CompareQuartetsMulti: Compare one tree's quartets against others'

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

Compare one tree's quartets against others'

Description

CompareQuartetsMulti() counts how many quartets in one tree are resolved in the same way or different ways in a forest of comparison trees.

Usage

CompareQuartetsMulti(x, cf)

Arguments

x	Object of class phylo representing the tree of interest.
cf	Comparison tree of class phylo, or list thereof, each with the same leaves as x.

Details

CompareQuartetsMulti() explicitly evaluates each quartet in each tree. As such its runtime will increase hyper-exponentially with the number of leaves in trees being compared. 30 leaves will take around 5 seconds; 40 closer to 20 s, and 50 around a minute.

Value

CompareQuartetsMulti() returns a named integer vector specifying the number of quartets whose resolution in x matches all or any of the resolutions in cf.

Named elements are:

N

The total number of quartet statements for the given number of n-leaf trees, i.e. n_trees × Q.

Q

The total number of quartets for n leaves.

s_all

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

s_any

The number of quartets that are resolved in x, and identically in at least one of cf.

d_all

The number of quartets that are resolved in every tree in cf, but never in the same way as they are resolved in in x.

d_any

The number of quartets in x that are resolved differently (i.e. contradicted) in at least one tree in cf.

r1_all

The number of quartets that are resolved in x, but not in any of cf.

r1_any

The number of quartets that are resolved in x, but unresolved in at least one of cf.

r2_all

The number of quartets that are resolved in all of cf, but not in x.

r2_any

The number of quartets that are resolved in at least one of cf, but not in x.

u_all

The number of quartets that are unresolved in all trees.

u_any

The number of quartets that are unresolved in x and at least one tree in cf.

x_only

The number of quartets in x that are not resolved the same way in any of cf.

Author(s)

Martin R. Smith ([e-mail])

See Also

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

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

Examples

library("TreeTools")
CompareQuartetsMulti(x  = CollapseNode(as.phylo(42, 6), 8:9),
                     cf = list(BalancedTree(6), PectinateTree(6), 
                               CollapseNode(as.phylo(1337, 6), 9:10)))

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