R: Phylogenetic principal components analysis

phyl.pca {phytools}

R Documentation

Phylogenetic principal components analysis

Description

This function performs phylogenetic PCA (e.g., Revell 2009; Evolution).

Usage

phyl.pca(tree, Y, method="BM", mode="cov", ...)
## S3 method for class 'phyl.pca'
biplot(x, ...)

Arguments

`tree`	phylogeny as an object of class `"phylo"`.
`Y`	data matrix with traits in columns.
`method`	method to obtain the correlation structure: can be `"BM"` or `"lambda"`.
`mode`	is the mode for the PCA: can be `"cov"` or `"corr"`.
`x`	object of class `"phyl.pca"` for `biplot.phyl.pca`.
`...`	for S3 plotting method `biplot.phyl.pca`, other arguments to be passed to `biplot`.

Details

If method="lambda" λ is optimized on the interval (0,1) using optimize. 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.

Value

An object of class phyl.pca which is a list with some or all of the following components:

`Eval`	diagonal matrix of eigenvalues.
`Evec`	matrix with eigenvectors in columns.
`S`	matrix with scores.
`L`	matrix with loadings.
`lambda`	fitted value of lambda (`method="lambda"` only).
`logL`	log-likelihood for lambda model (`method="logL"` only).

Author(s)

Liam Revell liam.revell@umb.edu, Joan Maspons

References

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.