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
phyDatobject or to return a vector specifying to each individual character, decompressed using the dataset'sindexattribute.
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.
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)
#> [1] 1 1 2 2 3 4 4 5 1 6 1 1 2 1 2 4 2 5 2 4 1 1 2 1 1
#> [26] 2 2 2 5 1 1 1 2 1 4 3 6 5 5 1 2 1 2 1 1 1 1 1 1 1
#> [51] 2 1 1 8 3 7 3 3 2 5 2 1 2 2 2 9 10 5 5 2 4 3 5 1 1
#> [76] 5 6 3 5 5 3 3 2 7 2 1 9 5 7 5 1 7 1 5 2 2 8 1 2 2
#> [101] 1 1 3 2 3 4 12 6 8 4 5 8 7 1 1 2 2 1 1 4 6 2 3 6 6
#> [126] 1 1 1 1 2 1 1 1 2 1 1 6
CharacterLength(tree, dataset, compress = TRUE)
#> [1] 1 1 2 2 3 4 4 5 1 6 1 1 2 1 2 4 2 5 2 4 1 2 1 1 2
#> [26] 2 2 5 1 1 1 2 4 3 6 5 5 1 2 2 2 1 8 3 7 3 3 2 5 2
#> [51] 1 2 2 9 10 5 5 2 4 3 5 1 1 5 6 3 5 5 3 3 2 7 2 1 9
#> [76] 5 7 5 1 7 1 5 2 2 8 1 2 2 1 3 2 3 4 12 6 8 4 5 8 7
#> [101] 1 2 2 1 4 6 2 3 6 6 1 1 1 1 2 1 2 6