Description Usage Arguments Value Author(s) References Examples
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.
1 2 | GetMeansModified(x, phy, flow, actual.params)
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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. |
the species mean
Brian O'Meara, Dwueng-Chwuan Jhwueng.
Jhwueng D.C. and O'Meara B.C. 2015. Trait evolution on phylogenetic networks. Submitted.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | #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)
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