Maximum entropy modeling of species geographic distributions

Ecological Modelling

Volumn 190, Issue 3-4, 2006, Pages 231-259

  Phillips, Steven J ^a   Anderson, Robert P ^b,c   Schapire, Robert E ^d  

^a AT AND T LABS RESEARCH   (United States)

^b CITY COLLEGE OF NEW YORK   (United States)

^c DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^d Princeton University   (United States)

Author keywords

Distribution; Maximum entropy; Modeling; Niche; Range

Indexed keywords

DATABASE SYSTEMS; ENTROPY; LEARNING SYSTEMS;

MAXIMUM ENTROPY; NICHE; RANGE;

BIODIVERSITY;

ENTROPY; GEOGRAPHICAL DISTRIBUTION; NICHE; POPULATION MODELING; PREDICTION;

BRADYPUS VARIEGATUS; EDENTATA; MAMMALIA; MICRORYZOMYS MINUTUS; MURIDAE; RODENTIA;

EID: 27944446350     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2005.03.026     Document Type: Article

References (92)

1. R.P. Anderson Real vs. artefactual absences in species distributions: tests for Oryzomys albigularis(Rodentia: Muridae) in Venezuela J. Biogeogr. 30 2003 591 605
2. R.P. Anderson, M. Gómez-Laverde, and A.T. Peterson Geographical distributions of spiny pocket mice in South America: insights from predictive models Global Ecol. Biogeogr. 11 2002 131 141
3. R.P. Anderson, and C.O. Handley Jr. A new species of three-toed sloth (Mammalia: Xenarthra) from Panamá, with a review of the genus Bradypus Proceedings of the Biological Society of Washington 114 2001 1 33
4. R.P. Anderson, D. Lew, and A.T. Peterson Evaluating predictive models of species' distributions: criteria for selecting optimal models Ecol. Model. 162 2003 211 232
5. R.P. Anderson, and E. Martínez-Meyer Modeling species' geographic distributions for preliminary conservation assessments: an implementation with the spiny pocket mice (Heteromys) of Ecuador Biol. Conser. 116 2004 167 179
6. R.P. Anderson, A.T. Peterson, and M. Gómez-Laverde Using niche-based GIS modeling to test geographic predictions of competitive exclusion and competitive release in South American pocket mice Oikos 98 2002 3 16
7. S. Anderson Problems in the retrieval of information from natural history museums Proceedings of the Conference on Data Acquisition and Processing in Biology and Medicine 1963 Pergamon Press New York 55 57
8. I. Aoki Holological study of lakes from an entropy viewpoint-Lake Mendota Ecol. Model. 45 1989 81 93
9. R. Aspinall An inductive modeling procedure based on Bayes' theorem for analysis of pattern in spatial data Int. J. Geogr. Inform. Syst. 6 2 1992 105 121
10. M. Austin Spatial prediction of species distribution: an interface between ecological theory and statistical modelling Ecol. Model. 157 2002 101 118
11. R.J. Baker, C.J. Phillips, R.D. Bradley, J.M. Burns, D. Cooke, G.F. Edson, D.R. Haragan, C. Jones, R.R. Monk, J.T. Montford, D.J. Schmidly, and N.C. Parker Bioinformatics, museums, and society: integrating biological data for knowledge-based decisions Occasional Papers Museum Texas Tech Univ. 187 1998 1 4
12. A.L. Berger, S.A. Della Pietra, and V.J. Della Pietra A maximum entropy approach to natural language processing Comput. Linguist. 22 1 1996 39 71
13. F.A. Bisby The quiet revolution: biodiversity informatics and the internet Science 289 2000 2309 2312
14. J.H. Brown, and M.V. Lomolino Biogeography 2nd ed. 1998 Sinauer Associates Sunderland, Massachusetts
15. J.R. Busby A biogeographical analysis of Nothofagus cunninghamii (Hook.) Oerst. in southeastern Australia Aust. J. Ecol. 11 1986 1 7
16. M.D. Carleton, and G.G. Musser Systematic studies of oryzomyine rodents (Muridae, Sigmodontinae): a synopsis of Microryzomys Bull. Am. Museum Nat. History 119 1989 1 83
17. G. Carpenter, A.N. Gillison, and J. Winter DOMAIN: a flexible modeling procedure for mapping potential distributions of plants, animals Biodivers. Conserv. 2 1993 667 680
18. F. Corsi, J. de Leeuw, and A. Skidmore Modeling species distribution with GIS L. Boitani T. Fuller Research Techniques in Animal Ecology 2000 Columbia University Press New York 389 434
19. F. Corsi, E. Duprè, and L. Boitani A large-scale model of wolf distribution in Italy for conservation planning Conserv. Biol. 13 1999 150 159
