html

Shotwell, S. K., & Dame, R. (2024). Appendix 1A. Ecosystem and socioeconomic profile of the Walleye Pollock stock in the Gulf of Alaska — report card. In C. C. Monnahan, G. D. Adams, B. E. Ferriss, S. K. Shotwell, D. R. McKelvey, & D. W. McGowan (Eds.), Assessment of the Walleye Pollock stock in the Gulf of Alaska.

Shotwell, S. K., & Dame, R. (2024). Appendix 2.1. Ecosystem and socioeconomic profile of the Pacific Cod stock in the Gulf of Alaska — report card. In P. J. F. Hulson, S. J. Barbeaux, B. Ferriss, K. Echave, J. Nielsen, S. McDermott, B. Laurel, A. Abookire, I. Spies, & S. K. Shotwell (Eds.), Assessment of the Pacific Cod stock in the Gulf of Alaska.

Zimmermann, F., Stokkeland, M. M., Wiech, M., Jenssen, M., Olssøn, R., Danielsen, J. E. H., & Sundet, J. H. (2024). Survey of Iceland scallop beds north of Svalbard (Toktrapport 2023-17; pp. 37 p.).

Babcock, E. A., Harford, W. J., Gedamke, T., Anderson, S C, & Goodyear, C. P. (2023). Simulation-testing model-based and design-based bycatch estimators. Collect. Vol. Sci. Pap. ICCAT, 80(6), 51–79. https://www.iccat.int/Documents/CVSP/CV080_2023/n_6/CV080060051.pdf

Bastardie, F., Baudron, A., Berg, C., Berger, A., Binch, L., Bitetto, I., Blanco, C., Bluemel, J. K., Bolser, D., Calderwood, J., Carvalho, N., Celie, L., Chen, C., Chust, G., Couce, E., Damalas, D., Depestele, J., Fallon, N., Fernandes, P., … Zupa, W. (2023). Workshop 2 on Fish Distribution (WKFISHDISH2; outputs from 2022 meeting). In Workshop 2 on Fish Distribution (WKFISHDISH2; outputs from 2022 meeting) Report. International Council for the Exploration of the Sea (ICES). https://doi.org/10.17895/ices.pub.21692246

Correa, G. moron, Kaplan, D., Grande, M., Uranga, J., Ramos Alonso, M.-L., Pascual Alayón, P., Rojo, V., Merino, G., Santiago, J., Grande, M., Uranga, J., Ramos Alonso, M.-L., Pascual Alayón, P., Rojo, V., Merino, G., & Santiago, J. (2023). Standardized catch per unit effort of yellowfin tuna in the Atlantic Ocean for the European purse seine fleet operating on floating objects. ICCAT Recueil de Documents Scientifiques / Collective Volume of Scientific Paper, 81(2), 1–26. https://archimer.ifremer.fr/doc/00897/100928/

Huynh, Q. C., & Carruthers, T. (2023). Development of spatial operating models to test survey design and calibrate a new survey index for Northwest Atlantic Fisheries Organization Subarea 0+1 (offshore) Greenland Halibut (Reinhardtius Hippoglossoides). DFO Can. Sci. Advis. Sec. Res. Doc., 2023/038. https://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2023/2023_038-eng.html

Shotwell, S. K., Ferriss, B., Hulson, P.-J. F., Laurel, B., Matta, B., & Rogers, L. (2023). Appendix 2.1. Ecosystem and socioeconomic profile of the Pacific Cod stock in the Gulf of Alaska — report card. In P.-J. F. Hulson, S. J. Barbeaux, B. Ferriss, K. Echave, J. Nielsen, S. K. Shotwell, B. Laurel, & I. Spies (Eds.), Assessment of the Pacific Cod stock in the Gulf of Alaska.

ICES. (2022). Benchmark workshop on Pandalus stocks (WKPRAWN). ICES Sci. Rep., 4(20), 249 pp. https://doi.org/10.17895/ices.pub.19714204

NAFO. (2022). Report of the Scientific Council Meeting (NAFO Scientific Council Studies Serial No. N7322(22/18)). https://www.nafo.int/Portals/0/PDFs/sc/2022/scs22-18.pdf

Tanaka, K. R., & Oliver, T. A. (2022). A simulation framework for evaluating multiple fishery-independent survey strategies in the Main Hawaiian Islands. NOAA Technical Memorandum, NMFS-PIFSC-134. https://doi.org/10.25923/dqaf-wa04

Haggarty, D. R., Huynh, Q. C., Forrest, R. E., Anderson, S. C., Bresch, M. J., & Keppel, E. A. (2020). Evaluation of potential rebuilding strategies for Inside Yelloweye Rockfish (Sebastes Ruberrimus) in British Columbia. DFO Can. Sci. Advis. Sec. Res. Doc., 2021/008, vi + 139 p. https://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2021/2021_008-eng.html

Anderson, S. C., Keppel, E. A., & Edwards, A. M. (2019). A reproducible data synopsis for over 100 species of British Columbia groundfish. DFO Can. Sci. Advis. Sec. Res. Doc., 2019/041, vii + 321 p.

pbs-assess/sdmTMB documentation built on June 2, 2025, 10:22 a.m.