Improving generalized regression analysis for the spatial prediction of forest communities

Journal of Biogeography

Volumn 33, Issue 10, 2006, Pages 1729-1749

  Maggini, Ramona ^a   Lehmann, Anthony ^b   Zimmermann, Niklaus E ^c   Guisan, Antoine ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b Centre Suisse de Cartographie de la Faune   (Switzerland)

^c SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

Author keywords

Cross validation; Forest communities; Generalized additive models; Generalized regression analysis; Potential distribution modelling; Predictor interactions; Receiver operating characteristic; Spatial autocorrelation; Spatial predictions

Indexed keywords

DATA SET; ENVIRONMENTAL MODELING; FOREST ECOSYSTEM; NUMERICAL MODEL; PREDICTION; REGRESSION ANALYSIS;

CENTRAL EUROPE; EURASIA; EUROPE; SWITZERLAND; VAUD;

EID: 33745719239     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2006.01465.x     Document Type: Article

References (112)

1. Akaike, H. (1973) Information theory as an extension of the maximum likelihood principle. Second International Symposium on Information Theory (ed. by B.N. Petrov and F. Csaki), pp. 267-281. Akademiai Kiado, Budapest.
2. Anselin, L., Syabi, I. & Kho, Y. (2006) GeoDa: an introduction to spatial data analysis. Geographical Analysis, 38, 5-22.
3. Araújo, M.B., Williams, P.H. & Fuller, R.J. (2002) Dynamics of extinction and the selection of nature reserves. Proceedings of the Royal Society of London Series B - Biological Sciences, 269, 1971-1980.
4. Araújo, M.B., Pearson, R.G., Thuiller, W. & Erhard, M. (2005a) Validation of species-climate impact models under climate change. Global Change Biology, 11, 1504-1513.
5. Araújo, M.B., Whittaker, R.J., Ladle, R.J. & Erhard, M. (2005b) Reducing uncertainty in projections of extinction risk from climate change. Global Ecology and Biogeography, 14, 529-528.
6. Araújo, M.B., Thuiller, W. & Pearson, R.G. (2006) Climate warming and the decline of amphibians and reptiles in Europe. Journal of Biogeography, doi: 10.1111/j.1365-2699.2006.01482.x.
7. Augustin, N.H., Mugglestone, M.A. & Buckland, S.T. (1996) An autologistic model for the spatial distribution of wildlife. Journal of Applied Ecology, 33, 339-347.
8. Austin, M.P. (1999) The potential contribution of vegetation ecology to biodiversity research. Ecography, 22, 465-484.
9. Austin, M.P. (2002) Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecological Modelling, 157, 101-118.
10. Austin, M.P. & Barry, S.C. (1998) Improved methods for modelling species distributions using GAMS. Report to Environment Australia. CSIRO Wildlife and Ecology, Canberra, Australia.
11. Austin, M.P. & Meyers, J.A. (1996) Current approaches to modelling the environmental niche of eucalypts: implication for management of forest biodiversity. Forest Ecology and Management, 85, 95-106.
12. Austin, M.P. & Smith, T.M. (1989) A new model for the continuum concept. Vegetatio, 83, 35-47.
13. Borcard, D. & Legendre, P. (1994) Environmental control and spatial structure in ecological communities, an example using orbatid mites (Acari, Oribatei). Environmental and Ecological Statistics, 1, 37-61.
14. Brzeziecki, B., Kienast, F. & Wildi, O. (1993) A simulated map of the potential natural forest vegetation of Switzerland. Journal of Vegetation Science, 4, 499-508.
15. Brzeziecki, B., Kienast, F. & Wildi, O. (1995) Modeling potential impacts of climate change on the spatial-distribution of zonal forest communities in Switzerland. Journal of Vegetation Science, 6, 257-268.
16. Burnham, K.P. & Anderson, D.R. (2002) Model selection and multimodel inference. A practical information-theoretic approach, 2nd edn. Springer-Verlag, New York.
17. Burnham, K.P. & Anderson, D.R. (2004) Multimodel inference - understanding AIC and BIC in model selection. Sociological Methods & Research, 33, 261-304.
18. Castella, E., Adalsteinsson, H., Brittain, J.E., Gislasson, G.M., Lehmann, A., Lencioni, V., Lods-Crozet, B., Maiolini, B., Milner, A.M., Olafson, J., Saltveit, S.J. & Snook, D.L., (2001) Macrobenthic invertebrate richness and composition along a latitudinal gradient of European glacier-fed streams. Freshwater Biology, 46, 1811-1831.
