Non-parametric multivariate analyses of changes in community structure
Citations
12,328 citations
9,509 citations
Cites background or methods from "Non-parametric multivariate analyse..."
...Clarke & Warwick (1994) described a procedure for ecological data termed SIMPER (similarity percentages) for determining which species (variables) are contributing most to the dissimilarity between groups of object (sampling units)....
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...Clarke & Ainsworth (1993) proposed a procedure for ecological data that basically measures the correlation between dissimilarities between sampling units based on species composition and the dissimilarities between sampling units based on environmental variables. They provided an algorithm called BIO-ENV that first calculates a dissimilarity matrix (e.g. Bray–Curtis) between sampling units based on species abundances and a separate dissimilarity matrix (e.g. Euclidean distance) between sampling units based on environmental variables. It then measures any correlation between the rank-orders of these two matrices using the Spearman rank correlation coefficient. Each pair of observations for the correlation will be the rank of the Bray–Curtis dissimilarity (from species abundances) between objects h and i and the rank of the Euclidean distance (from environmental variables) between objects h and i. Legendre & Legendre (1998) pointed out that the BIO-ENV procedure basically calculates the same correlation as a Mantel test (Chapter 15 and Section 18....
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...Clarke & Warwick (1994) argued that fourth-root transformations should always be used for species abundance data before calculating dissimilarities to reduce the influence of very abundant species....
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...Clarke & Ainsworth (1993) proposed a procedure for ecological data that basically measures the correlation between dissimilarities between sampling units based on species composition and the dissimilarities between sampling units based on environmental variables....
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...Clarke & Ainsworth (1993) proposed a procedure for ecological data that basically measures the correlation between dissimilarities between sampling units based on species composition and the dissimilarities between sampling units based on environmental variables. They provided an algorithm called BIO-ENV that first calculates a dissimilarity matrix (e.g. Bray–Curtis) between sampling units based on species abundances and a separate dissimilarity matrix (e.g. Euclidean distance) between sampling units based on environmental variables. It then measures any correlation between the rank-orders of these two matrices using the Spearman rank correlation coefficient. Each pair of observations for the correlation will be the rank of the Bray–Curtis dissimilarity (from species abundances) between objects h and i and the rank of the Euclidean distance (from environmental variables) between objects h and i. Legendre & Legendre (1998) pointed out that the BIO-ENV procedure basically calculates the same correlation as a Mantel test (Chapter 15 and Section 18.1.3), except the former is based on rank transformed data. The Mantel test could be used for the global test of no correlation between the two matrices, or even between the dissimilarities based on species composition and differences between sampling units for each environmental variable separately. It can also be extended to compare more than two matrices (Diniz-Filho & Bini 1996). Clarke & Ainsworth (1993) and Clarke & Warwick (1994) incorporated a stepwise routine into their BIO-ENV procedure, to find the combinations of environmental variables that produce dissimilarities between sampling units with the highest correlations with dissimilarities between sampling units based on species composition....
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3,640 citations
Cites methods from "Non-parametric multivariate analyse..."
...ANOSIM is a permutation-based test of the null hypothesis that within-group distances are not significantly smaller than between-group distances....
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...We used the analysis of similarities (ANOSIM) (44) function in the program PRIMER (45) to test for differences in community composition among various sample groups....
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3,468 citations
Cites background or methods from "Non-parametric multivariate analyse..."
...It is generally agreed that the Euclidean distance measure is not appropriate for use with ecological data of species abundances (e.g., Faith et al. 1987, Clarke 1993, Legendre and Legendre 1998)....
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...Email: mja@stat.auckland.ac.nz Several nonparametric multivariate methods for use in biology, ecology, and the social sciences have been proposed (Mantel 1967, Mantel and Valand 1970, Hubert and Schultz 1976, Mielke et al. 1976, Smith et al. 1990, McArdle 1991, Clarke 1993, Pillar and Orlóci 1996)....
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...…seems to provide the most meaningful intuitive measure of dissimilarity in ecological community structure (Odum 1950, Hajdu 1981, Faith et al. 1987, Clarke 1993, Legendre and Legendre 1998), the mathematically complex portion of the information inherent in the measure has generally been ignored....
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...First, there are those that can be based on any distance measure of choice, including semimetric measures such as the Bray-Curtis measure (Mantel 1967, Hubert and Schultz 1976, Smith et al. 1990, Clarke 1993)....
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2,255 citations
Cites background or methods from "Non-parametric multivariate analyse..."
...This led Warwick and Clarke (1993) to propose that increased multivariate dispersion, as measured by the Bray–Curtis dissimilarity, may in general be a sign of increased environmental stress....
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...Euclidean distance is inappropriate here for these reasons, and also because it is not generally considered useful for measuring the ecological dissimilarity among species assemblages (Faith et al., 1987; Clarke, 1993)....
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...For measures such as Euclidean distance or Bray–Curtis, some form of standardization or transformation of variables may also be done before calculating distances, so that variables have equal weight or are placed on similar scales (Faith et al., 1987; Clarke, 1993)....
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...Euclidean distance is inappropriate here for these reasons, and also because it is not generally considered useful for measuring the ecological dissimilarity among species assemblages (Faith et al., 1987; Clarke, 1993)....
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...Several robust dissimilarity-based tests for equality of multivariate locations have been described (Mielke, Berry, and Johnson, 1976; Smith, Pontasch, and Cairns, 1990; Clarke, 1993; Pillar and Orlóci, 1996; Gower and Krzanowski, 1999; Legendre and Anderson, 1999; Anderson, 2001)....
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References
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