Calculate parsimony score with inapplicable data
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)
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.
Object of class morphy, perhaps created with
PhyDat2Morphy().
Integer vector corresponding to the first column of the edge
matrix of a tree of class phylo, i.e. tree$edge[, 1].
Integer vector corresponding to the second column of the edge
matrix of a tree of class phylo, i.e. tree$edge[, 2].
Integer vector containing, for each tip and each node in sequential order, the integer index its parent node. The root node should be its own parent.
integer vector containing, for each node, starting at the
root and proceeding in sequential order, the integer corresponding to its
left child. Tip numbering begins at 0; the root node is numbered nTip.
integer vector containing, for each node, the index of its right child.
For each node, numbered in postorder, the number of its parent node.
For each internal node, numbered in postorder, the number of its left child node or tip.
For each internal node, numbered in postorder, the number of its right child node or tip.
The length of the tree (after weighting)
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.
PhyDat2Morphy
Other tree scoring: CharacterLength,
Fitch, IWScore
Other tree scoring: CharacterLength,
Fitch, IWScore