19. Cawsey, E.M., Austin, M.P. & Baker, B.L. (2002) Regional vegetation mapping in Australia: a case study in the practical use of statistical modelling. Biodiversity and Conservation, 11, 2239-2274.
20. Clarkson, B.R., Schipper, L.A. & Lehmann, A. (2004) Vegetation and peat characteristics in the development of lowland restiad peat bogs, North Island, New Zealand. Wetlands, 24, 133-151.
21. Clot, F. & Delarze, R. (1998) Banque de données phyto des forêts vaudoises. Résultats de l'analyse des relevés du Nord vaudois. Département de la sécurité et de l'environnement; Service des forêts, de la faune et de la nature, Canton de Vaud, Switzerland.
22. Coudun, C., Gegout, J.-C., Piedallu, C. & Rameau, J.-C. (2006) Soil nutritional factors improve models of plant species distribution: an illustration with Acer campestre (L.) in France. Journal of Biogeography, doi: 10.1111/j.1365-2699.2005.01443.x.
23. Dambacher, J.M., Li, H.W. & Rossignol, P.A. (2002) Relevance of community structure in assessing indeterminacy of ecological predictions. Ecology, 83, 1372-1385.
24. Delarze, R., Gonseth, Y. & Galland, P. (1998) Guide des milieux de Suisse. Ecologie - menaces - espèces caractéristiques. Delachaux & Niestlé, Lausanne, Switzerland.
25. Dirnböck, T. & Dullinger, S. (2004) Habitat distribution models, spatial autocorrelation, functional traits and dispersal capacity of alpine plant species. Journal of Vegetation Science, 15, 77-84.
26. Dutilleul, P., Clifford, P., Richardson, S. & Hemon, D. (1993) Modifying the t test for assessing the correlation between two spatial processes. Biometrics, 49, 305-314.
27. Efron, B. & Tibshirani, R. (1993) An introduction to the bootstrap. Chapman & Hall, New York.
28. Ferrier, S., Drielsma, M., Manion, G. & Watson, G. (2002) Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales. II. Community-level modelling. Biodiversity and Conservation, 11, 2309-2338.
29. Fielding, A.H. & Bell, J.F. (1997) A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation, 24, 38-49.
30. Franklin, J. (1995) Predictive vegetation mapping: geographic modeling of biospatial patterns in relation to environmental gradients. Progress in Physical Geography, 19, 474-499.
31. Franklin, J. (1998) Predicting the distribution of shrub species in southern California from climate and terrain-derived variables. Journal of Vegetation Science, 9, 733-748.
32. Franklin, J., McCullough, P. & Gray, C. (2000) Terrain variables used for predictive mapping of vegetation communities in southern California. Terrain analysis: principles and applications (ed. by J. Wilson and J. Gallant), pp. 331-353. Wiley, New York.
33. Garza-Pérez, J.R., Lehmann, A. & Arias-González, J.E. (2004) Spatial prediction of coral reef habitats: integrating ecology with spatial modeling and remote sensing. Marine Ecology Progress Series, 269, 141-152.
34. Graham, C.H., Ferrier, S., Huettman, F., Moritz, C. & Peterson, A.T. (2004) New developments in museum-based informatics and applications in biodiversity analysis. Trends in Ecology & Evolution, 19, 497-503.
35. Guisan, A. & Harrell, F.E. (2000) Ordinal response regression models in ecology. Journal of Vegetation Science, 11, 617-626.
36. Guisan, A. & Hofer, U. (2003) Predicting reptile distributions at the mesoscale: relation to climate and topography. Journal of Biogeography, 30, 1233-1243.
37. Guisan, A. & Thuiller, W. (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8, 993-1009.
38. Guisan, A. & Zimmermann, N.E. (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135, 147-186.
39. Guisan, A., Theurillat, J.P. & Kienast, F. (1998) Predicting the potential distribution of plant species in an Alpine environment. Journal of Vegetation Science, 9, 65-74.
40. Guisan, A., Weiss, S.B. & Weiss, A.D. (1999) GLM versus CCA spatial modeling of plant species distribution. Plant Ecology, 143, 107-122.
41. Guisan, A., Edwards, J., Thomas, C. & Hastie, T. (2002) Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modelling, 157, 89-100.
