TINNIKdist {MSCquartets}

Compute TINNIK distance from quartets and hypothesis test p-values

Description

Apply the B-quartet inference algorithm of Allman et al. (2022), Allman et al. (2024) 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

critical value for cut or T3 test

beta

critical value 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

Allman ES, Baños H, Mitchell JD, Rhodes JA (2022). “The tree of blobs of a species network: identifiability under the coalescent.” Journal of Mathematical Biology, 86(1), 10. doi:10.1007/s00285-022-01838-9.

Allman ES, Baños H, Mitchell JD, Rhodes JA (2024). “TINNIK: Inference of the Tree of Blobs of Species Networks Under the Coalescent.” draft.

See Also

quartetTable,quartetTableResolved,quartetStarTest, quartetCutTest, quartetStarTestInd, quartetCutTestInd

Examples

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