Chapter 6 Species Distribution Modeling

As usual, course materials not in the github repository can be found in the course Google Drive course-materials folder. Everything will of course be linked to here on the website.

09/29

Guest Lecture on TMB by Dr. Eric Ward, NOAA Northwest Fisheries Science Center.
(Class fully remote via Zoom)

Link to 9/29 materials

Reading

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

Additional readings on these topics

Kleisner, K.M., Fogarty, M.J., McGee, S., Hare, J.A., Moret, S., Perretti, C.T. and Saba, V.S., 2017. Marine species distribution shifts on the US Northeast Continental Shelf under continued ocean warming. Progress in Oceanography, 153, pp.24-36.

Nye, J.A., Link, J.S., Hare, J.A. and Overholtz, W.J., 2009. Changing spatial distribution of fish stocks in relation to climate and population size on the Northeast United States continental shelf. Marine Ecology Progress Series, 393, pp.111-129.

Carroll, G., Holsman, K.K., Brodie, S., Thorson, J.T., Hazen, E.L., Bograd, S.J., Haltuch, M.A., Kotwicki, S., Samhouri, J., Spencer, P. and Willis‐Norton, E., 2019. A review of methods for quantifying spatial predator–prey overlap. Global Ecology and Biogeography, 28(11), pp.1561-1577.

Thorson, J.T., Barnett, L.A.K., 2017. Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat. ICES J. Mar. Sci. 74, 1311–1321.

Thorson, J.T., Ianelli, J.N., Larsen, E., Ries, L., Scheuerell, M.D., Szuwalski, C., and Zipkin, E. 2016. Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. Glob. Ecol. Biogeogr. 25(9): 1144–1158. doi:10.1111/geb.12464.