42. Guisan, A., Broennimann, O., Engler, R., Yoccoz, N.G., Vust, M., Zimmermann, N.E. & Lehmann, A. (in press) Using niche-based models to improve the sampling of rare species. Conservation Biology.
43. Hampe, A. (2004) Bioclimate envelope models: what they detect and what they hide. Global Ecology and Biogeography, 13, 469-476.
44. Harrell, F.E. (2001) Regression modeling strategies with applications to linear models, logistic regression and survival analysis. Springer-Verlag, New York.
45. Hastie, T. & Tibshirani, R.J. (1990) Generalized additive models. Chapman & Hall, London.
46. Hastie, T.J., Tibshirani, R.J. & Friedman, J. (2001) Elements of statistical learning: data mining, inference and prediction. Springer, New York.
47. Hurlbert, S.H. (1984) Pseudoreplication and the design of ecological field experiments. Ecological Monographs, 54, 187-211.
48. Jaberg, C. & Guisan, A. (2001) Modelling the distribution of bats in relation to landscape structure in a temperate mountain environment. Journal of Applied Ecology, 38, 1169-1181.
49. Johnson, J.B. & Omland, K.S. (2004) Model selection in ecology and evolution. Trends in Ecology & Evolution, 19, 101-108.
50. Joly, P., Miaud, C., Lehmann, A. & Grolet, O. (2001) Habitat matrix effect on pond occupancy in newts. Conservation Biology, 15, 239-248.
51. Keitt, T.H., Bjornstad, O.N., Dixon, P.M. & Citron-Pousty, S. (2002) Accounting for spatial pattern when modeling organism-environment interactions. Ecography, 25, 616-625.
52. Kuha, J. (2004) AIC and BIC - comparisons of assumptions and performance. Sociological Methods & Research, 33, 188-229.
53. Leathwick, J.R. (1998) Are New Zealand's Nothofagus species in equilibrium with their environment? Journal of Vegetation Science, 9, 719-732.
54. Leathwick, J.R. (2002) Intra-generic competition among Nothofagus in New Zealand's primary indigenous forests. Biodiversity and Conservation, 11, 2177-2187.
55. Leathwick, J.R. & Austin, M.P. (2001) Competitive interactions between tree species in New Zealand's old-growth indigenous forests. Ecology, 82, 2560-2573.
56. Leathwick, J.R. & Whitehead, D. (2001) Soil and atmospheric water deficits and the distribution of New Zealand indigenous tree species. Functional Ecology, 15, 233-242.
57. Leathwick, J.R., Whitehead, D. & McLeod, M. (1996) Predicting changes in the composition of New Zealand's indigenous forests in response to global warming: a modelling approach. Environmental Software, 11, 81-90.
58. Legendre, P. (1993) Spatial autocorrelation: trouble or new paradigm? Ecology, 74, 1659-1673.
59. Legendre, P., Dale, M.R.T., Fortin, M.-J., Gurevitch, J., Hohn, M. & Myers, D. (2002) The consequences of spatial structure for the design and analysis of ecological field surveys. Ecography, 25, 601-615.
60. Lehmann, A., Leathwick, J.R. & Overton, J.McC. (2002a) Assessing New Zealand fern diversity from spatial predictions of species assemblages. Biodiversity and Conservation, 11, 2217-2238.
61. Lehmann, A., Overton, J.McC. & Austin, M.P. (2002b) Regression models for spatial prediction: their role for biodiversity and conservation. Biodiversity and Conservation, 11, 2085-2092.
62. Lehmann, A., Overton, J.McC. & Leathwick, J.R. (2002c) GRASP: generalized regression analysis and spatial prediction. Ecological Modelling, 157, 189-207.
63. Lehmann, A., Leathwick, J.R. & Overton, J.McC. (2005) grasp v. 3.2 user's manual. Swiss Center For Faunal Cartography, Neuchâtel, Switzerland (http://www.cscf.ch/grasp).
64. Lichstein, J.W., Simons, T.R., Shriner, S.A. & Franzreb, K.E. (2002) Spatial autocorrelation and autoregressive models in ecology. Ecological Monographs, 72, 445-463.
65. Liebhold, A.M. & Gurevitch, J. (2002) Integrating the statistical analysis of spatial data in ecology. Ecography, 25, 553-557.
66. Liu, C., Berry, P.M., Dawson, T.P. & Pearson, R.G. (2005) Selecting thresholds of occurrence in the prediction of species distributions. Ecography, 28, 385-393.
