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
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.
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)
#> [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