Phylogenetic Linear Regression

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Documentation for package ‘phylolm’ version 2.6.5

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phylolm-package Phylogenetic Linear Regression
AIC.logLik.phyloglm Methods for class 'phyloglm'.
AIC.logLik.phylolm Methods for class 'phylolm'.
AIC.phyloglm Methods for class 'phyloglm'.
AIC.phylolm Methods for class 'phylolm'.
confint.phylolm Methods for class 'phylolm'.
extractAIC.phylolm Methods for class 'phylolm'.
flowerSize Flower size of 25 Euphorbiaceae species
flowerTree Phylogenetic tree of 25 Euphorbiaceae species
guidetree Binary population tree within Arabidopsis thaliana
logLik.phyloglm Methods for class 'phyloglm'.
logLik.phylolm Methods for class 'phylolm'.
mace Multi-task learning for ancestral state estimation.
model.frame.phylolm Methods for class 'phylolm'.
nobs.phyloglm Methods for class 'phyloglm'.
nobs.phylolm Methods for class 'phylolm'.
OU1d.loglik Log likelihood of an one-dimensional Ornstein-Uhlenbeck model
OUshifts Detections of shifts in the OU process along a phylogeny.
phyloglm Phylogenetic Generalized Linear Model
phyloglmstep Stepwise model selection for Phylogenetic Generalized Linear Model
phylolm Phylogenetic Linear Model
phylostep Stepwise model selection for Phylogenetic Linear Model
plot.OUshifts Methods for class 'OUshifts'.
plot.phyloglm Methods for class 'phyloglm'.
plot.phylolm Methods for class 'phylolm'.
predict.phylolm Methods for class 'phylolm'.
print.logLik.phyloglm Methods for class 'phyloglm'.
print.logLik.phylolm Methods for class 'phylolm'.
print.phyloglm Methods for class 'phyloglm'.
print.phylolm Methods for class 'phylolm'.
print.summary.phyloglm Methods for class 'phyloglm'.
print.summary.phylolm Methods for class 'phylolm'.
pruningwise.branching.times Calculates internal node ages in an ultrametric "pruningwise" tree
pruningwise.distFromRoot Calculates node distance from the root in an "pruningwise" tree
quartetCF Quartet concordance factors across Arabidopsis thaliana
rbinTrait Binary trait simulation
residuals.phyloglm Methods for class 'phyloglm'.
residuals.phylolm Methods for class 'phylolm'.
rTrait Continuous trait simulation
stepwise.test.tree Fits a population tree to data from quartet concordance factors
summary.phyloglm Methods for class 'phyloglm'.
summary.phylolm Methods for class 'phylolm'.
test.one.species.tree Tests the fit of a population tree to quartet concordance factor data
test.tree.preparation data structure preparation for testing a population tree
three.point.compute Computations with a (generalized) three-point structured tree
transf.branch.lengths Creates a tree with branch lengths to represent the 3-point structure of a covariance matrix
vcov.phyloglm Methods for class 'phyloglm'.
vcov.phylolm Methods for class 'phylolm'.