This function performs phylogenetic PCA (e.g., Revell 2009; Evolution).
phyl.pca(tree, Y, method="BM", mode="cov", ...)
# S3 method for phyl.pca
biplot(x, ...)
scores(object, ...)
# S3 method for phyl.pca
scores(object, ...)phylogeny as an object of class "phylo".
data matrix with traits in columns.
method to obtain the correlation structure: can be "BM" or "lambda".
is the mode for the PCA: can be "cov" or "corr".
object of class "phyl.pca" for biplot method.
object of class "phyl.pca" for scores method.
for S3 plotting method biplot.phyl.pca, other arguments to be passed to biplot.
An object of class "phyl.pca" consisting of a list with some or all of the following components:
diagonal matrix of eigenvalues.
matrix with eigenvectors in columns.
matrix with scores.
matrix with loadings.
fitted value of \(\lambda\) (method="lambda" only).
log-likelihood for \(\lambda\) model (method="logL" only).
If method="lambda" then \(\lambda\) will be optimized on the interval (0,1) using optimize. Optimization method can be set using the option opt which can take values "ML", "REML", or "fixed". If the last of these is selected than the user should also specify a value of \(\lambda\) to use via the argument lambda.
S3 methods (print, summary, and biplot) are modified from code provided by Joan Maspons and are based on the same methods for objects of class "prcomp". Function biplot now permits the argument choices to be supplied, which should be a vector of length two indicated the two PC axes to be plotted.
S3 method scores extracts or computes (for a matrix of newdata) PC scores given an object of class "phyl.pca".
Revell, L. J. (2009) Size-correction and principal components for interspecific comparative studies. Evolution, 63, 3258-3268.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.