phytools (version 0.1-9)

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.

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 X^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