InapplicableFitch: Calculate parsimony score with inapplicable data

In ms609/inapplicable: Inapplicable data in parsimony analysis

Description

Uses code modified from the Morphy library to calculate a parsimony score in datasets that contain inapplicable data

Usage

InapplicableFitch(tree, dataset)

Arguments

tree	A tree of class phylo.
dataset	A phylogenetic data matrix of class phyDat, whose names correspond to the labels of any accompanying tree.

Value

This function returns the elements from a list containing:

• The total parsimony score

• The parsimony score associated with each character

• A matrix comprising character reconstructions for each node after the final pass

The elements to return are specified by the parameter detail. If a single element is requested (default) then just that element will be returned If multiple elements are requested then these will be returned in a list.

Author(s)

Martin R. Smith (using C code adapted from MorphyLib, author Martin Brazeau)

See Also

MorphyDat

BasicSearch

Examples

data(inapplicable.datasets)
tree <- TreeSearch::RandomTree(inapplicable.phyData[[1]])
result <- InapplicableFitch(tree, inapplicable.phyData[[1]])

ms609/inapplicable documentation built on May 23, 2019, 7:49 a.m.