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Last data update: 2014.03.03

R: Function to obtain the correlation between two matrices.

cor.matrix

R Documentation

Function to obtain the correlation between two matrices.

Description

Function obtains the correlation between two matrices, similar to the function mantel. The significance of the statistics is evaluated differently from mantel. For more details, see syncsa.

Usage

cor.matrix(m1, m2, x, y, method = "pearson", dist = "euclidean",
		permutations = 999, norm = FALSE, na.rm = FALSE)

Arguments

`m1`	Matrix that multiplied by m2 results in the matrix x.
`m2`	Matrix that when multiplied by m1 results in the matrix x. See 'details' below.
`x`	Matrix obtained by multiplication of m1 and m2.
`y`	Matrix that will be correlated with the matrix x.
`method`	Correlation method, as accepted by cor: "pearson", "spearman" or "kendall".
`dist`	Dissimilarity index, as accepted by vegdist: "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial" or "chao". However, some of these will not make sense in this case.
`permutations`	Number of permutations in assessing significance.
`norm`	Logical argument (TRUE or FALSE) to specify if x is standardized within variables (Default norm = FALSE).
`na.rm`	Logical argument (TRUE or FALSE) to specify if pairwise deletion of missing observations when computing dissimilarities (Default na.rm = FALSE).

Details

The null model is based on permutations in the matrix m2, typically the matrices B, U and Q.

Null model described by Pillar et al. (2009) and Pillar & Duarte (2010). For more details on the matrices and the null model, see syncsa.

Value

`Obs`	Correlation between matrices.
`p`	Significance level based on permutations.

Author(s)

Vanderlei JÃºlio Debastiani <vanderleidebastiani@yahoo.com.br>

References

Pillar, V.D.; Duarte, L.d.S. (2010). A framework for metacommunity analysis of phylogenetic structure. Ecology Letters, 13, 587-596.

Pillar, V.D., Duarte, L.d.S., Sosinski, E.E. & Joner, F. (2009). Discriminating trait-convergence and trait-divergence assembly patterns in ecological community gradients. Journal of Vegetation Science, 20, 334â348.