TINNIKdist: Compute TINNIK distance from quartets and hypothesis test p-values
Description
Apply the B-quartet inference algorithm of ABMR22;textualMSCquartets, ABMR24;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)
Value
a distance table output$dist and
a vector output$Bquartets with TRUE/FALSE entries indicating B-quartets
ordered as rows of pTable.
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.