TINNIKdist: Compute TINNIK distance from quartets and hypothesis test...

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

Compute TINNIK distance from quartets and hypothesis test p-values

Description

Apply the B-quartet inference algorithm of \insertCiteABMR22;textualMSCquartets, \insertCiteABMR24;textualMSCquartets to infer all B-quartets from results of hypothesis tests, and then compute an estimate of an intertaxon distance fitting the topological tree of blobs of the species network.

Usage

TINNIKdist(pTable, test = "T3", alpha = 0.05, beta = 0.05)

Arguments

pTable	table of resolved quartet counts, as produced by quartetTableResolved, with extra columns from both star hypothesis test, and either cut or T3 hypothesis tests
test	either "cut" or "T3"
alpha	level for cut or T3 test
beta	level for star test

Details

This function assumes pTable has columns for taxa and resolved quartet counts as originally produced by quartetTable, and hypothesis test results as produced by quartetStarTestInd, and either quartetTreeTestInd for the T3 test or quartetCutTestInd. Rows must be present for every 4-taxon subset. (Note: Of functions in this package, only HolmBonferroni might modify the row order from the required one.)

This function uses the Rcpp package for significant speed up in computation time.

Value

a distance table output$dist and a vector output$Bquartets with TRUE/FALSE entries indicating B-quartets ordered as rows of pTable.

References

\insertRef

ABMR22MSCquartets

\insertRef

ABMR24MSCquartets

See Also

quartetTable,quartetTableResolved,quartetStarTest, quartetCutTest, quartetStarTestInd, quartetCutTestInd

Examples

data(pTableYeastRokas)
out=TINNIKdist(pTableYeastRokas,test="T3",alpha=.05,beta=.05)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.