TreeSearch (version 0.4.3)

MorphyTreeLength: Calculate parsimony score with inapplicable data

Description

Calculate parsimony score with inapplicable data

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

The length of the tree (after weighting)

Functions

• MorphyLength: Faster function that requires internal tree parameters

• GetMorphyLength: Fastest function that requires internal tree parameters

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

See Also

PhyDat2Morphy

Other tree scoring: CharacterLength(), Fitch(), IWScore()

Other tree scoring: CharacterLength(), Fitch(), IWScore()