Variation partitioning of species data matrices: Estimation and comparison of fractions

Ecology

Volumn 87, Issue 10, 2006, Pages 2614-2625

  Peres Neto, Pedro R ^a,b   Legendre, Pierre ^a   Dray, Stéphane ^a   Borcard, Daniel ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF REGINA   (Canada)

Author keywords

Adjusted coefficient of determination; Bootstrap; Canonical analysis; Canonical correspondence analysis (CCA); Ecological community; Redundancy analysis (RDA); Variation partitioning

Indexed keywords

CANONICAL ANALYSIS; COMMUNITY STRUCTURE; COMPARATIVE STUDY; DATA ACQUISITION; ESTIMATION METHOD; SPECIES OCCURRENCE;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; ECOLOGY; GEOGRAPHY; METHODOLOGY; MITE;

ANIMALS; ECOLOGY; GEOGRAPHY; MITES; MODELS, BIOLOGICAL;

EID: 33845367389     PISSN: 00129658     EISSN: 00129658     Source Type: Journal    
DOI: 10.1890/0012-9658(2006)87[2614:VPOSDM]2.0.CO;2     Document Type: Article

References (43)

1. Anderson, M. J., and N. A. Gribble. 1998. Partitioning the variation among spatial, temporal and environmental components in a multivariate data set. Australian Journal of Ecology 23:158-167.
2. Azen, R., and D. V. Budescu. 2003. The dominance analysis approach for comparing predictors in multiple regression. Psychological Methods 8:129-148.
3. Birks, H. J. B., S. M. Peglar, and H. A. Austin. 1996. An annotated bibliography of canonical correspondence analysis and related constrained ordination methods 1986-1993. Abstracta Botanica 20:17-36.
4. Borcard, D., and P. Legendre. 1994. Environmental control and spatial structure in ecological communities: an example using oribatid mites (Acari, Oribatei). Environmental and Ecological Statistics 1:37-61.
5. Borcard, D., P. Legendre, and P. Drapeau. 1992. Partialling out the spatial component of ecological variation. Ecology 73:1045-1055.
6. Boyce, M. S., and L. L. McDonald. 1999. Relating populations to habitats using resource selection functions. Trends in Ecology and Evolution 14:268-272.
7. Cottenie, K. 2005. Integrating environmental and spatial processes in ecological community analysis. Ecology Letters 8:1175-1182.
8. 2 in small and moderate samples. Journal of Econometrics 35:253-266.
9. Cushman, S. A., and K. McGarigal. 2002. Hierarchical, multiscale decomposition of species-environment relationships. Landscape Ecology 17:637-646.
10. Dawson-Saunders, B. T. 1982. Correcting for the bias in the canonical redundancy statistic. Educational and Psychological Measurement 42:131-143.
11. Diniz, J. A. F., and L. M. Bini. 1996. Assessing the relationship between multivariate community structure and environmental variables. Marine Ecology Progress Series 143:303-306.
12. Dray, S., P. Legendre, and P. R. Peres-Neto. 2006. Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbor matrices (PCNM). Ecological Modelling, in press.
13. Ezekiel, M. 1930. Methods of correlational analysis. Wiley, New York, New York, USA.
14. Jackson, D. A., and H. H. Harvey. 1993. Fish and benthic invertebrates: community concordance and community-environment relationships. Canadian Journal of Fisheries and Aquatic Sciences 50:2641-2651.
15. Jenkins, D. G., and A. L. Buikema. 1998. Do similar communities develop in similar sites? A test with zooplankton structure and function. Ecological Monographs 68:421-443.
16. Kerlinger, F. N., and E. J. Pedhazur. 1973. Multiple regression in behavioral research. Holt, Rinehart and Winston, New York, New York, USA.
17. Kromrey, J. D., and C. V. Hines. 1995. Use of empirical estimates of shrinkage in multiple regression: a caution. Educational and Psychological Measurement 55:901-925.
18. Lambert, Z. V., A. R. Wildt, and R. M. Durand. 1988. Redundancy analysis - an alternative to canonical correlation and multivariate multiple-regression in exploring interset associations. Psychological Bulletin 104:282-289.
