This is a repository for useful or seminal papers in spatial\/temporal ecological modeling that are likely of use to marine mammalogists.\u00a0 If you have a favorite paper that isn’t listed here, please send it to Mark Baumgartner (mbaumgartner@whoi.edu<\/a>), let us know which category it belongs in, and we’ll post it here.<\/p>\n Austin, M.P. 2002. Spatial prediction of species distribution: an interface between ecological theory and statistical modelling.<\/a> Ecological Modelling 157:101-118.<\/p>\n Austin, M. 2007. Species distribution models and ecological theory: A critical assessment and some possible new approaches.<\/a> Ecological Modelling 200:1\u201319.<\/p>\n Guisan A. and N.E. Zimmermann. 2000. Predictive habitat distribution models in ecology.<\/a> Ecological Modelling 135:147\u2013186.<\/p>\n Guisan, A. and W. Thuiller. 2005. Predicting species distribution: offering more than simple habitat models.<\/a> Ecology Letters 8:993\u20131009.<\/p>\n Guisan, A., A. Lehmann, S. Ferrier, M. Austin, J. MC. C. Overton, R. Aspinall, and T. Hastie. 2006. Making better biogeographical predictions of species\u2019 distributions.<\/a> Journal of Applied Ecology 43:386\u2013392.<\/p>\n Redfern, J.V., M.C. Ferguson, E.A. Becker, K.D. Hyrenbach, C. Good, J. Barlow, K. Kaschner, M.F. Baumgartner, K.A. Forney, L.T. Ballance, P. Fauchald, P. Halpin, T. Hamazaki, A.J. Pershing, S.S. Qian, A. Read, S.B. Reilly, L. Torres, and F. Werner.\u00a0 2006.\u00a0 Techniques for cetacean-habitat modeling: A review.<\/a> Marine Ecology Progress Series 310:271-295.<\/p>\n Guisan, A., T.C. Edwards, Jr., and T. Hastie. 2002. Generalized linear and generalized additive models in studies of species distributions: setting the scene.<\/a> Ecological Modelling 157:89-100.<\/p>\n Pearce, J., and S. Ferrier. 2000. Evaluating the predictive performance of habitat models developed using logistic regression.<\/a> Ecological Modelling 133:225\u2013245.<\/p>\n Ecological Modelling, Volume 157, Issues 2-3, Pages 89-348 (30 November 2002) Applications<\/em><\/p>\n Gregr, E.J. and A.W. Trites. 2001. Predictions of critical habitat for five whale species in the waters of coastal British Columbia.<\/a> Canadian Journal of Fisheries and Aquatic Sciences 58:1265\u20131285.<\/p>\n Tittensor, D.P., A.R. Baco, P.E. Brewin, M.R. Clark, M. Consalvey, J. Hall-Spencer, A.A. Rowden, T. Schlacher, K.I. Stocks, and A.D. Rogers.\u00a0 2009.\u00a0 Predicting global habitat suitability for stony corals on seamounts.<\/a> Journal of Biogeography 36:1111\u20131128.<\/p>\n Methods<\/em><\/p>\n Carpenter, G., A.N. Gillison, and J. Winter. 1993. DOMAIN: a flexible modelling procedure for mapping potential distributions of plants and animals.<\/a> Biodiversity and Conservation 2:667-680.<\/p>\n Hengla, T., H. Sierdsema, A. Radovi\u0107, and A. Dilod. Spatial prediction of species\u2019 distributions from occurrence-only records: combining point pattern analysis, ENFA and regression-kriging.<\/a>\u00a0 Ecological Modelling. in press.\u00a0 (see website<\/a>)<\/em><\/p>\n Hirzel, A.H., J. Hausser, D. Chessel, and N. Perrin. 2002. Ecological-niche factor analysis: how to compute habitat-siutability maps without absence data?<\/a> Ecology 83:2027\u20132036.<\/p>\n Kaschner, K., R. Watson, A.W. Trites, and D. Pauly. 2006. Mapping world-wide distributions of marine mammal species using a relative environmental suitability (RES) model.