GetMeansModified: The species means for the network model

In BMhyd: PCM for Hybridization

Description

This function returns the species mean for the network model. For the non hybrid species, it returns as a parameter μ and for hybrid species it returns μ+ \log β.

Usage

	GetMeansModified(x, phy, flow, actual.params)
	

Arguments

x	vector of the parameters: including rate of evolution σ^2, overall mean μ, measurement error SE, hybrid vigor β, variation at the burst of hybridization v_H.
phy	a class of phylo tree.
flow	a flow struture of gene flow.
actual.params	The parameters that are related to the hybridzation including the hybrid vigor β and variation at the burst of hybridization v_H.

Value

the species mean

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

	#number of nonhybrd species
	ntax.nonhybrid<-5	
	#number of hybridspecies
	ntax.hybrid<-2
	#simulate 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)
    #set the parameter values
    sigma.sq <- 0.01;mu <- 1;SE <- 0;bt<-12;vh<-0
    par<-c(sigma.sq,mu,SE,bt,vh)
    names(par)<-c("sigma.sq","mu","SE","bt","vh")
    actual.params<-12
    names(actual.params)<-"bt"
	#calculate the species means
	GetMeansModified(par, network$phy, network$flow,actual.params)
	

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