Comparative interpretation of count, presence-absence and point methods for species distribution models

Methods in Ecology and Evolution

Volumn 3, Issue 1, 2012, Pages 177-187

  Aarts, Geert ^a,b   Fieberg, John ^c   Matthiopoulos, Jason ^d  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^c MINNESOTA DEPARTMENT OF NATURAL RESOURCES   (United States)

^d UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

Accessibility; Availability; Case control; Line transect; Occupancy; Presence only; Resource selection; Telemetry; Usage; Utilization distribution

Indexed keywords

EID: 84867412542     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2011.00141.x     Document Type: Article

References (58)

1. Aarts, G., MacKenzie, M., McConnell, B., Fedak, M. & Matthiopoulos, J. (2008) Estimating space-use and habitat preference from wildlife telemetry data. Ecography, 31, 140-160.
2. Austin, M.P. (2002) Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecological Modelling, 157, 101-118.
3. Baddeley, A. & Turner, R. (2000) Practical maximum pseudolikelihood for spatial point patterns. Australian & New Zealand Journal of Statistics, 42, 283-315.
4. Baddeley, A., Berman, M., Fisher, N.I., Hardegen, A., Milne, R.K., Schuhmacher, D., Shah, R. & Turner, R. (2010) Spatial logistic regression and change-of-support in Poisson point processes. Electronic Journal of Statistics, 4, 1151-1201.
5. Boyce, M.S. & McDonald, L.L. (1999) Relating populations to habitats using resource selection functions. Trends in Ecology and Evolution, 14, 268-272.
6. Buckland, S.T.E. & Elston, D.A. (1993) Empirical models for the distribution of wildlife. Journal of Applied Ecology, 30, 478-495.
7. Buckland, S.T., Anderson, D.R., Burnham, K.P., Laake, J.L., Borchers, D.L. & Thomas, L. (2004) Advanced Distance Sampling. Oxford University press, New York.
8. Cramer, E.M. (1985) Multicollinearity. Encyclopaedia of Statistics (eds S. Kotz, N.L. Johnson & C.B. Read ), pp. 639-643. John Wiley and Sons, New York.
9. Cressie, N.A.C. (1993) Spatial Statistics for Spatial Data. Wiley-Interscience, New York.
10. Diggle, P.J. (1990) A point process modeling approach to raised incidence of a rare phenomenon in the vicinity of a prespecified point. Journal of the Royal Statistical Society. Series A, (Statistics in Society), 153, 349-362.
11. Diggle, P.J., Kaimi, I. & Abellana, R. (2010a) Partial-likelihood analysis of spatio-temporal point-process data. Biometrics, 66, 347-354.
12. Diggle, P.J., Menezes, R. & Su, T.L. (2010b) Geostatistical inference under preferential sampling. Journal of the Royal Statistical Society. Series C, Applied statistics, 59, 191-232.
13. Diggle, P.J. & Rowlingson, B.S. (1994) A conditional approach to point process modeling of elevated risk. Journal of the Royal Statistical Society. Series A, (Statistics in Society), 157, 433-440.
14. Dormann, C. (2007) Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Global Ecology and Biogeography, 16, 129-138.
15. Dormann, C., McPherson, J.M., Araujo, M.B., Bivand, R., Bolliger, J., Carl, G., Davies, R.G., Hirzel, A., Jetz, W., Kissling, W.D., Kuhn, I., Ohlemuller, R., Peres-Neto, P.R., Reineking, B., Schroder, B., Schurr, F.M. & Wilson, R. (2007) Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography, 30, 609-628.
16. Drake, J.M., Randin, C. & Guisan, A. (2006) Modelling ecological niches with support vector machines. Journal of Applied Ecology, 43, 424-432.
17. Dungan, J.L., Perry, J.N., Dale, M.R.T., Legendre, P., Citron-Pousty, S., Fortin, M.-J., Jakomulska, A., Miriti, M. & Rosenberg, M.S. (2002) A balanced view of scale in spatial statistical analyses. Ecography, 25, 626-640.
