Publications using sdmTMB

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

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., and 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. doi:10.1073/pnas.2316419121.

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

Lindmark, M., Ohlberger, J., and Gårdmark, A. 2024, May 9. Stronger effect of temperature on body growth in cool than in warm populations suggests lack of local adaptation. bioRxiv. doi:10.1101/2024.01.17.575983.

Bass, A., Anderson, S., Bateman, A., Connors, B., Peña, M., Li, S., Kaukinen, K., Patterson, D., Hinch, S., and Miller, K. 2024. Intrinsic and extrinsic factors associated with the spatio-temporal distribution of infectious agents in early marine Chinook and coho salmon. Mar. Ecol. Prog. Ser. 736: 107–127. doi:10.3354/meps14581.

Riekkola, L., Liu, O.R., Ward, E.J., Holland, D.S., Feist, B.E., and 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. doi:10.1016/j.jenvman.2023.119735.

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

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

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

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

Pan, K., Marshall, L., de Snoo, G.R., and Biesmeijer, J.C. (2024). Dutch landscapes have lost insect-pollinated plants over the past 87 years. Journal of Applied Ecology. In press. doi:10.1111/1365-2664.14649.

Mullowney, D., Baker, K., Pantin, J., Coffey, W., Lefort, K., and Morrissey, K. 2024. Merits of Multi-Indicator Precautionary Approach Management in a Male-Only Crab Fishery. Fishes 9(5): 187. doi:10.3390/fishes9050187.

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

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

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

Thompson, P.L., and 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. URL.

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

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., and Martone, R. 2024. Evaluating the design of the first marine protected area network in Pacific Canada under a changing climate. FACETS 9: 1–18. doi:10.1139/facets-2023-0126.

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

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

Cristiani, J., Rubidge, E.M., Thompson, P.L., Robb, C., Lewis, M.H.-, and O’Connor, M.I. 2023. Quantifying marine larval dispersal to assess MPA network connectivity and inform future national and transboundary planning efforts. bioRxiv. doi:10.1101/2023.05.01.538971.

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., Moss, J., Surma, S., and Weise, M.T. 2024. Linking climate stressors to ecological processes in ecosystem models, with a case study from the Gulf of Alaska. ICES Journal of Marine Science: fsae002. doi:10.1093/icesjms/fsae002.

Babcock, E.A., Harford, W.J., Gedamke, T., Anderson, S.C., and Goodyear, C.P. 2023. Simulation-testing model-based and design-based bycatch estimators. Collect. Vol. Sci. Pap. ICCAT 80(6): 51–79. PDF

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., and Libralato, S. 2023. Identifying priority areas for spatial management of mixed fisheries using ensemble of multi-species distribution models. Fish and Fisheries. In press. doi:10.1111/faf.12802.

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. In press. doi:10.1002/pan3.10554

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, Sweden. https://gupea.ub.gu.se/handle/2077/77483

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

Cardinale, M., Zimmermann, F., Søvik, G., Griffiths, C.A., Bergenius Nord, M., and 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. doi:10.1093/icesjms/fsad111.

Asciutto, E., Maioli, F., Manfredi, C., Anibaldi, A., Cimini, J., Isailović, I., Marčeta, B., and Casini, M. 2023. Spatio-temporal patterns of whiting (Merlangius merlangus) in the Adriatic Sea under environmental forcing. bioRxiv 2023.08.01.551447. doi:10.1101/2023.08.01.551447.

Yalcin, S., Anderson, S.C., Regular, P.M., and English, P.A. 2023. Exploring the limits of spatiotemporal and design-based index standardization under reduced survey coverage. ICES Journal of Marine Science: fsad155. doi:10.1093/icesjms/fsad155.

Nephin, J., Thompson, P.L., Anderson, S.C., Park, A.E., Rooper, C.N., Aulthouse, B., and Watson, J. 2023. Integrating disparate survey data in species distribution models demonstrate the need for robust model evaluation. Can. J. Fish. Aquat. Sci. In press. doi:10.1139/cjfas-2022-0279.

Zimmermann, F., Tengvall, J., Strand, H.K., Nedreaas, K., Thangstad, T.H., Husson, B., and 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. doi:10.1016/j.ecss.2023.108435.

Baker, K.D., Anderson, S.C., Mullowney, D.R.J., Walkusz, W., and 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. doi:10.1016/j.fishres.2023.106898.

Blake, K., Anderson, S., Gleave, A., and Veríssimo, D. 2023. Impact on species’ online attention when named after celebrities. Conservation Biology. In press. doi:10.1111/cobi.14184.

Morant, J., Arrondo, E., Sánchez-Zapata, J.A., Donázar, J.A., Margalida, A., Carrete, M., Blanco, G., Guil, F., Serrano, D., and 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. doi:10.1016/j.eiar.2023.107339.

Barbato, M., Zampieri, C., D’Acunto, S., Pennino, M.G., Barausse, A., and 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. doi:10.1111/1365-2664.14494.

