Calculate parsimony score from Morphy object

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

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.

See also

PhyDat2Morphy

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

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

Author

Martin R. Smith