quartetNetworkDist: Compute network quartet distance between taxa
Description
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.
Usage
quartetNetworkDist(pTable, alpha, beta)
Value
a distance table
Arguments
pTable
a table of quartets and p-values, as computed by NANUQ, or
quartetTreeTestInd and quartetStarTestInd
alpha
a scalar significance level for judging p-values p_T3 indicating hybridization on quartet;
smaller value gives fewer hybridization decisions
beta
a scalar significance level for judging p-values p_star indicating quartet star tree;
smaller value gives fewer resolved tree decisions
Details
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.