Entry: aldous.test
Aliases: aldous.test
Keywords: htest
Description: Visualizing balance via scatter diagrams
URL: ../../../library/apTreeshape/html/aldous.test.html

Entry: all.equal.treeshape
Aliases: all.equal.treeshape
Keywords: manip
Description: Compare two objects of class treeshape
URL: ../../../library/apTreeshape/html/all.equal.treeshape.html

Entry: apTreeshape-internal
Aliases: as.treeshape.treebalance is.binary.phylo pandit raldous rbiased rpda ryule treebalance treebase
Keywords: internal
Description: Internal apTreeshape Functions
URL: ../../../library/apTreeshape/html/apTreeshape-internal.html

Entry: as.phylo.treeshape
Aliases: as.phylo.treeshape
Keywords: manip
Description: Conversion among tree objects
URL: ../../../library/apTreeshape/html/as.phylo.treeshape.html

Entry: as.treeshape
Aliases: as.treeshape as.treeshape.phylo
Keywords: manip
Description: Conversion among tree objects
URL: ../../../library/apTreeshape/html/as.treeshape.html

Entry: cladesize
Aliases: cladesize
Keywords: univar
Description: Compute the number of children of a randomly chosen node
URL: ../../../library/apTreeshape/html/cladesize.html

Entry: colless
Aliases: colless
Keywords: univar
Description: Compute the Colless' shape statistic on tree data
URL: ../../../library/apTreeshape/html/colless.html

Entry: cutreeshape
Aliases: cutreeshape
Keywords: manip
Description: Cut objects of class "treeshape"
URL: ../../../library/apTreeshape/html/cutreeshape.html

Entry: dbtrees
Aliases: dbtrees
Keywords: manip IO
Description: Download trees from internet databases.
URL: ../../../library/apTreeshape/html/dbtrees.html

Entry: hivtree.treeshape
Aliases: hivtree.treeshape
Keywords: datasets
Description: Phylogenetic Tree of 193 HIV-1 Sequences
URL: ../../../library/apTreeshape/html/hivtree.treeshape.html

Entry: index.test
Aliases: colless.test sackin.test
Keywords: htest
Description: Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
URL: ../../../library/apTreeshape/html/index.test.html

Entry: likelihood.test
Aliases: likelihood.test
Keywords: htest
Description: Test the Yule model vs PDA (uniform) model.
URL: ../../../library/apTreeshape/html/likelihood.test.html

Entry: pandit
Aliases: cytochromc rhodopsin
Keywords: datasets
Description: Phylogenetic trees from the Pandit database
URL: ../../../library/apTreeshape/html/pandit.html

Entry: plot.treeshape
Aliases: plot.treeshape
Keywords: hplot
Description: Plot phylogenetic treeshapes.
URL: ../../../library/apTreeshape/html/plot.treeshape.html

Entry: rtreeshape
Aliases: rtreeshape
Keywords: datagen
Description: Generate a list of random binary trees according to a given model
URL: ../../../library/apTreeshape/html/rtreeshape.html

Entry: sackin
Aliases: sackin
Keywords: univar
Description: Compute the Sackin's index of a tree
URL: ../../../library/apTreeshape/html/sackin.html

Entry: shape.statistic
Aliases: shape.statistic
Keywords: univar
Description: Computes the log of the likelihood ratio (yule/pda)
URL: ../../../library/apTreeshape/html/shape.statistic.html

Entry: smaller.clade.spectrum
Aliases: smaller.clade.spectrum
Keywords: univar
Description: Compute the smaller clade spectrum of a tree.
URL: ../../../library/apTreeshape/html/smaller.clade.spectrum.html

Entry: spectrum.treeshape
Aliases: spectrum.treeshape
Keywords: univar
Description: Compute the spectrum of a tree
URL: ../../../library/apTreeshape/html/spectrum.treeshape.html

Entry: subtree.test
Aliases: subtree.test
Keywords: htest
Description: Test the Yule or PDA hypothesis
URL: ../../../library/apTreeshape/html/subtree.test.html

Entry: summary.treeshape
Aliases: summary.treeshape
Keywords: manip
Description: Print a summary of an object of class "treeshape"
URL: ../../../library/apTreeshape/html/summary.treeshape.html

Entry: tipsubtree
Aliases: tipsubtree
Keywords: manip
Description: Extract a subtree that contains pre-specified tip names or labels
URL: ../../../library/apTreeshape/html/tipsubtree.html

Entry: treebase
Aliases: primates carnivora.treeshape
Keywords: datasets
Description: Phylogenetic trees from the TreeBASE database
URL: ../../../library/apTreeshape/html/treebase.html

Entry: treeshape
Aliases: treeshape
Keywords: datagen
Description: Builds an object of class treeshape
URL: ../../../library/apTreeshape/html/treeshape.html

Entry: universal.treeshape
Aliases: universal.treeshape
Keywords: datasets
Description: Universal phylogenetic tree of life
URL: ../../../library/apTreeshape/html/universal.treeshape.html
