Analyses of Phylogenetic Treeshape

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Documentation for package ‘apTreeshape’ version 1.4-1

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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
carnivora.treeshape Phylogenetic trees from the TreeBASE database
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"
cytochromc Phylogenetic trees from the Pandit database
dbtrees Download trees from internet databases.
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.
primates Phylogenetic trees from the TreeBASE database
rhodopsin Phylogenetic trees from the Pandit database
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