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apTreeshape (version 1.2.1)

Analyses of Phylogenetic Treeshape

Description

apTreeshape is mainly dedicated to simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily.

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Version

Install

install.packages('apTreeshape')

Monthly Downloads

99

Version

1.2.1

License

GPL version 2 or later

Maintainer

Nicolas Bortolussi

Last Published

October 12th, 2020

Functions in apTreeshape (1.2.1)

summary.treeshape

Print a summary of an object of class "treeshape"

Phylogenetic trees from the Pandit database

Builds an object of class treeshape

all.equal.treeshape

Compare two objects of class treeshape

Extract a subtree that contains pre-specified tip names or labels

as.phylo.treeshape

Conversion among tree objects

likelihood.test

Test the Yule model vs PDA (uniform) model.

Conversion among tree objects

Phylogenetic trees from the TreeBASE database

universal.treeshape

Universal phylogenetic tree of life

apTreeshape-internal

Internal apTreeshape Functions

spectrum.treeshape

Compute the spectrum of a tree

Download trees from internet databases.

hivtree.treeshape

Phylogenetic Tree of 193 HIV-1 Sequences

smaller.clade.spectrum

Compute the smaller clade spectrum of a tree.

Compute the Colless' shape statistic on tree data

Compute the Sackin's index of a tree

Cut objects of class "treeshape"

Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic

Plot phylogenetic treeshapes.

Generate a list of random binary trees according to a given model

Test the Yule or PDA hypothesis

Visualizing balance via scatter diagrams

shape.statistic

Computes the log of the likelihood ratio (yule/pda)

Compute the number of children of a randomly chosen node