20. S. Della Pietra, V. Della Pietra, and J. Lafferty Inducing features of random fields IEEE Trans. Pattern Anal. Mach. Intell. 19 4 1997 1 13
21. E.R. DeLong, D.M. DeLong, and D.L. Clarke-Pearson Comparing the areas under two or more correlated receiver operating characteristic curves: a non-parametric approach Biometrics 44 1988 837 845
22. E. Dinerstein, D.M. Olson, D.J. Graham, A.L. Webster, S.A. Primm, M.P. Bookbinder, and G. Ledec Ecoregions of Latin America and the Caribbean (inset map) A Conservation Assessment of the Terrestrial Ecoregions of Latin America and the Caribbean 1995 The World Bank Washington, DC
23. M. Dudík, S.J. Phillips, and R.E. Schapire Performance guarantees for regularized maximum entropy density estimation Proceedings of the 17th Annual Conference on Computational Learning Theory 2004 ACM Press New York 655 662
24. J.F. Eisenberg, and K.H. Redford Mammals of the Neotropics. vol. 3, the central Neotropics: Ecuador, Peru, Bolivia, Brazil 1999 University of Chicago Press Chicago
25. J. Elith Quantitative methods for modeling species habitat: comparative performance and an application to Australian plants S. Ferson M. Burgman Quantitative Methods for Conservation Biology 2002 Springer-Verlag New York 39 58
26. L.H. Emmons Neotropical Rainforest Mammals: A Field Guide 2nd ed. 1997 University of Chicago Press Chicago
27. R. Engler, A. Guisan, and L. Rechsteiner An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data J. Appl. Ecol. 41 2004 263 274
28. Fawcett, T., 2003. ROC graphs: notes and practical considerations for data mining researchers. Technical Report HPL-2003-4, Palo Alto, CA: HP Laboratories.
29. Ferrier, S., Watson, G., 1996. An evaluation of the effectiveness of environmental surrogates and modelling techniques in predicting the distribution of biological diversity. Canberra, Australia: NSW National Parks and Wildlife Service. http://www. deh.gov.au/biodiversity/publications/technical/surrogates.
30. S. Ferrier, G. Watson, J. Pearce, and M. Drielsma Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales. 1. Species-level modeling Biodivers. Conserv. 11 2002 2275 2307
31. A.H. Fielding, and J.F. Bell A review of methods for the assessment of prediction errors in conservation presence/absence models Env. Conserv. 24 1997 38 49
32. E. Gouvêa, and F.D. de Ávila Pires Mamíferos do Parque Nacional do Itatiaia Revista Científica do Centro Universitário do Barra Mansa, UBM 1 2 1999 11 26
33. C.H. Graham, S. Ferrier, F. Huettman, C. Moritz, and A.T. Peterson New developments in museum-based informatics and applications in biodiversity analysis Trends Ecol. Evol. 19 9 2004 497 503
34. A. Guisan, T.C. Edwards, and T. Hastie Jr. Generalized linear and generalized additive models in studies of species distributions: setting the scene Ecol. Model. 157 2002 89 100
35. A. Guisan, and N.E. Zimmerman Predictive habitat distribution models in ecology Ecol. Model. 135 2000 147 186
36. J. Hanley, and B. McNeil The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 143 1982 29 36
37. J. Hanley, and B. McNeil A method of comparing the areas under receiver operating characteristic curves derived from the same cases Radiology 148 1983 839 843
38. P. Hershkovitz Report on some sigmodontine rodents collected in southeastern Brazil with descriptions of a new genus and six new species Bonner zoologische Beiträge 47 1998 193 256
39. A.H. Hirzel, J. Hausser, D. Chessel, and N. Perrin Ecological-niche factor analysis: how to compute habitat-suitability maps without absence data? Ecology 87 2002 2027 2036
40. L. Holdridge, W. Grenke, W. Hatheway, T. Liang, and J. Tosi Jr. Forest Environments In Tropical Life Zones: A Pilot Study 1971 Pergamon Press New York
41. G.E. Hutchinson Concluding remarks Cold Spring Harbor Symposia on Quantitative Biology 22 1957 415 427
42. E.T. Jaynes Information theory and statistical mechanics Phys. Rev. 106 1957 620 630
