CharacterLength {TreeSearch}

Character length

Description

Homoplasy length of each character in a dataset on a specified tree.

Usage

CharacterLength(tree, dataset, compress = FALSE)

FitchSteps(tree, dataset)

FastCharacterLength(tree, dataset)

Arguments

tree

A tree of class phylo.

dataset

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

compress

Logical specifying whether to retain the compression of a phyDat object or to return a vector specifying to each individual character, decompressed using the dataset's index attribute.

Value

CharacterLength() returns a vector listing the contribution of each character to tree score, according to the algorithm of Brazeau et al. (2019).

Functions

• FastCharacterLength(): Do not perform checks. Use with care: may cause erroneous results or software crash if variables are in the incorrect format.

Author(s)

Martin R. Smith ([e-mail])

References

Brazeau MD, Guillerme T, Smith MR (2019). “An algorithm for morphological phylogenetic analysis with inapplicable data.” Systematic Biology, 68(4), 619–631. doi:10.1093/sysbio/syy083.

See Also

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

Examples

data("inapplicable.datasets")
dataset <- inapplicable.phyData[[12]]
tree <- TreeTools::NJTree(dataset)
CharacterLength(tree, dataset)
CharacterLength(tree, dataset, compress = TRUE)