phytools: phyl.cca – R documentation

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phyl.cca

Phylogenetic canonical correlation analysis

This function performs phylogenetic canonical correlation analysis (e.g., Revell & Harrison 2008; Bioinformatics).

phyl.cca(tree, X, Y, lambda=1.0, fixed=TRUE)

`tree`	a phylogenetic tree in `"phylo"` format.
`X`	a data matrix with traits in columns.
`Y`	data matrix with traits in columns, to be correlated with `X`.
`lambda`	optionally, a (fixed) value for λ.
`fixed`	optionally, a logical value indicating whether or not to estimate λ using likelihood.

(Optional) joint optimization of λ is performed using optimize on the interval (0,1).

An object of class "phyl.cca" containing the following components:

`cor`	canonical correlations.
`xcoef`	coefficients for the canonical variables for `X`.
`ycoef`	coefficients for the canonical variables for `Y`.
`xscores`	matrix with the canonical scores for `X`.
`yscores`	matrix with the canonical scores for `Y`.
`chisq`	vector of χ^2 values.
`p`	P-values for the hypothesis test that the ith and all subsequent correlations are zero.

Revell, L. J., Harrison, A. S. (2008) PCCA: A program for phylogenetic canonical correlation analysis. Bioinformatics, 24, 1018-1020.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.