MSCquartets: quartetTableDominant – R documentation

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quartetTableDominant

Produce table of dominant quartets, with estimates of internal edge lengths

Description

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.

Usage

quartetTableDominant(rqt, bigweights = "infinite")

Arguments

`rqt`	a table, as produced by `quartetTableResolved` of size (n choose 4)x(n+3);
`bigweights`	`"infinite"` or `"finite"`, to indicate whether the weight (internal edge length) of a quartet for which only one topology appears is given as `Inf` or a finite, but large, numerical value

Details

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).

Value

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 4-taxon tree, of the quartets' central edge lengths, in coalescent units

Examples

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,]

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

v1.1.0

MIT + file LICENSE

Authors

Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)

Initial release