quartetNetworkDist: Compute network quartet distance between taxa

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

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 \insertCiteABR19;textualMSCquartets, generalizes the quartet distance of \insertCiteRho19;textualMSCquartets.

Usage

quartetNetworkDist(pTable, alpha, beta)

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.

Value

a distance table

References

\insertRef

ABR19MSCquartets

\insertRef

Rho19MSCquartets

See Also

NANUQ, NANUQdist

Examples

data(pTableYeastRokas)
dist=quartetNetworkDist(pTableYeastRokas, alpha=.05, beta=.95)

MSCquartets documentation built on Nov. 2, 2023, 5:32 p.m.