quartetTableResolved: Modify quartet table to show only resolved quartets

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

Modify quartet table to show only resolved quartets

Description

Converts table of all quartet counts, including unresolved ones, by either dropping unresolved ones, or distributing them uniformly among the three resolved counts.

Usage

quartetTableResolved(qt, omit = FALSE)

Arguments

qt	table, as produced by quartetTable for n taxa, with n+4 columns
omit	TRUE deletes unresolved quartets column; FALSE deletes the column but redistributes unresolved counts as (1/3,1/3,1/3) to resolved counts

Value

a table of quartet counts similar to qt, but with columns showing only resolved quartet counts

See Also

quartetTable, quartetTableDominant

Examples

gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
QT=quartetTable(gtrees,tnames[1:6])
QT[1:6,]
RQT=quartetTableResolved(QT)
RQT[1:6,]

MSCquartets documentation built on Nov. 2, 2023, 5:32 p.m.