<\/a> Marine Ecology Progress Series 316:285\u2013310.<\/p>\n Phillips, S.J. , R.P. Anderson, and R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions.<\/a> Ecological Modelling 190:231\u2013259.<\/p>\n Phillips, S.J. and M. Dudik. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation.<\/a> Ecography 31:161-175.<\/p>\n Dangers Lozier, J.D., P. Aniello, and M.J. Hickerson. 2009. Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling.<\/a> Journal of Biogeography 36:1623\u20131627.<\/p>\n Phillips, S.J., M. Dudik, J. Elith, C.H. Graham, A. Lehmann, J. Leathwick, and S. Ferrier. 2009. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data.<\/a> Ecological Applications 19:181\u2013197.<\/p>\n Performance evaluation<\/em><\/p>\n Elith, J., C.H. Graham, R.P. Anderson, M. Dudik, S. Ferrier, A. Guisan, R.J. Hijmans, F. Huettmann, J.R. Leathwick, A. Lehmann, J. Li, L.G. Lohmann, B.A. Loiselle, G. Manion, C. Moritz, M. Nakamura, Y. Nakazawa, J. McC. Overton, A.T. Peterson, S.J. Phillips, K.S. Richardson, R. Scachetti-Pereira, R.E. Schapire, J. Soberon, S. Williams, M.S. Wisz, and N.E. Zimmermann. 2006. Novel methods improve prediction of species\u2019 distributions from occurrence data.<\/a> Ecography 29:129-151.<\/p>\n Farber, O. and R. Kadmon. 2003. Assessment of alternative approaches for bioclimatic modeling with special emphasis on the Mahalanobis distance.<\/a> Ecological Modelling 160:115-130.<\/p>\n Gregr, E.J. and A.W. Trites. 2008. A novel presence-only validation technique for improved Steller sea lion Eumetopias jubatus<\/em> critical habitat descriptions.<\/a> Marine Ecology Progress Series 365:247\u2013261.<\/p>\n Hirzel, A.H. , G. Le Lay, V. Helfer, C. Randin, and A. Guisan. 2006. Evaluating the ability of habitat suitability models to predict species presences.<\/a> Ecological Modelling 199:142-152.<\/p>\n Aarts, G., M. MacKenzie, B. McConnell, M. Fedak and J. Matthiopoulos. 2008. Estimating space-use and habitat preference from wildlife telemetry data.<\/a> Ecography 31: 140-160.<\/p>\n Austin, D., W.D. Bowen, and J.I. McMillan. 2004. Intraspecific variation in movement patterns: modeling individual behaviour in a large marine predator.<\/a> Oikos 105:15-30.<\/p>\n Bailey, H., B.R. Mate, D.M. Palacios, L. Irvine, S.J. Bograd, and D.P. Costa. 2009. Behavioural estimation of blue whale movements in the Northeast Pacific from state-space model analysis of satellite tracks.<\/a> Endangered Species Research.<\/p>\n Bailey, H., G. Shillinger, D. Palacios, S. Bograd, J. Spotila, F. Paladino, and B. Block. 2008. Identifying and comparing phases of movement by leatherback turtles using state-space models.<\/a> Journal of Experimental Marine Biology and Ecology 356:128-135.<\/p>\n Baumgartner, M.F. and B.R. Mate.\u00a0 2005.\u00a0 Summer and fall habitat of North Atlantic right whales (Eubalaena glacialis<\/em>) inferred from satellite telemetry.<\/a> Canadian Journal of Fisheries and Aquatic Sciences 62:527-543.<\/p>\n Breed, G.A., I.D. Jonsen, R.A. Myers, W.D. Bowen, and M.L. Leonard. 2009. Sex-specific, seasonal foraging tactics of adult grey seals (Halichoerus grypus<\/em>) revealed by state-space analysis.<\/a> Ecology 90:3209-3221.<\/p>\n Eckert, S.A., J.E. Moore, D.C. Dunn, R.S. van Buiten, K.L. Eckert, and P.N. Halpin. 2008. Modeling loggerhead turtle movement in the Mediterranean: importance of body size and oceanography.