ResolvedQuartets {Quartet}

Count resolved quartets

Description

Counts how many quartets are resolved or unresolved in a given tree, following Brodal et al. (2013).

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

• Brodal GS, Fagerberg R, Mailund T, Pedersen CNS, Sand A (2013). “Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree.” SODA '13 Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms, 1814–1832. doi:10.1137/1.9781611973105.130.

See Also

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

Examples

data(sq_trees)

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

vapply(sq_trees, ResolvedQuartets, integer(2))