as.phylo is a generic function - described in the APE package - which converts an object into a tree of class "phylo". This method is an adataption of this generic method to convert objects of class "treeshape" in objects of class "phylo".
● Data Source:
CranContrib
● Keywords: manip
● Alias: as.phylo.treeshape
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Internal apTreeshape functions.
● Data Source:
CranContrib
● Keywords: internal
● Alias: Delta, ancestor, as.treeshape.treebalance, is.binary.phylo, logratio, pandit, raldous, rbiased, read.tree2, rpda, ryule, smaller.clade.spectrum2, treebalance, treebase
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This function makes a global comparison of two phylogenetic trees.
● Data Source:
CranContrib
● Keywords: manip
● Alias: all.equal.treeshape
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aldous.test
(Package: apTreeshape) :
Visualizing balance via scatter diagrams
A graphical test to decide if tree data fit the Yule or the PDA models.
● Data Source:
CranContrib
● Keywords: htest
● Alias: aldous.test
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treeshape
(Package: apTreeshape) :
Builds an object of class treeshape
treeshape builds a tree of class "treeshape" from a n*2 matrix, where n is the number of internal nodes of the tree. There are no informations about the heights of the branches in an object of class "treeshape". Formally, a "tree shape" is a phylogenetic tree where the label of the tips are ignored. Here, the label of the tips can be kept or ignored. If a names vector is provided, then the names of species are attached to the tips of the tree. Otherwise, tips are simply labeled with their numbers in the tree. Trees of class "treeshape" are always binary.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: treeshape
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tipsubtree
(Package: apTreeshape) :
Extract a subtree that contains pre-specified tip names or labels
tipsubtree returns an object of class "treeshape" that contains pre-specified tip names or labels. The name of the tips are conserved. It extracts the smallest tree that contains the common ancestors of the given tips.
● Data Source:
CranContrib
● Keywords: manip
● Alias: tipsubtree
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summary.treeshape
(Package: apTreeshape) :
Print a summary of an object of class "treeshape"
This function prints a compact summary of a phylogenetic tree of class "treeshape")
● Data Source:
CranContrib
● Keywords: manip
● Alias: summary.treeshape
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subtree.test tests the likelihood of the Yule or the PDA hypothesis and computes the p-value of the test. The test is based on the number of subtrees of a given size in the tree.
● Data Source:
CranContrib
● Keywords: htest
● Alias: subtree.test
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This function returns a sequence containing the number of subtrees of size n, n-1, ..., 3, 2 where n is the size of the tree. The 'k'th element of the sequence is the number of subtrees of size n-k+1 in the tree, where n is the number of tips of the tree.
● Data Source:
CranContrib
● Keywords: univar
● Alias: spectrum.treeshape
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smaller.clade.spectrum returns a n*2 matrix where n is the number of internal nodes of the tree. For each i in 1:n, the [i,1] element of the matrix is the size of the clade rooted at the 'i'th node of the tree. [i,2] is the size of the smaller daughter clade of the 'i'th node of the tree.
● Data Source:
CranContrib
● Keywords: univar
● Alias: smaller.clade.spectrum
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providing 
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