43. E.T. Jaynes Notes on present status and future prospects W.T. Grandy L.H. Schick Jr. Maximum Entropy and Bayesian Methods 1990 Kluwer Dordrecht, The Netherlands 1 13
44. J.R. Jensen Introductory Digital Image Processing, A Remote Sensing Perspective 1996 Prentice Hall Upper Saddle River, NJ
45. L. Joseph, and D.R.B. Stockwell Climatic modeling of the distribution of some Pyrrhura parakeets of northwestern South America with notes on their systematics and special reference to Pyrrhura caeruleiceps Todd, 1947 Ornitología Neotropical 13 2002 1 8
46. J.W. Karl, L.K. Svancara, P.J. Heglund, N.M. Wright, and J.M. Scott Species commonness and the accuracy of habitat-relationship models J.M. Scott P.J. Heglund M.L. Morrison J.B. Haufler M.G. Raphael W.A. Wall F.B. Samson Predicting Species Occurrences: Issues of Accuracy and Scale 2002 Island Press Washington, DC 573 580
47. B.G. Mackey, and D.B. Lindenmayer Towards a hierarchical framework for modelling the spatial distribution of animals J. Biogeogr. 28 2001 1147 1166
48. A. McPherson A biogeographical analysis of factors influencing the distribution of Costa Rican rodents Brenesia 23 1985 97 273
49. Minitab Minitab, Release 12.1 1998 Minitab, Inc. State College, PA
50. M. New, M. Hulme, and P. Jones Representing twentieth-century space-time climate variability. Part 1. Development of a 1961-90 mean monthly terrestrial climatology J. Climate 12 1999 829 856. Data available at http://ipcc-ddc.cru. uea.ac.uk/cru_data/examine/cru_climate.html
51. A.Y. Ng, and M.I. Jordan On discriminative versus generative classifiers: a comparison of logistic regression and naive Bayes Adv. Neural Inform. Process. Syst. 14 2001 605 610
52. H. Nix A biogeographic analysis of Australian elapid snakes Atlas of Elapid Snakes of Australia 1986 Australian Government Publishing Service Canberra, Australia 4 15
53. B.D. Patterson, G. Ceballos, W. Sechrest, M.F. Tognelli, T. Brooks, L. Luna, P. Ortega, I. Salazar, and B.E. Young Digital Distribution Maps of the Mammals of the Western Hemisphere, Version 1.0 2003 NatureServe Arlington, VA
54. R.A. Paynter Jr. Ornithological Gazetteer of Venezuela 1982 Museum of Comparative Zoology, Harvard University Cambridge, MA
55. R.G. Pearson, T.P. Dawson, and C. Lin Modelling species distributions in Britain: a hierarchical integration of climate and land-cover data Ecography 27 2004 285 298
56. R. Pérez-Hernández, G. Colomine, and G. Villarroel Los museos de historia natural vinculados con la universidad venezolana y sus perspectivas hacia el siglo XXI Acta Científica Venezolana 48 1997 177 181
57. A.T. Peterson, and K.P. Cohoon Sensitivity of distributional prediction algorithms to geographic data completeness Ecol. Model. 117 1999 154 164
58. A.T. Peterson, and R.D. Holt Niche differentiation in Mexican birds: using point occurrences to detect ecological innovation Ecol. Lett. 6 2003 774 782
59. A.T. Peterson, and D.A. Kluza New distributional modeling approaches for gap analysis Anim. Conserv. 6 2003 47 54
60. A.T. Peterson, and C.R. Robins Using ecological-niche modeling to predict barred owl invasions with implications for spotted owl conservation Conserv. Biol. 17 2003 1161 1165
61. A.T. Peterson, and J. Shaw Lutzomyia vectors for cutaneous leishmaniasis in southern Brazil: ecological niche models, predicted geographic distribution, and climate change effects Int. J. Parasitol. 33 2003 919 931
62. A.T. Peterson, J. Soberón, and V. Sánchez-Cordero Conservatism of ecological niches in evolutionary time Science 285 1999 1265 1267
63. S.J. Phillips, M. Dudík, and R.E. Schapire A maximum entropy approach to species distribution modeling Proceedings of the 21st International Conference on Machine Learning 2004 ACM Press New York 655 662
64. W.F. Ponder, G.A. Carter, P. Flemons, and R.R. Chapman Evaluation of museum collection data for use in biodiversity assessment Conserv. Biol. 15 2001 648 657
65. F.J. Provost, and T. Fawcett Analysis and visualization of classifier performance: comparison under imprecise class and cost distributions Knowledge Discovery and Data Mining 1997 ACM Press New York 43 48
