phytools (version 0.1-9)

phyl.pca: Phylogenetic principal components analysis

Description

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

Usage

phyl.pca(tree,Y,method="BM",mode="cov")

Arguments

tree

a phylogenetic tree in "phylo" format.

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".

Value

• a list with 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).

Details

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

References

Revell, L. J. 2009. Size-correction and principal components for interspecific comparative studies. Evolution, 63, 3258--3268.

See Also

phyl.resid