blobDistance: Compute empirical distance between taxon groups.

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

Compute empirical distance between taxon groups.

Description

From gene quartet counts, computes NANUQ or modNANUQ distances between groups of taxa (which should be those around a multifurcation in a tree of blobs. If these groups are not singletons, averaging is done over group elements.

Usage

blobDistance(pTable, taxa, groupvec, test = "T3", alpha, beta, dist = "NANUQ")

Arguments

pTable	table of giving empirical gene quartet counts for the taxa on tree, with columns p_star and p_test
taxa	a list of taxon names, who positions are used in 'groups'
groupvec	taxon groups encoded in vector
test	to be used for detecting hybridizations in quartete ("T3" or "cut")
alpha	test level for p_test
beta	test level for p_star
dist	the distance to compute, either "NANUQ" or "modNANUQ"

Value

the distance matrix, ordered by taxon group number

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.