66. H.R. Pulliam On the relationship between niche and distribution Ecol. Lett. 3 2000 349 361
67. Ratnaparkhi, A., 1998. Maximum entropy models for natural language ambiguity resolution. Ph.D. Thesis, University of Pennsylvania, Philadelphia, PA.
68. S. Reddy, and L.M. Dávalos Geographical sampling bias and its implications for conservation priorities in Africa J. Biogeogr. 30 2003 1719 1727
69. T. Root Environmental factors associated with avian distributional boundaries J. Biogeogr. 15 1988 489 505
70. E. Schneider, and J. Kay Life as a manifestation of the second law of thermodynamics Math. Comput. Model. 19 6-8 1994 25 48
71. J.M. Scott P.J. Heglund M.L. Morrison J.B. Haufler M.G. Raphael W.A. Wall F.B. Samson Predicting Species Occurrences: Issues of Accuracy and Scale 2002 Island Press Washington, DC
72. C.E. Shannon A mathematical theory of communication Bell Syst. Tech. J. 27 1948 379 423 623-656
73. J. Soberón Linking biodiversity information sources Trends Ecol. Evol. 14 1999 291
74. J. Soberón, and A.T. Peterson Biodiversity informatics: managing and applying primary biodiversity data Philos. Trans. Royal Soc. Lond. B 359 2004 689 698
75. B.R. Stein, and J. Wieczorek Mammals of the world: MaNIS as an example of data integration in a distributed network environment Biodivers. Inform. 1 1 2004 14 22
76. D. Stockwell, and D. Peters The GARP modeling system: problems and solutions to automated spatial prediction Int. J. Geograph. Inform. Sci. 13 1999 143 158
77. D.R.B. Stockwell, and I.R. Noble Induction of sets of rules from animal distribution data: a robust and informative method of data analysis Math. Comput. Simul. 33 1992 385 390
78. D.R.B. Stockwell, and A.T. Peterson Controlling bias in biodiversity data J.M. Scott P.J. Heglund M.L. Morrison J.B. Haufler M.G. Raphael W.A. Wall F.B. Samson Predicting Species Occurrences: Issues of Accuracy and Scale 2002 Island Press Washington, DC 537 546
79. D.R.B. Stockwell, and A.T. Peterson Effects of sample size on accuracy of species distribution models Ecol. Model. 148 2002 1 13
80. A.V. Suarez, and N.D. Tsutsui The value of museum collections for research and society BioScience 54 1 2004 66 74
81. G.H.H. Tate The mammals of the Guiana region Bull. Am. Museum Nat. History 76 1939 151 229
82. C.D. Thomas, A. Cameron, R.E. Green, M. Bakkenes, L.J. Beaumont, Y.C. Collingham, B.F.N. Erasmus, M.F. de Siqueira, A. Grainger, L. Hannah, L. Hughes, B. Huntley, A.S. van Jaarsveld, G.F. Midgley, L. Miles, M.A. Ortega-Huerta, A.T. Peterson, O.L. Phillips, and S.E. Williams Extinction risk from climate change Nature 427 2004 145 148
83. USGS, 2001. HYDRO 1k, elevation derivative database. United States Geological Survey, Sioux Falls, South Dakota. Available at http://www.edcdaac. usgs.gov/gtopo30/hydro.
84. S. Vida A computer program for non-parametric receiver operating characteristic analysis Comput. Meth. Prog. Biomed. 40 1993 95 101
85. E. Welk, K. Schubert, and M.H. Hoffmann Present and potential distribution of invasive mustard (Alliara petiolata) in North America Divers. Distributions 8 2002 219 233
86. E.O. Wiley, K.M. McNyset, A.T. Peterson, C.R. Robins, and A.M. Stewart Niche modeling and geographic range predictions in the marine environment using a machine-learning algorithm Oceanography 16 3 2003 120 127
87. P.M. Williams Bayesian regularization and pruning using a Laplace prior Neural Comput. 7 1 1995 117 143
88. T.W. Yee, and N.D. Mitchell Generalized additive models in plant ecology J. Veg. Sci. 2 1991 587 602
89. Y. Yom-Tov, and R. Kadmon Analysis of the distribution of insectivorous bats in Israel Divers. Distributions 4 1998 63 70
90. B. Zadrozny Learning and evaluating classifiers under sample selection bias Proceedings of the 21st International Conference on Machine Learning 2004 903 910
91. A.E. Zaniewski, A. Lehmann, and J.M. Overton Predicting species spatial distributions using presence-only data: a case study of native New Zealand ferns Ecol. Model. 157 2002 261 280
92. M.H. Zweig, and G. Campbell Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine Clin. Chem. 39 4 1993 561 577