19. Legendre, P., and M. J. Anderson. 1999. Distance-based redundancy analysis: testing multi-species responses in multi-factorial ecological experiments. Ecological Monographs 69:1-24.
20. Legendre, P., D. Borcard, and P. R. Peres-Neto. 2005. Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecological Monographs 75:435-450.
21. Legendre, P., and M.-J. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107-138.
22. Legendre, P., and E. Gallagher. 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129:271-280.
23. Legendre, P., and L. Legendre. 1998. Numerical ecology. Second English edition. Elsevier Science BV, Amsterdam, The Netherlands.
24. Manly, B. F. J. 1997. Randomization, bootstrap, and Monte Carlo methods in biology. Second edition. Chapman and Hall, London, UK.
25. Martin, T. G., B. A. Wintle, J. R. Rhodes, P. M. Kuhnert, S. A. Field, S. J. Low-Choy, A. J. Tyre, and H. P. Possingham. 2005. Zero tolerance ecology: improving ecology inference by modeling the source of zero observations. Ecology Letters 8:1235-1246.
26. Miller, J. K. 1975. The sampling distribution and a test for the significance of the bimultivariate redundancy statistic: a Monte Carlo study. Multivariate Behavioral Research 10:233-244.
27. Miller, J. K., and S. D. Farr. 1971. Bimultivariate redundancy: a comprehensive measure of interbattery relationship. Multivariate Behavioral Research 6:313-324.
28. Mood, A. M. 1969. Macro-analysis of the American educational system. Operations Research 17:770-784.
29. Økland, R. H. 2003. Partitioning the variation in a plot-by-species data matrix that is related to n sets of explanatory variables. Journal of Vegetation Science 14:693-700.
30. Oksanen, J., R. Kindt, P. Legendre, and R. B. O'Hara. 2005. vegan: community ecology package. Version 1.7-81. 〈http://cran.r-project.org/ 〉
31. Peres-Neto, P. R. 2004. Patterns in the co-occurrence of stream fish metacommunties: the role of site suitability, morphology and phylogeny versus species interactions. Oecologia 140:352-360.
32. Peres-Neto, P. R., and D. A. Jackson. 2001. How well do multivariate data sets match? The robustness and flexibility of a Procrustean superimposition approach over the Mantel test. Oecologia 129:169-178.
33. Peres-Neto, P. R., D. A. Jackson, and K. M. Somers. 2003. Giving meaningful interpretation to ordination axes: assessing the significance of eigenvector coefficients in principal component analysis. Ecology 84:2347-2363.
34. Peres-Neto, P. R., and J. D. Olden. 2001. Assessing the robustness of randomization tests: examples from behavioural studies. Animal Behaviour 61:79-86.
35. Peres-Neto, P. R., J. D. Olden, and D. A. Jackson. 2001. Environmentally constrained null models: site suitability as occupancy criterion. Oikos 93:110-120.
36. Rao, C. R. 1964. The use and interpretation of principal component analysis in applied research. Sankhyaá, Series A 26:329-358.
37. Rodríguez, M. A., and W. M. Lewis, Jr. 1997. Structure of fish assemblages along environmental gradients in floodplain lakes of the Orinoco River. Ecological Monographs 67:109-128.
38. Royston, P., and S. G. Simpson. 1995. Comparing non-nested regression models. Biometrics 51:114-127.
39. ter Braak, C. J. F. 1986. Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 67:1167-1179.
40. ter Braak, C. J. F., and P. Smilauer. 2002. Canoco reference manual and CanoDraw for Windows user's guide: software for canonical community ordination (Version 4.5). Microcomputer Power, Ithaca, New York, USA.
41. Watnik, M., W. Johnson, and E. J. Bedrick. 2001. Nonnested linear model selection revisited. Communications in statistics - theory and methods 30:1-20.
42. Wu, C. F. J. 1986. Jackknife, bootstrap and other resampling methods in regression-analysis. Annals of Statistics 14:1261-1295.
43. Zar, J. H. 1999. Biostatistical analysis. Third edition. Prentice Hall, London, UK.