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.

Author
Nicolas Bortolussi, Eric Durand, Michael Blum <michael.blum@imag.fr>, Olivier Francois <olivier.francois@imag.fr>
Date of publication
2012-11-09 07:03:26
Maintainer
Michael Blum <michael.blum@imag.fr>
License
GPL (>= 2)
Version
1.4-5

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