MorphyTreeLength: Calculate parsimony score from Morphy object

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Calculate parsimony score from Morphy object

Description

This function must be passed a valid Morphy object, or R may crash. For most users, the function TreeLength() will be more appropriate.

Usage

MorphyTreeLength(tree, morphyObj)

MorphyLength(
  parent,
  child,
  morphyObj,
  inPostorder = FALSE,
  nTaxa = mpl_get_numtaxa(morphyObj)
)

GetMorphyLength(parentOf, leftChild, rightChild, morphyObj)

C_MorphyLength(parentOf, leftChild, rightChild, morphyObj)

Arguments

tree	A tree of class phylo, with tip labels in the order generated by RenumberTips, i.e. corresponding to the sequence of taxa in the corresponding Morphy object.
morphyObj	Object of class morphy, perhaps created with PhyDat2Morphy().
parent	Integer vector corresponding to the first column of the edge matrix of a tree of class phylo, i.e. tree[["edge"]][, 1]
child	Integer vector corresponding to the second column of the edge matrix of a tree of class phylo, i.e. tree[["edge"]][, 2].
parentOf	For each node, numbered in postorder, the number of its parent node.
leftChild	For each internal node, numbered in postorder, the number of its left child node or tip.
rightChild	For each internal node, numbered in postorder, the number of its right child node or tip.

Value

MorphyTreeLength() returns the length of the tree, after applying weighting.

Functions

• MorphyLength(): Faster function that requires internal tree parameters. Node numbering must increase monotonically away from root.

• GetMorphyLength(): Fastest function that requires internal tree parameters

• C_MorphyLength(): Direct call to C function. Use with caution.

Author(s)

Martin R. Smith

See Also

PhyDat2Morphy

Other tree scoring: CharacterLength(), IWScore(), LengthAdded(), MinimumLength(), TaxonInfluence()

Other tree scoring: CharacterLength(), IWScore(), LengthAdded(), MinimumLength(), TaxonInfluence()

TreeSearch documentation built on April 11, 2025, 5:49 p.m.