Produce network quartet distance table for the NANUQ algorithm, from a table of quartets and p-values, and specified levels of quartet hypothesis tests. The network quartet distance, which is described more fully by ABR19;textualMSCquartets, generalizes the quartet distance of Rho19;textualMSCquartets.
quartetNetworkDist(pTable, alpha, beta)a distance table
a table of quartets and p-values, as computed by NANUQ, or
quartetTreeTestInd and quartetStarTestInd
a scalar significance level for judging p-values p_T3 indicating hybridization on quartet;
smaller value gives fewer hybridization decisions
a scalar significance level for judging p-values p_star indicating quartet star tree;
smaller value gives fewer resolved tree decisions
In case of a triple of quartet counts with the two largest equal and the third slighltly smaller,
along with alpha and beta leading to a star quartet being rejected and a tree not being rejected,
this function chooses a resolved quartet topology uniformly at random from the two largest counts. This is the only
stochastic element of the code, and its impact is usually negligible.
ABR19MSCquartets
Rho19MSCquartets
NANUQ, NANUQdist
data(pTableYeastRokas)
dist=quartetNetworkDist(pTableYeastRokas, alpha=.05, beta=.95)
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