quartetTableCollapse: Reduce quartet table by combining some taxa

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Reduce quartet table by combining some taxa

Description

Form a smaller resolved quartet table by lumping some taxa into a composite taxon.

Usage

quartetTableCollapse(rqt, taxaA, taxaB)

Arguments

rqt	a resolved quartet table, as from quartetTableResolved
taxaA	a vector of taxon names in rqt to be included in the output table
taxaB	a vector of taxon names in rqt to form new composite taxon in the output table

Details

This function is needed for the recursive calls in WQDSrec. It should only be applied to a resolved quartet table which includes counts for all possible quartets on the taxa (though counts can be zero).

The sets taxaA and taxaB must be disjoint. Their union need not be all taxa in rqt.

Value

a resolved quartet table with length(taxaA)+1 taxa; the composite taxon is named as the concatenation of the sorted names in taxaB

See Also

WQDCrecursive

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.