phyl.cca: Phylogenetic canonical correlation analysis

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Phylogenetic canonical correlation analysis

Description

Phylogenetic canonical correlation analysis, following Revell & Harrison (2008).

Usage

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

Arguments

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 \lambda.
fixed	optionally, a logical value indicating whether or not to estimate \lambda using likelihood.

Details

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

Value

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

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 \chi^2 values.
p	P-values for the hypothesis test that the ith and all subsequent correlations are zero.

Author(s)

Liam Revell [e-mail]

References

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

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

phyl.pca

phytools documentation built on June 22, 2024, 10:39 a.m.