BMhyd (version 1.2-8)

LumpIntoClades: Lump into clades

Description

This function Lump the hybrid species into a clades

Usage

LumpIntoClades(phy,flow)

Arguments

phy

a phylogeny of phylo class

flow

structure of gene flow

Value

a flow table that contains the donor clade, recipient clade, proportion of the gene flow,time from root donor, and time from root recipient.

Details

The function summaries the flow structure into the clade where the donor clades contribute more than one recipient clades.

References

Jhwueng D.C. and O'Meara B.C. 2015. Trait evolution on phylogenetic networks. Submitted.

Examples

	#set the number of non hybrid species
	ntax.nonhybrid<-5
	#set the number of hybrid species
	ntax.hybrid<-2
	#simulate a network
	network<-SimulateNetwork(ntax.nonhybrid=ntax.nonhybrid, ntax.hybrid=ntax.hybrid, 
	flow.proportion=0.5, origin.type='clade', birth = 1, death = 0.5, sample.f = 0.5, 
	tree.height = 1, allow.ghost=FALSE)
	#show the flow
	network$flow	
	#show the new flow table
	LumpIntoClades(network$phy, network$flow)