Readings

Barve, Narayani, Vijay Barve, Alberto Jim’enez-Valverde, Andr’es Lira-Noriega, Sean P. Maher, A. Townsend Peterson, Jorge Sober’on, and Fabricio Villalobos. 2011. “The Crucial Role of the Accessible Area in Ecological Niche Modeling and Species Distribution Modeling.” Ecological Modelling 222 (11). Elsevier BV: 1810–19. doi:10.1016/j.ecolmodel.2011.02.011.

Beale, Colin M., Jack J. Lennon, Jon M. Yearsley, Mark J. Brewer, and David A. Elston. 2010. “Regression Analysis of Spatial Data.” Ecology Letters 13 (2). Wiley-Blackwell: 246–64. doi:10.1111/j.1461-0248.2009.01422.x.

Beguin, Julien, Sara Martino, Havard Rue, and Steven G. Cumming. 2012. “Hierarchical Analysis of Spatially Autocorrelated Ecological Data Using Integrated Nested Laplace Approximation.” Methods in Ecology & Evolution 3 (5): 921–29. doi:10.1111/j.2041-210X.2012.00211.x.

Breiman, Leo. 2001. “Statistical Modeling: The Two Cultures (with Comments and a Rejoinder by the Author).” Statistical Science 16 (3). Institute of Mathematical Statistics: 199–231. doi:10.1214/ss/1009213726.

Crawley, Michael J. 2007. The R Book. Wiley-Blackwell. doi:10.1002/9780470515075.

Domingos, Pedro. 2016. “A Few Useful Things to Know About Machine Learning.” https://homes.cs.washington.edu/~pedrod/papers/cacm12.pdf.

Drake, John M. 2014. “Ensemble Algorithms for Ecological Niche Modeling from Presence-Background and Presence-Only Data.” Ecosphere 5 (6). Ecological Society of America: art76. doi:10.1890/es13-00202.1.

———. 2015. “Range Bagging: A New Method for Ecological Niche Modelling from Presence-Only Data.” J. R. Soc. Interface 12 (107). The Royal Society: 20150086. doi:10.1098/rsif.2015.0086.

Drake, John M., Christophe Randin, and Antoine Guisan. 2006. “Modelling Ecological Niches with Support Vector Machines.” Journal of Applied Ecology 43 (3): 424–32. doi:10.1111/j.1472-4642.2010.00725.x.

Elith, J., J. R. Leathwick, and T. Hastie. 2008. “A Working Guide to Boosted Regression Trees.” Journal of Animal Ecology 77 (4). Wiley-Blackwell: 802–13. doi:10.1111/j.1365-2656.2008.01390.x.

Elith, Jane, and John R. Leathwick. 2009. “Species Distribution Models: Ecological Explanation and Prediction Across Space and Time.” Annu. Rev. Ecol. Evol. Syst. 40 (1). Annual Reviews: 677–97. doi:10.1146/annurev.ecolsys.110308.120159.

Elith, Jane, Steven J. Phillips, Trevor Hastie, Miroslav Dudik, Yung En Chee, and Colin J. Yates. 2010. “A Statistical Explanation of MaxEnt for Ecologists.” Diversity and Distributions 17 (1): 43–57. doi:10.1111/j.1472-4642.2010.00725.x.

Fawcett, Tom. 2006. “An Introduction to ROC Analysis.” Pattern Recognition Letters 27 (8). Elsevier BV: 861–74. doi:10.1016/j.patrec.2005.10.010.

Franklin, Janet. 2009. Mapping Species Distributions. Cambridge University Press (CUP). doi:10.1017/cbo9780511810602.

Hijmans, Robert J., Susan E. Cameron, Juan L. Parra, Peter G. Jones, and Andy Jarvis. 2005. “Very High Resolution Interpolated Climate Surfaces for Global Land Areas.” International Journal of Climatology 25 (15). Wiley-Blackwell: 1965–78. doi:10.1002/joc.1276.

Hijmans, Robert J., Steven Phillips, John Leathwick, and Jane Elith. 2013. Dismo: Species Distribution Modeling. https://CRAN.R-project.org/package=dismo.

Hutchinson, G. Evelyn. 1957. “Concluding Remarks.” Cold Spring Harbor Symposium on Quantitative Biology 22: 415–27. http://symposium.cshlp.org/content/22/415.

Kearney, M., S. J. Simpson, D. Raubenheimer, and B. Helmuth. 2010. “Modelling the Ecological Niche from Functional Traits.” Philosophical Transactions of the Royal Society B: Biological Sciences 365 (1557). The Royal Society: 3469–83. doi:10.1098/rstb.2010.0034.

Kelling, S. 2009. Data-intensive science: A new paradigm for biodiversity studies. Bioscience 59:607-613. doi:10.1525/bio.2009.59.7.12.

Leibold, Matthew A. 1995. “The Niche Concept Revisited: Mechanistic Models and Community Context.” Ecology 76 (5). JSTOR: 1371. doi:10.2307/1938141.

Peterson, A. Townsend, Jorge Soberon, Richard G. Pearson, Robert P. Anderson, Enrique Martinez-Meyer, Miguel Nakamura, and Miguel B. Araujo. 2011. Ecological Niches and Geographic Distributions. Princeton, NJ: Princeton University Press. http://press.princeton.edu/titles/9641.html.

Phillips, Steven J., Miroslav Dudik, and Robert E. Shapire. 2004. “A Maximum Entropy Approach to Species Distribution Modeling.” In Proceedings of the Twenty-First International Conference on Machine Learning, edited by Carla Brodley, 665–62. https://www.cs.princeton.edu/~schapire/papers/maxent_icml.pdf.

Phillips, Steven J., Miroslav Dudik, Jane Elith, Catherine H. Graham, Anthony Lehman, John Leathwick, and Simon Ferrier. 2009. “Sample Selection Bias and Presence-Only Distribution Models: Implications for Background and Pseudo-Absence Data.” Ecological Applications 19: 181–97. doi:10.1890/07-2153.1.

Pulliam, H.R. 2000. “On the Relationship Between Niche and Distribution.” Ecology Letters 3 (4). Wiley-Blackwell: 349–61. doi:10.1046/j.1461-0248.2000.00143.x.

Renner, Ian W., and David I. Warton. 2013. “Equivalence of MAXENT and Poisson Point Process Models for Species Distribution Modeling in Ecology.” Biometrics 69 (1). Wiley-Blackwell: 274–81. doi:10.1111/j.1541-0420.2012.01824.x.

Royle, J. Andrew, Richard B. Chandler, Charles Yackulic, and James D. Nichols. 2012. “Likelihood Analysis of Species Occurrence Probability from Presence-Only Data for Modelling Species Distributions.” Methods in Ecology and Evolution 3 (3). Wiley-Blackwell: 545–54. doi:10.1111/j.2041-210x.2011.00182.x.

Vel’asquez-Tibat’a, Jorge, Catherine H. Graham, and Stephan B. Munch. 2015. “Using Measurement Error Models to Account for Georeferencing Error in Species Distribution Models.” Ecography, May. Wiley-Blackwell, n/a–/a. doi:10.1111/ecog.01205.

Venables, W. N., and B. D. Ripley. 2002. Modern Applied Statistics with S. Springer New York. doi:10.1007/978-0-387-21706-2.

Ward, Gill, Trevor Hastie, Simon Barry, Jane Elith, and John R. Leathwick. 2008. “Presence-Only Data and the EM Algorithm.” Biometrics 65 (2). Wiley-Blackwell: 554–63. doi:10.1111/j.1541-0420.2008.01116.x.