ResolvedQuartets: Count resolved quartets

In ms609/SlowQuartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

Count resolved quartets

Description

Counts how many quartets are resolved or unresolved in a given tree, following \insertCiteBrodal2013;textualQuartet.

Usage

ResolvedQuartets(tree, countTriplets = FALSE)

ResolvedTriplets(tree)

Arguments

tree	A tree of class phylo.
countTriplets	Logical; if TRUE, the function will return the number of triplets instead of the number of quartets.

Details

Trees with more than 477 leaves risk encountering integer overflow errors, as the number of quartets is larger than can be stored in R's signed 32-bit integer representation. If warnings are thrown, check subsequent calculations for errors.

Value

ResolvedQuartets() returns a vector of length two, listing the number of quartets (or triplets) that are ⁠[1]⁠ resolved; ⁠[2]⁠ unresolved in the specified tree.

Functions

• ResolvedTriplets(): Convenience function to calculate the number of resolved/unresolved triplets.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

Other quartet counting functions: AllQuartets(), CompareQuartets(), CompareQuartetsMulti()

Examples

data(sq_trees)

ResolvedTriplets(sq_trees$collapse_some)
# Equivalent to:
ResolvedQuartets(sq_trees$collapse_some, countTriplets = TRUE)

vapply(sq_trees, ResolvedQuartets, integer(2))

ms609/SlowQuartet documentation built on Nov. 5, 2024, 8:48 a.m.