67. Lobo, J.M., Castro, I. & Moreno, J.C. (2001) Spatial and environmental determinants of vascular plant species richness distribution in the Iberian Peninsula and Balearic Islands. Biological Journal of the Linnean Society, 73, 233-253.
68. Luoto, L., Heikkinen, R.K., Pöyry, J. & Saarinen, K. (2006) Determinants of biogeographical distribution of butterflies in boreal regions. Journal of Biogeography, doi: 10.1111/j.1365-2699.2005.01395.x.
69. Maggini, R., Guisan, A. & Cherix, D. (2002) A stratified approach for modeling the distribution of a threatened ant species in the Swiss National Park. Biodiversity and Conservation, 11, 2117-2141.
70. Manel, S., Dias, J.M., Buckton, S.T. & Ormerod, S.J. (1999a) Alternative methods for predicting species distribution: an illustration with Himalayan river birds. Journal of Applied Ecology, 36, 734-747.
71. Manel, S., Dias, J.M. & Ormerod, S.J. (1999b) Comparing discriminant analysis, neural networks and logistic regression for predicting species distributions: a case study with a Himalayan river bird. Ecological Modelling, 120, 337-347.
72. Manel, S., Williams, H.C. & Ormerod, S.J. (2001) Evaluating presence-absence models in ecology: the need to account for prevalence. Journal of Applied Ecology, 38, 921-931.
73. Manly, B.F.J., McDonald, L.L., Thomas, D.L., McDonald, T.L. & Erickson, W.P. (2002) Resource selection by animals, 2nd edn. Kluwer Academic, Dordrecht.
74. McPherson, J.M., Jetz, W. & Rogers, D.J. (2004) The effects of species' range sizes on the accuracy of distribution models: ecological phenomenon or statistical artefact? Journal of Applied Ecology, 41, 811-823.
75. Moisen, G.G. & Frescino, T.S. (2002) Comparing five modelling techniques for predicting forest characteristics. Ecological Modelling, 157, 209-225.
76. Moser, D., Dullinger, S., Englisch, T., Niklfeld, H., Plutzar, C., Sauberer, N., Zechmeister, H.G. & Grabherr, G. (2005) Environmental determinants of vascular plant species richness in the Austrian Alps. Journal of Biogeography, 32, 1117-1127.
77. Nogués-Bravo, D. & Martinez-Rica, J.P. (2004) Factors controlling the spatial species richness pattern of four groups of terrestrial vertebrates in an area between two different biogeographic regions in northern Spain. Journal of Biogeography, 31, 629-640.
78. OFS (2003) GEOSTAT: Manuel de l'utilisateur. Office Fédéral de la Statistique, Berne, Switzerland.
79. OFT (1990) Atlas de Suisse. Office Fédéral de la Topographie, Wabern-Bern, Switzerland.
80. Opdam, P. & Washer, D. (2004) Climate change meets habitat fragmentation: linking landscape and biogeographical scale levels in research and conservation. Biological Conservation, 117, 285-297.
81. Overton, J.McC., Stephens, R.T.T., Leathwick, J.R. & Lehmann, A. (2002) Information pyramids for informed biodiversity conservation. Biodiversity and Conservation, 11, 2093-2116.
82. Ozesmi, S.L. & Ozesmi, U. (1999) An artificial neural network approach to spatial habitat modelling with interspecific interaction. Ecological Modelling, 116, 15-31.
83. Palomares, F., Ferreras, P., Travaini, A. & Delibes, M. (1998) Co-existence between Iberian lynx and Egyptian mongooses: estimating interaction strength by structural equation modelling and testing by an observational study. Journal of Animal Ecology, 67, 967-978.
84. Pearce, J. & Ferrier, S. (2000) An evaluation of alternative algorithms for fitting species distribution models using logistic regression. Ecological Modelling, 128, 127-147.
85. Pearson, R.G., Thuiller, W., Araújo, M.B., Martinez-Meyer, E., Brotons, L., McClean, C., Miles, L., Segurado, P., Dawson, T.P. & Lees, D.C. (2006) Model-based uncertainty in species' range prediction. Journal of Biogeography, doi: 10.1111/j.1365-2699.2006.01460.x.
86. Pereira, J.M.C. & Itami, R.M. (1991) GIS-based habitat modelling using logistic multiple regression: a study of the Mt Graham red squirrel. Engineering & Remote Sensing, 57, 1475-1486.
87. Perry, J.N., Liebhold, A.M., Rosenberg, M.S., Dungan, J., Miriti, M., Jakomulska, A. & Citron-Pousty, S. (2002) Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data. Ecography, 25, 578-600.
