quartetTableDominant  R Documentation 
Converts table of counts of resolved quartets on n
taxa to show only dominant one, with
maximum likelihood estimate of internal edge weight under the MSC.
quartetTableDominant(rqt, bigweights = "infinite")
rqt 
a table, as produced by 
bigweights 

If bigweights="finite"
, when for a set of 4 taxa the quartet counts are (m,0,0) then
the edge weight is computed as if the relative frequency of the dominant topology were m/(m+1).
an (n choose 4)x(n+1) array with dominant quartet topology encoded by 1,1,1,1 in
taxon columns, with signs indicating cherries; the (n+1)th column "weight"
contains the maximum likelihood estimates,
under MSC on a 4taxon tree, of the quartets' central edge lengths, in coalescent units
quartetTable
, quartetTableResolved
gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
RQT[1:6,]
DQT=quartetTableDominant(RQT)
DQT[1:6,]
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