apTreeshape: Analyses of Phylogenetic Treeshape

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.

AuthorNicolas Bortolussi, Eric Durand, Michael Blum <michael.blum@imag.fr>, Olivier Francois <olivier.francois@imag.fr>
Date of publication2012-11-09 07:03:26
MaintainerMichael Blum <michael.blum@imag.fr>
LicenseGPL (>= 2)
Version1.4-5

View on CRAN

Man pages

aldous.test: Visualizing balance via scatter diagrams

all.equal.treeshape: Compare two objects of class treeshape

apTreeshape-internal: Internal apTreeshape Functions

as.phylo.treeshape: Conversion among tree objects

as.treeshape: Conversion among tree objects

carnivora.treeshape: Phylogeny of carnivores.

cladesize: Compute the number of children of a randomly chosen node

colless: Compute the Colless' shape statistic on tree data

cutreeshape: Cut objects of class "treeshape"

cytochromc: Phylogeny of the cytochrome C family.

hivtree.treeshape: Phylogenetic Tree of 193 HIV-1 Sequences

index.test: Perform a test on the Yule or PDA hypothesis based on the...

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: Phylogeny of the primates.

rhodopsin: Phylogeny of rhodopsin proteins.

rtreeshape: Generate a list of random binary trees according to a given...

sackin: Compute the Sackin's index of a tree

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...

treeshape: Builds an object of class treeshape

universal.treeshape: Universal phylogenetic tree of life

Files in this package

apTreeshape
apTreeshape/MD5
apTreeshape/R
apTreeshape/R/treeshape.R apTreeshape/R/treebalance.R apTreeshape/R/tipsubtree.R apTreeshape/R/summary.treeshape.R apTreeshape/R/subtree.test.R apTreeshape/R/spectrum.treeshape.R apTreeshape/R/smaller.clade.spectrum2.R apTreeshape/R/smaller.clade.spectrum.R apTreeshape/R/shift.test.R apTreeshape/R/shape.statistic.R apTreeshape/R/sackin.test.R apTreeshape/R/sackin.R apTreeshape/R/ryule.R
apTreeshape/R/rtreeshape.R
apTreeshape/R/rpda.R apTreeshape/R/read.tree2.R apTreeshape/R/rbiased.R apTreeshape/R/raldous.R apTreeshape/R/plot.treeshape.R apTreeshape/R/maxlik.betasplit.R apTreeshape/R/logratio.R apTreeshape/R/likelihood.test.R apTreeshape/R/is.binary.phylo.R apTreeshape/R/Delta.R apTreeshape/R/cutreeshape.R apTreeshape/R/colless.test.R apTreeshape/R/colless.R apTreeshape/R/cladesize.R apTreeshape/R/as.treeshape.treebalance.R apTreeshape/R/as.treeshape.R apTreeshape/R/as.treeshape.phylo.R apTreeshape/R/as.phylo.treeshape.R apTreeshape/R/ancestor.R apTreeshape/R/all.equal.treeshape.R apTreeshape/R/aldous.test.R
apTreeshape/NAMESPACE
apTreeshape/man
apTreeshape/man/universal.treeshape.Rd apTreeshape/man/treeshape.Rd apTreeshape/man/tipsubtree.Rd apTreeshape/man/summary.treeshape.Rd apTreeshape/man/subtree.test.Rd apTreeshape/man/spectrum.treeshape.Rd apTreeshape/man/smaller.clade.spectrum.Rd apTreeshape/man/shift.test.Rd apTreeshape/man/shape.statistic.Rd apTreeshape/man/sackin.Rd apTreeshape/man/rtreeshape.Rd apTreeshape/man/rhodopsin.Rd apTreeshape/man/primates.Rd apTreeshape/man/plot.treeshape.Rd apTreeshape/man/maxlik.betasplit.Rd apTreeshape/man/likelihood.test.Rd apTreeshape/man/index.test.Rd apTreeshape/man/hivtree.treeshape.Rd apTreeshape/man/cytochromc.Rd apTreeshape/man/cutreeshape.Rd apTreeshape/man/colless.Rd apTreeshape/man/cladesize.Rd apTreeshape/man/carnivora.treeshape.Rd apTreeshape/man/as.treeshape.Rd apTreeshape/man/as.phylo.treeshape.Rd apTreeshape/man/apTreeshape-internal.Rd apTreeshape/man/all.equal.treeshape.Rd apTreeshape/man/aldous.test.Rd
apTreeshape/DESCRIPTION
apTreeshape/demo
apTreeshape/demo/apTreeshape.R
apTreeshape/demo/00Index
apTreeshape/data
apTreeshape/data/universal.treeshape.rda
apTreeshape/data/rhodopsin.rda
apTreeshape/data/primates.rda
apTreeshape/data/hivtree.treeshape.rda
apTreeshape/data/cytochromc.rda
apTreeshape/data/carnivora.treeshape.rda
apTreeshape/CHANGES

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.