LumpIntoClades: Lump into clades

Description Usage Arguments Details Value Author(s) References Examples

Description

This function Lump the hybrid species into a clades

Usage

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LumpIntoClades(phy,flow)

Arguments

phy

a phylogeny of phylo class

flow

structure of gene flow

Details

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

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.

Author(s)

Brian O'Meara, Dwueng-Chwuan Jhwueng.

References

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

Examples

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	#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) 
	

BMhyd documentation built on May 2, 2019, 8:27 a.m.

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