phytools (version 0.2-40)

phyl.cca: Phylogenetic canonical correlation analysis

Description

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

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.

Value

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

Details

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

References

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

See Also

phyl.pca