Monteiro, G.M., Djogbénou, L.S., Donnelly, M.J., and Sedda, L. 2023. Development and deployment of improved Anopheles gambiae s.l. field surveillance by adaptive spatial sampling design. bioRxiv 2023.06.16.545360; doi: https://doi.org/10.1101/2023.06.16.545360

Vogel, E.F., Skalmerud, S., Biuw, M., Blanchet, M.-A., Kleivane, L., Skaret, G., Øien, N., and 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. doi:10.3389/fmars.2023.1254761.

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., and Samhouri, J.F. 2023. Species redistribution creates unequal outcomes for multispecies fisheries under projected climate change. Science Advances 9(33): eadg5468. doi:10.1126/sciadv.adg5468.

Freshwater, C., Duguid, W., Juanes, F., and 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. doi:10.1139/cjfas-2022-0259.

Kochprapa, P., Savini, C., Ngoprasert, D., Savini, T., and Gale, G.A. 2023. Spatio-temporal dynamics of human−elephant conflict in a valley of pineapple plantations. Integrative Conservation. In press. doi:10.1002/inc3.23.

Stokkeland, M.M. 2023. Improved Stock Estimation for Iceland Scallops (Chlamys Islandica) in the Svalbard Area. MSc Thesis. University of Bergen. URL

Evans, R., English, P.A., Gauthier, S., and 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. doi:10.3389/fmars.2023.1031485.

Huynh, Q.C., and 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

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., and 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. Royal Society. doi:10.1098/rstb.2022.0191.

Ohyama, L., Booher, D.B., and 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. In press. doi:10.1111/1365-2435.14355.

Stompe, D.K., Moyle, P.B., Oken, K.L., Hobbs, J.A., and 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

Hebert, N. 2023. A Comparison of Spatio-temporal Species Distribution Modelling Frameworks Using Cucumaria frondosa as a Case Study. MSc thesis. http://hdl.handle.net/10222/82354

ICES. 2022. Benchmark workshop on Pandalus stocks (WKPRAWN). ICES Scientific Reports https://doi.org/10.17895/ices.pub.19714204.v1.

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

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., and 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

Bugaj, M., 2022. Species distribution and abundance of Bering Sea tunicates with implications for coastal food security. MSc thesis. Western Washington University. https://cedar.wwu.edu/wwuet/1148

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

Latour, R.J., Gartland, J. and Peterson, C.D. 2022. Ontogenetic niche structure and partitioning of immature sandbar sharks within the Chesapeake Bay nursery. Marine Biology, 169(6), pp.1-17. https://doi.org/10.1007/s00227-022-04066-3

Brodie, S., Smith, J.A., Muhling, B.A., Barnett, L.A., Carroll, G., Fiedler, P., Bograd, S.J., Hazen, E.L., Jacox, M.G., Andrews, K.S. and Barnes, C.L., 2022. Recommendations for quantifying and reducing uncertainty in climate projections of species distributions. Global Change Biology, 28(22), pp.6586-6601. https://doi.org/10.1111/gcb.16371

Watson, J., Edwards, A. and Auger-Méthé, M., 2022. A statistical censoring approach accounts for hook competition in abundance indices from longline surveys. Canadian Journal of Fisheries and Aquatic Sciences. In press. https://doi.org/10.1139/cjfas-2022-0159

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

Anderson, S.C., E.J. Ward, P.A. English, L.A.K. Barnett. 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.

Lindmark, M., S.C. Anderson, M. Gogina, M. Casini. 2022. Evaluating drivers of spatiotemporal individual condition of a bottom-associated marine fish. bioRxiv 2022.04.19.488709. https://doi.org/10.1101/2022.04.19.488709.

Essington, T.E. S.C. Anderson, L.A.K. Barnett, H.M. Berger, S.A. Siedlecki, E.J. Ward. 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. In press at Ecography. https://doi.org/10.1111/ecog.06249.

Commander, C.J.C, L.A.K. Barnett, E.J. Ward, S.C. Anderson, T.E. Essington. 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.

English, P., E.J. Ward, C.N. Rooper, R.E. Forrest, L.A. Rogers, K.L. Hunter, A.M. Edwards, B.M. Connors, S.C. Anderson. 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. Open access preprint: https://doi.org/10.32942/osf.io/b87ng.

Evans R., P.A. English , S.C. Anderson, S. Gauthier, C.L.K. Robinson. Factors affecting the seasonal distribution and biomass of E. pacifica and T. spinifera along the Pacific coast of Canada: A spatiotemporal modelling approach. 2021. PLOS ONE. 2021 May 14;16(5):e0249818. https://doi.org/10.1371/journal.pone.0249818.

Katzenberger, J. 2021. Habitat use and population viability of the Red Kite (Milvus milvus) in Germany. PhD Thesis. Georg-August-Universität Göttingen. [Research Gate URL]

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

Haggarty D.R., Q.C. Huynh, R.E. Forrest, S.C. Anderson, M.J. Bresch, E.A. Keppel. 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

Katzenberger, J. 2019. Modelling distribution and habitat suitability for the Red Kite Milvus milvus in Germany. Vogelwelt 139: 117–128. [PDF]

Anderson, S.C., E.A. Keppel, A.M. Edwards. 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. http://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2019/2019_041-eng.html