Compare quartet states by explicit enumeration

CompareQuartets() uses explicit enumeration to compare two lists of quartet states (Estabrook et al. 1985) , detailing how many are identical and how many are unresolved. For most purposes, the faster function QuartetStatus() will be preferable.

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.

References

Estabrook GF, McMorris FR, Meacham CA (1985). “Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units.” Systematic Zoology, 34(2), 193--200. doi:10.2307/2413326 .

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()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

  trees <- list(TreeTools::BalancedTree(6),
                TreeTools::PectinateTree(6))
  quartets <- QuartetStates(trees)
  CompareQuartets(quartets[[1]], quartets[[2]])
#>  N  Q  s  d r1 r2  u 
#>  2  1  1  0  0  0  0