18. Elith, J., Graham, C.H., Anderson, R.P., Dudík, M., Ferrier, S., Guisan, A., Hijmans, R.J., Huettmann, F., Leathwick, J.R., Lehmann, A., Li, J., Lohmann, L.G., Loiselle, B.A., Manion, G., Moritz, C., Nakamura, M., Nakazawa, Y., Overton, J.M., Peterson, A.T., Phillips, S.J., Richardson, K., Scachetti-Pereira, R., Schapire, R.E., Soberon, J., Williams, S., Wisz, M.S. & Zimmermann, N.E. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography, 29, 129-151.
19. Embling, C.B., Fernandes, P.G., Hammond, P.S., Armstrong, F. & Gordon, J. (2005) Investigations into the relationship between pelagic fish and dolphin distributions off the west coast of Scotland. ICES Anual Science Conference, pp. 15. Aberdeen.
20. Fauchald, P. & Tveraa, T. (2003) Using first-passage time in the analysis of area-restricted search and habitat selection. Ecology, 84, 282-288.
21. Fieberg, J., Matthiopoulos, J., Hebblewhite, M., Boyce, M.S. & Frair, J.L. (2010) Correlation and studies of habitat selection: problem, red herring or opportunity? Philosophical Transactions of the Royal Society. B, Biological Sciences, 365, 2233-2244.
22. Frair, J.L., Nielsen, S.E., Merrill, E.H., Lele, S.R., Boyce, M.S., Munro, R.H.M., Stenhouse, G.B. & Beyer, H.L. (2004) Removing GPS collar bias in habitat selection studies. Journal of Applied Ecology, 41, 201-212.
23. Gilbert, P.B., Lele, S.R. & Vardi, Y. (1999) Maximum likelihood estimation in semiparametric selection bias models with application to AIDS vaccine trials. Biometrika, 86, 27-43.
24. Gotway, C.A. & Young, L.J. (2002) Combining incompatible spatial data. Journal of the American Statistical Association, 97, 632-648.
25. Gruijter, J.D., Brus, D.J., Bierkens, M. & Knotters, M. (2006) Sampling for Natural Resource Monitoring. Springer-Verlag, Berlin.
26. Guisan, A., Edwards, T.C. & Hastie, T. (2002) Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modelling, 157, 89-100.
27. Guisan, A. & Thuiller, W. (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8, 993-1009.
28. Guisan, A. & Zimmermann, N.E. (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135, 147-186.
29. Guisan, A., Zimmermann, N.E., Elith, J., Graham, C.H., Phillips, S. & Peterson, A.T. (2007) What matters for predicting the occurrences of trees: techniques, data, or species' characteristics? Ecological Monographs, 77, 615-630.
30. Hebblewhite, M. & Merrill, E. (2008) Modelling wildlife-human relationships for social species with mixed-effects resource selection models. Journal of Applied Ecology, 45, 834-844.
31. Hirzel, A. & Guisan, A. (2002) Which is the optimal sampling strategy for habitat suitability modelling. Ecological Modelling, 157, 331-341.
32. Jelinski, D.E. & Wu, J.G. (1996) The modifiable areal unit problem and implications for landscape ecology. Landscape Ecology, 11, 129-140.
33. Jimenez-Valverde, A., Diniz, F., de Azevedo, E.B. & Borges, P.A.V. (2009) Species distribution models do not account for abundance: the case of arthropods on Terceira Island. Annales Zoologici Fennici, 46, 451-464.
34. Johnson, D.H. (1980) The comparison of usage and availability measurements for evaluating resource preference. Ecology, 6, 65-71.
35. Johnson, D.S., Thomas, D.L., Hoef, J.M.V. & Christ, A. (2008) A general framework for the analysis of animal resource selection from telemetry data. Biometrics, 64, 968-976.
36. Keating, K.A. & Cherry, S. (2004) Use and interpretation of logistic regression in habitat selection studies. The Journal of Wildlife Management, 68, 774-789.