88. Peterson, A.T. (2003) Predicting the geography of species' invasions via ecological niche modeling. Quarterly Review of Biology, 78, 419-433.
89. Randin, C.F., Dirnböck, T., Dullinger, S., Zimmermann, N.E., Zappa, M. & Guisan, A. (2006) Are niche-based species distribution models transferable in space? Journal of Biogeography, doi: 10.1111/j.1365-2699.2006. 01466.x.
90. Ray, N., Lehmann, A. & Joly, P. (2002) Modeling spatial distribution of amphibian populations: a GIS approach based on habitat matrix permeability. Biodiversity and Conservation, 11, 2143-2165.
91. Schmieder, K. & Lehmann, A. (2004) A spatio-temporal framework for efficient inventories of natural resources: a case study with submersed macrophytes. Journal of Vegetation Science, 15, 807-816.
92. Schwarz, G. (1978) Estimating the dimension of a model. Annals of Statistics, 6, 461-464.
93. Schwarz, P.A., Fahey, T.J. & McCulloch, C.E. (2003) Factors controlling spatial variation of tree species abundance in a forested landscape. Ecology, 84, 1862-1878.
94. Scott, J.M., Heglund, P.J., Morrison, M.L., Raphael, M.G., Wall, W.A. & Samson, F.B. (2002) Predicting species occurrences: issues of accuracy and scale. Island Press, Covelo, CA.
95. Segurado, P. & Araújo, M.B. (2004) An evaluation of methods for modelling species distributions. Journal of Biogeography, 31, 1555-1568.
96. Stockwell, D.R.B. & Peterson, A.T. (2002) Effects of sample size on accuracy of species distribution models. Ecological Modelling, 148, 1-13.
97. Stone, M. (1977) An asymptotic equivalence of choice of model by cross-validation and Akaike's criterion. Journal of the Royal Statistical Society, Series B, 39, 44-47.
98. Suarez-Seoane, S., Osborne, P.E. & Alonso, J.C. (2002) Large-scale habitat selection by agricultural steppe birds in Spain: identifying species-habitat responses using generalized additive models. Journal of Applied Ecology, 39, 755-771.
99. Svenning, J.C. & Skov, F. (2005) The relative roles of environment and history as controls of tree species composition and richness in Europe. Journal of Biogeography, 32, 1019-1033.
100. Swets, J.A. (1988) Measuring the accuracy of diagnostic systems. Science, 240, 1285-1293.
101. Thuiller, W. (2004) Patterns and uncertainties of species' range shifts under climate change. Global Change Biology, 10, 2020-2027.
102. Thuiller, W., Brotons, L., Araújo, M.B. & Lavorel, S. (2004) Effects of restricting environmental range of data to project current and future species distributions. Ecography, 27, 165-172.
103. Tibshirani, R. (1996) Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society, Series B, 58, 267-288.
104. Turc, L., (1963) Evaluation des besoins en eau d'irrigation, évapotranspiration potentielle, formulation simplifié et mise à jour. Annales Agronomiques, 12, 13-49.
105. Van den Berg, M.S., Joosse, W. & Coops, H. (2003) A statistical model predicting the occurrence and dynamics of submerged macrophytes in shallow lakes in the Netherlands. Hydrobiologia, 506, 611-623.
106. Wagner, H.H. & Fortin, M.J. (2005) Spatial analysis of landscapes: concepts and statistics. Ecology, 86, 1975-1987.
107. Yee, T.W. & Mackenzie, M. (2002) Vector generalized additive models in plant ecology. Ecological Modelling, 157, 141-156.
108. Yee, T.W. & Mitchell, N.D. (1991) Generalized additive models in plant ecology. Journal of Vegetation Science, 2, 587-602.
109. Zaniewski, A.E., Lehmann, A. & Overton, J.M.C. (2002) Predicting species spatial distributions using presence-only data: a case study of native New Zealand ferns. Ecological Modelling, 157, 261-280.
110. Zhang, L.J., Gove, J.H. & Heath, L.S. (2005) Spatial residual analysis of six modeling techniques. Ecological Modelling, 186, 154-177.
111. Zimmermann, N.E. & Kienast, F. (1999) Predictive mapping of alpine grasslands in Switzerland: species versus community approach. Journal of Vegetation Science, 10, 469-482.
112. Zimmermann, N.E. & Roberts, D.W. (2001) Final report of the MLP climate and biophysical mapping project. Scientific project report. WSL, Birmensdorf, Switzerland.