phyl.resid | R Documentation |
Computes the residuals from the phylogenetic regression of multiple y variables (in a matrix) on a single x.
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 |
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).
Optionally fits \lambda
for each regression model. Likelihood optimization of \lambda
is performed for method=
"lambda"
using optimize
on the interval (0,1).
This function is theoretically redundant with residuals
applied to a "gls"
object class in which the correlation structure is based on corBrownian
or corPagel
; however 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 elements:
beta |
a vector or matrix of regression coefficients. |
resid |
a vector or matrix of residuals for species. |
lambda |
a vector of |
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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
phyl.pca
, gls
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