LumpIntoClades: Lump into clades
In BMhyd: PCM for Hybridization

Description Usage Arguments Details Value Author(s) References Examples

This function Lump the hybrid species into a clades

1	LumpIntoClades(phy,flow)

`phy`	a phylogeny of phylo class
`flow`	structure of gene flow

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

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

Brian O'Meara, Dwueng-Chwuan Jhwueng.

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

	#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)