fit_sgd <- function(phylo, tot_time, par, f=1, meth="Nelder-Mead")
{
nobs <- Ntip(phylo)
p<-length(par)
lambert <- Phylo2Lambert(phylo)
lambert[1] <- tot_time
init<-par
optim_LH <- function(init)
{
likel <- LikelihoodSGDFromLambert(lambert, abs(init[1]), abs(init[2]), abs(init[3]), f)
LH <- likel[3]+likel[4]
return(-log(LH))
}
temp <- optim(init, optim_LH)
res<-list(model="sgd", LH=-temp$value, aicc=2*temp$value+2*p+(2*p*(p+1))/(nobs-p-1), par=c(birth = abs(temp$par[1]), growth = abs(temp$par[1])-abs(temp$par[2]), mutation = abs(temp$par[3])))
return(res)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.