CompareQuartets: Compare quartet states by explicit enumeration

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

Compare quartet states by explicit enumeration

Description

CompareQuartets() uses explicit enumeration to compare two lists of quartet states \insertCiteEstabrook1985Quartet, detailing how many are identical and how many are unresolved. For most purposes, the faster function QuartetStatus() will be preferable.

Usage

CompareQuartets(x, cf)

Arguments

x, cf

List of quartet states, perhaps generated by QuartetStates().

Value

Returns an array of seven numeric elements, corresponding

N

The total number of quartet statements for two trees of n leaves, i.e. 2 Q.

Q

The total number of quartets for n leaves.

s

The number of quartets that are resolved identically in both trees.

d

The number of quartets that are resolved differently in each tree.

r1

The number of quartets that are resolved in tree 1, but not in tree 2.

r2

The number of quartets that are resolved in tree 2, but not in tree 1.

u

The number of quartets that are unresolved in both trees.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

• QuartetStatus() generates the same output from a list of trees.

Other element-by-element comparisons: CompareQuartetsMulti(), CompareSplits(), PairSharedQuartetStatus(), QuartetState(), SharedQuartetStatus(), SplitStatus()

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

Examples

  trees <- list(TreeTools::BalancedTree(6),
                TreeTools::PectinateTree(6))
  quartets <- QuartetStates(trees)
  CompareQuartets(quartets[[1]], quartets[[2]])

ms609/SlowQuartet documentation built on April 22, 2024, 5:41 p.m.