<\/a> Ecological Applications 18:290-308.<\/p>\n Freitas, C., K.M. Kovacs, C. Lydersen, and R.A. Ims. 2008. A novel method for quantifying habitat selection and predicting habitat use.<\/a> Journal of Applied Ecology 45:1213-1220.<\/p>\n Gurarie, E., R. Andrews, and K.L. Laidre. 2009. A novel method for identifying behavioral changes in animal movement data.<\/a> Ecology Letters 12:395-408.<\/p>\n Johnson, D.S., J.M. London, M.A. Lea, and J.W. Durban. 2008. Continuous-time correlated random walk model for animal telemetry data.<\/a> Ecology 89:1208-1215.<\/p>\n Jonsen, I.D., J.M. Fleming, and R.A. Myers. 2005. Robust state-space modeling of animal movement data.<\/a> Ecology 86:2874-2880.<\/p>\n Jonsen, I.D., R.A. Myers, and M.C. James. 2007. Identifying leatherback turtle foraging behaviour from satellite-telemetry using a switching state-space model.<\/a> Marine Ecology Progress Series 337:255-264.<\/p>\n Laidre K.L., M.P. Heide-J\u00f8rgensen, M.L. Lodgson, R.C. Hobbs, R. Dietz, and G.R. VanBlaricom. 2004. Fractal analysis of narwhal space use patterns.<\/a> Zoology 107:3-11.<\/p>\n Laidre K.L., M.P. Heide-J\u00f8rgensen, M.L. Logdson, R.C. Hobbs, P. Heagerty, R. Dietz, O.A. J\u00f8rgensen, and M.A. Treble. 2004. Seasonal narwhal habitat associations in the high Arctic.<\/a> Marine Biology 145:821-831.<\/p>\n Patterson, T.A., L. Thomas, C. Wilcox, O. Ovaskainen, and J. Matthiopoulos. 2008. State-space models of individual animal movement.<\/a> Trends in Ecology and Evolution 23:87-94.<\/p>\n Schick, R.S., S.R. Loarie, F. Colchero, B.D. Best, A. Boustany, D.A. Conde, P.N. Halpin, L.N. Joppa, C.M. McClellan, and J.S. Clark. 2008. Understanding movement data and movement processes: current and emerging directions.<\/a> Ecology Letters 11:1338\u20131350.<\/p>\n Tremblay, Y., S.A. Shaffer, S.L. Fowler, C.E. Kuhn, B.I. McDonald, M.J. Weise, C.A. Bost, H. Weimerskirch, D.E. Crocker, M.E. Goebel, and D.P. Costa. 2006. Interpolation of animal tracking data in a fluid environment.<\/a> Journal of Experimental Biology 209:128-140.<\/p>\n Tremblay, Y., A.J. Roberts, and D.P. Costa. 2007. Fractal landscape method: an alternative approach to measuring area-restricted searching behavior.<\/a> Journal of Experimental Biology 210:935-945.<\/p>\n Tremblay, Y., P.W. Robinson, and D.P. Costa. 2009. A parsimonious approach to modeling animal movement data.<\/a>\u00a0 PLoS ONE 4:e4711. doi:4710.1371\/journal.pone.0004711.<\/p>\n Weng, K.C., D.G. Foley, J.E. Ganong, C. Perle, G.L. Shillinger, and B.A. Block. 2008. Migration of an upper trophic level predator, the salmon shark Lamna ditropis<\/em>, between distant ecoregions.<\/a> Marine Ecology Progress Series 372:253-264.<\/p>\n Whitehead, H., A. Coakes, N. Jaquet, and S. Lusseau. 2008. Movements of sperm whales in the tropical Pacific.<\/a> Marine Ecology Progress Series 361:291-300.<\/p>\n Carl, G. and I. K\u00fchn. 2007. Analyzing spatial autocorrelation in species distributions using Gaussian and logit models.<\/a> Ecological Modelling 207:159\u2013170.<\/p>\n Dormann, C.F. 2007. Effects of incorporating spatial autocorrelation into the analysis of species distribution data.<\/a> Global Ecology and Biogeography 16:129\u2013138.<\/p>\n Dormann, C. F., J.M. McPherson, M.B. Ara\u00fajo, R. Bivand, J. Bolliger, G. Carl, R.G. Davies, A. Hirzel, W. Jetz, W.D. Kissling, I. K\u00fchn, R. Ohlem\u00fcller, P.R. Peres-Neto, B. Reineking, B. Schr\u00f6der, F.M. Schurr, and R. Wilson. 