quartetNetworkDist {MSCquartets}

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 Allman et al. (2019), generalizes the quartet distance of Rhodes (2020).

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

Allman ES, Baños H, Rhodes JA (2019). “NANUQ: A method for inferring species networks from gene trees under the coalescent model.” Algorithms Mol. Biol., 14(24), 1-25. doi:10.1186/s13015-019-0159-2.

Rhodes JA (2020). “Topological metrizations of trees, and new quartet methods of tree inference.” IEEE/ACM Trans. Comput. Biol. Bioinform., 17(6), 2107-2118. doi:10.1109/TCBB.2019.2917204.

See Also

NANUQ, NANUQdist

Examples

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