phyl.resid {phytools} | R Documentation |
This function fits one or multiple phylogenetic regressions (depending on the number of columns in Y
) and computes the residuals. Designed for phylogenetic size correction using GLS regression (e.g., Revell 2009; Evolution).
phyl.resid(tree, x, Y, method="BM")
tree |
a phylogenetic tree in |
x |
vector containing the single independent variable (e.g., size), or matrix with multiple independent variables in columns. |
Y |
vector or matrix with one or multiple dependent variables in columns. |
method |
method to obtain the correlation structure: can be |
Optionally fits λ for each regression model. Likelihood optimization of λ is performed for method="lambda"
using optimize
on the interval (0,1). This function is redundant with residuals(gls(...,correlation=corPagel(...)))
, but some users may find this method simpler, and it provides a good way to cross-check your results & make sure that you are using gls
correctly.
A list with the following components:
beta |
a vector or matrix of regression coefficients. |
resid |
a vector or matrix of residuals for species. |
lambda |
a vector of lambda values ( |
logL |
a vector of log-likelihoods ( |
Liam Revell liam.revell@umb.edu
Revell, L. J. (2009) Size-correction and principal components for interspecific comparative studies. Evolution, 63, 3258-3268.
Revell, L. J. (2010) Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution, 1, 319-329.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.