phyl.cca: Phylogenetic canonical correlation analysis

View source: R/phyl.cca.R

phyl.ccaR Documentation

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 liam.revell@umb.edu

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.