MSCquartets: quartetTableResolved – R documentation

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quartetTableResolved

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

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

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