phyl.cca {phytools} | R Documentation |
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 |
X |
a data matrix with traits in columns. |
Y |
data matrix with traits in columns, to be correlated with |
lambda |
optionally, a (fixed) value for |
fixed |
optionally, a logical value indicating whether or not to estimate |
(Optional) joint optimization of λ is performed using optimize
on the interval (0,1).
A list with the following components:
cor |
canonical correlations. |
xcoef |
coefficients for the canonical variables for |
ycoef |
coefficients for the canonical variables for |
xscores |
matrix with the canonical scores for |
yscores |
matrix with the canonical scores for |
chisq |
vector of χ^2 values. |
p |
P-values for the hypothesis test that the ith and all subsequent correlations are zero. |
Liam Revell liam.revell@umb.edu
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.