Analyses of Phylogenetic Treeshape

Documentation for package ‘apTreeshape’ version 1.4-3

aldous.test	Visualizing balance via scatter diagrams
all.equal.treeshape	Compare two objects of class treeshape
as.phylo.treeshape	Conversion among tree objects
as.treeshape	Conversion among tree objects
as.treeshape.phylo	Conversion among tree objects
cladesize	Compute the number of children of a randomly chosen node
colless	Compute the Colless' shape statistic on tree data
colless.test	Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
cutreeshape	Cut objects of class "treeshape"
hivtree.treeshape	Phylogenetic Tree of 193 HIV-1 Sequences
likelihood.test	Test the Yule model vs PDA (uniform) model.
maxlik.betasplit	Maximum likelihood of beta in the Beta-splitting model
plot.treeshape	Plot phylogenetic treeshapes.
rtreeshape	Generate a list of random binary trees according to a given model
sackin	Compute the Sackin's index of a tree
sackin.test	Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
shape.statistic	Computes the log of the likelihood ratio (yule/pda)
shift.test	Testing diversification rate variation in phylogenetic trees
smaller.clade.spectrum	Compute the smaller clade spectrum of a tree.
spectrum.treeshape	Compute the spectrum of a tree
subtree.test	Test the Yule or PDA hypothesis
summary.treeshape	Print a summary of an object of class "treeshape"
tipsubtree	Extract a subtree that contains pre-specified tip names or labels
treeshape	Builds an object of class treeshape
universal.treeshape	Universal phylogenetic tree of life