MSCquartets: quartetStarTestInd – R documentation

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quartetStarTestInd

Multiple independent hypothesis tests for gene quartet counts fitting a species quartet star tree under the MSC

Description

Perform hypothesis tests for a species quartet star tree vs. any alternative for all quartet counts in an input table, as if the quartets are independent.

Usage

quartetStarTestInd(rqt)

Arguments

rqt

Table of resolved quartet counts, as produced by quartetTableResolved, or quartetTreeTestInd

Details

This function assumes all quartets are resolved. The test performed is described in quartetStarTest.

Value

the same table as the input rqt with column "p_star" appended, containing p-values for judging fit to MSC on a star tree

Examples

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