combineCycleResolutions: Combine several cycle resolutions on a tree of blobs to...

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

Combine several cycle resolutions on a tree of blobs to create a network

Description

Given a list of resolutions of different multifurcations on a tree of blobs (each as produced by resolveCycle), combine these with the tree of blobs to form a network.

Usage

combineCycleResolutions(ToB, resolutions, plot = 1, titletext = NULL)

Arguments

ToB	an unrooted tree of blobs for the network, with multifurcating nodes labelled by labelIntNodes
resolutions	a list of resolutions (each of which may be a list) for different nodes with elements in format described in output of resolveCycle
plot	if FALSE (0), no plots; if TRUE (>0) plot networks
titletext	a string of text for plot

Details

This function is useful for forming near-optimal networks when there are several resolutions that have similar fit for some of the multifurcations.

Value

a list of Newick strings for the networks, with all edge lengths 1

See Also

TINNIK, labelIntNodes, resolveCycle, resolveLevel1

Examples

data(pTableYeastRokas)
out=TINNIK(pTableYeastRokas, alpha=.01, beta=.05)
ToB=labelIntNodes(out$ToB)
R9=resolveCycle(ToB, node=9, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")
R10=resolveCycle(ToB, node=10, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")
combineCycleResolutions(ToB, resolutions=list(R9,R10),plot=TRUE)

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