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Calculate the parsimony score of a tree given a dataset

Source: R/IWScore.R, R/tree_length.R
TreeLength.Rd

TreeLength() uses the Morphy library Brazeau2017TreeSearch to calculate a parsimony score for a tree, handling inapplicable data according to the algorithm of Brazeau2019;textualTreeSearch. Trees may be scored using equal weights, implied weights Goloboff1993TreeSearch, or profile parsimony Faith2001TreeSearch.

Usage

IWScore(tree, dataset, concavity = 10L, ...)

TreeLength(tree, dataset, concavity = Inf)

# S3 method for class 'phylo'
TreeLength(tree, dataset, concavity = Inf)

# S3 method for class 'numeric'
TreeLength(tree, dataset, concavity = Inf)

# S3 method for class 'list'
TreeLength(tree, dataset, concavity = Inf)

# S3 method for class 'multiPhylo'
TreeLength(tree, dataset, concavity = Inf)

Fitch(tree, dataset)

Arguments

tree

A tree of class phylo, a list thereof (optionally of class multiPhylo), or an integer – in which case tree random trees will be uniformly sampled.

dataset

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

concavity

Determines the degree to which extra steps beyond the first are penalized. Specify a numeric value to use implied weighting Goloboff1993TreeSearch; concavity specifies k in k / e + k. A value of 10 is recommended; TNT sets a default of 3, but this is too low in some circumstances Goloboff2018,Smith2019TreeSearch. Better still explore the sensitivity of results under a range of concavity values, e.g. k = 2 ^ (1:7). Specify Inf to weight each additional step equally. Specify "profile" to employ profile parsimony Faith2001TreeSearch.

...

unused; allows additional parameters specified within ... to be received by the function without throwing an error.

Value

TreeLength() returns a numeric vector containing the score for each tree in tree.

References

See also

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

Author

Martin R. Smith (using Morphy C library, by Martin Brazeau)

Examples

data("inapplicable.datasets")
tree <- TreeTools::BalancedTree(inapplicable.phyData[[1]])
TreeLength(tree, inapplicable.phyData[[1]])
#> [1] 1117
TreeLength(tree, inapplicable.phyData[[1]], concavity = 10)
#> [1] 52.75785
TreeLength(tree, inapplicable.phyData[[1]], concavity = "profile")
#> → Inapplicable tokens treated as ambiguous for profile parsimony
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> [1] 3941.387
TreeLength(5, inapplicable.phyData[[1]])
#> [1] 1974 1985 1907 1948 1926