TreeSearch (version 1.1.1)

CharacterLength: 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 Brazeau2018;textualTreeTools.

Functions

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

References

See Also

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

Examples

# NOT RUN {
data('inapplicable.datasets')
dataset <- inapplicable.phyData[[12]]
tree <- TreeTools::NJTree(dataset)
CharacterLength(tree, dataset)
CharacterLength(tree, dataset, compress = TRUE)
# }