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review.<\/a> Ecography 30:609-628.<\/p>\n Betts, M.G., L.M. Ganio, M.M.P. Huso, N.A. Som, F. Huettmann, J. Bowman, and B.A. Wintle. 2009. Comment on \u2018\u2018Methods to account for spatial autocorrelation in the analysis of species distributional data: a review\u2019\u2019<\/a> Ecography 32:374-378.<\/p>\n Dormann, C.F. 2009. Response to comment on \u201cMethods to account for spatial autocorrelation in the analysis of species distributional data: a review\u201d<\/a> Ecography 32: 379-381.<\/p>\n Millar, R.B. and M.J. Anderson. 2004. Remedies for pseudoreplication.<\/a> Fisheries Research 70:397\u2013407.<\/p>\n Segurado, P., M.B. Ara\u00fajo, and W.E. Kunin. 2006. Consequences of spatial autocorrelation for niche-based models.<\/a> Journal of Applied Ecology 43:433\u2013444.<\/p>\n Boyce, M.S., P.R. Vernier, S.E. Nielsen, and F.K.A. Schmiegelow. 2002. Evaluating resource selection functions.<\/a> Ecological Modelling 157:281-300.<\/p>\n Lobo, J.M., A. Jim\u00e9nez-Valverde, and R. Real. 2008. AUC: a misleading measure of the performance of predictive distribution models.<\/a> Global Ecology and Biogeography 17:145\u2013151.<\/p>\n Peterson, A.T., M. Papes, and J. Sober\u00f3n. 2008. Rethinking receiver operating characteristic analysis applications in ecological niche modeling.<\/a> Ecological Modelling 213:63\u201372.<\/p>\n Rykiel, E.J., Jr. 1996. Testing ecological models: the meaning of validation.<\/a> Ecological Modelling 90:229-244.<\/p>\n MacLeod, C.D., L. Mandleberg, C. Schweder, S.M. Bannon, and G.J. Pierce. 2008. A comparison of approaches for modelling the occurrence of marine animals.<\/a> Hydrobiologia 612:21\u201332.<\/p>\n Praca, E., A. Gannier, K. Das, and S. Laran. 2009. Modelling the habitat suitability of cetaceans: Example of the sperm whale in the northwestern Mediterranean Sea.<\/a> Deep-Sea Research I 56:648\u2013657.<\/p>\n Hamazaki, T. 2002. Spatiotemporal prediction models of cetacean habitats in the mid-western North Atlantic Ocean (from Cape Hatteras, North Carolina, U.S.A. to Nova Scotia, Canada).<\/a> Marine Mammal Science 18:920-939.<\/p>\n Gregr, E.J. 2004. Modeling species-habitat relationships in the marine environment: a comment on Hamazaki (2002).<\/a> Marine Mammal Science 20:353-355.<\/p>\n Hamazaki, T. 2004. Modeling species-habitat relationship in the marine environment: a response to Gregr (2004).<\/a> Marine Mammal Science 20:356-358.<\/p>\n Guisan, A., C.H. Graham, J. Elith, F. Huettmann and the NCEAS Species Distribution Modelling Group. 2007. Sensitivity of predictive species distribution models to change in grain size.<\/a> Diversity and Distributions 13:332\u2013340.<\/p>\nReview and general papers<\/h3>\n
Generalized linear and additive models<\/h3>\n
\n<\/a>
\nFisheries Research, Volume 70, Issues 2-3, Pages 137-428 (December 2004)
\n<\/a>
\nEcological Modelling, Volume 199, Issue 2, Pages 129-216 (16 November 2006)<\/a><\/p>\nPresence-only techniques<\/h3>\n
\n<\/em><\/p>\nMovement analyses<\/h3>\n
Autocorrelation and pseudoreplication<\/h3>\n
Model evaluation<\/h3>\n
Model comparisons<\/h3>\n
Some exciting and useful controversy in marine mammal habitat modeling!<\/h3>\n
Scale and resolution<\/h3>\n
Other<\/h3>\n