Counts how many quartets are resolved or unresolved in a given tree, following Brodal et al. (2013) .
ResolvedQuartets(tree, countTriplets = FALSE)
ResolvedTriplets(tree)A tree of class phylo.
Logical; if TRUE, the function will return the number
of triplets instead of the number of quartets.
ResolvedQuartets() returns a vector of length two, listing the
number of quartets (or triplets) that are [1] resolved; [2] unresolved
in the specified tree.
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.
ResolvedTriplets(): Convenience function to calculate the number of
resolved/unresolved triplets.
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 .
Other quartet counting functions:
AllQuartets(),
CompareQuartets(),
CompareQuartetsMulti()
data(sq_trees)
ResolvedTriplets(sq_trees$collapse_some)
#> [1] 144 21
# Equivalent to:
ResolvedQuartets(sq_trees$collapse_some, countTriplets = TRUE)
#> [1] 144 21
vapply(sq_trees, ResolvedQuartets, integer(2))
#> ref_tree move_one_near move_one_mid move_one_far move_two_near
#> [1,] 330 330 330 330 330
#> [2,] 0 0 0 0 0
#> move_two_mid move_two_far collapse_one collapse_some m1mid_col1
#> [1,] 330 330 322 207 322
#> [2,] 0 0 8 123 8
#> m1mid_colsome m2mid_col1 m2mid_colsome opposite_tree caterpillar
#> [1,] 265 322 125 330 330
#> [2,] 65 8 205 0 0
#> top_and_tail anti_pectinate random_tree
#> [1,] 330 330 330
#> [2,] 0 0 0