37. Leathwick, J.R., Elith, J., Francis, M.P., Hastie, T. & Taylor, P. (2006) Variation in demersal fish species richness in the oceans surrounding New Zealand: an analysis using boosted regression trees. Marine Ecology Progress Series, 321, 267-281.
38. Lehmann, A., Overton, J.M. & Leathwick, J.R. (2002) GRASP: generalized regression analysis and spatial prediction. Ecological Modelling, 157, 189-207.
39. Lele, S.R. (2009) A new method for estimation of resource selection probability function. The Journal of Wildlife Management, 73, 122-127.
40. Lele, S.R. & Keim, J.L. (2006) Weighted distributions and estimation of resource selection probability functions. Ecology, 87, 3021-3028.
41. Mackenzie, D.I. & Royle, J.A. (2005) Designing occupancy studies: general advice and allocating survey effort. Journal of Applied Ecology, 42, 1105-1114.
42. MacKenzie, D.I., Nichols, J.D., Royle, J.A., Pollock, K.H., Hines, J.E. & Bailey, L.L. (2005) Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence. Elsevier, San Diego.
43. Manly, B.F.J., McDonald, L.L., Thomas, D.L., McDonald, T.L. & Erickson, W.P. (2002) Resource selection by animals. Statistical Design and Analysis for Field Studies. Kluwer Academic Publisher, Dordrecht.
44. Matthiopoulos, J. (2003a) Model-supervised kernel smoothing for the estimation of spatial usage. Oikos, 102, 367-377.
45. Matthiopoulos, J. (2003b) The use of space by animals as a function of accessibility and preference. Ecological Modelling, 159, 239-268.
46. Matthiopoulos, J., Hebblewhite, M., Aarts, G. & Fieberg, J. (2011) Generalized functional responses for species distributions. Ecology, 92, 583-589.
47. McCullagh, P. & Nelder, J.A. (1989) Generalized Linear Models, 2nd edn. Chapman & Hall, London.
48. Mysterud, A. & Ims, R.A. (1998) Functional responses in habitat use: availability influences relative use in trade-off situations. Ecology, 79, 1435-1441.
49. Nielsen, S.E., Johnson, C.J., Heard, D.C. & Boyce, M.S. (2005) Can models of presence-absence be used to scale abundance? - Two case studies considering extremes in life history. Ecography, 28, 197-208.
50. Pearce, J.L. & Boyce, M.S. (2006) Modelling distribution and abundance with presence-only data. Journal of Applied Ecology, 43, 405-412.
51. Pearce, J. & Ferrier, S. (2001) The practical value of modelling relative abundance of species for regional conservation planning: a case study. Biological Conservation, 98, 33-43.
52. Phillips, S.J., Anderson, R.P. & Schapire, R.E. (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
53. Prentice, R.L. & Gloeckler, L.A. (1978) Regression-analysis of grouped survival data with application to breast-cancer data. Biometrics, 34, 57-67.
54. Royle, J.A., Nichols, J.D. & Kery, M. (2005) Modelling occurrence and abundance of species when detection is imperfect. Oikos, 110, 353-359.
55. Svancara, L.K., Garton, E.O., Chang, K.T., Scott, J.M., Zager, P. & Gratson, M. (2002) The inherent aggravation of aggregation: an example with elk aerial survey data. The Journal of Wildlife Management, 66, 776-787.
56. Warton, D.I. & Shepherd, L.C. (2010) Poisson point process models solve the 'pseudo-absence problem' for presence-only data in ecology. The Annals of Applied Statistics, 4, 1383-1402.
57. Webb, N.F., Hebblewhite, M. & Merrill, E.H. (2008) Statistical methods for identifying wolf kill sites using global positioning system locations. The Journal of Wildlife Management, 72, 798-807.
58. Wood, S.M. (2006) Generalized Additive Models: An Introduction with R. Chapman & Hall/CRC, Boca Raton.