Homoplasy length of each character in a dataset on a specified tree.
CharacterLength(tree, dataset, compress = FALSE)
FitchSteps(tree, dataset)
FastCharacterLength(tree, dataset)A tree of class phylo.
A phylogenetic data matrix of phangorn class
phyDat, whose names correspond to the labels of any accompanying tree.
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.
CharacterLength() returns a vector listing the contribution of each
character to tree score, according to the algorithm of
Brazeau et al. (2019)
.
FastCharacterLength(): Do not perform checks. Use with care: may cause
erroneous results or software crash if variables are in the incorrect format.
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 .
Other tree scoring:
IWScore(),
LengthAdded(),
MinimumLength(),
MorphyTreeLength(),
TaxonInfluence()
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