R: Phylogenetic Linear Regression

# Phylogenetic Linear Regression

## Documentation for package ‘phylolm’ version 2.6.5

- DESCRIPTION file.

## Help Pages

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'.