EM_phylo <- function(wt, init_par, n_trees=10, n_it=30, printpar=TRUE, mu=0.1, impsam=FALSE, tol=0.0001, parallel=F, method=1){
n_pars = length(init_par)
pars = init_par
Pars = matrix(nrow=(n_it+1),ncol=n_pars)
#El = vector(mode='numeric',length = n_it) #?
#x1 = c(0,2,1)
#x2 = c(20,2,1)
i = 1
qt = c(0,0,0)
q = vector(mode='numeric',length = n_it)
Pars[i,] = pars
while(i <= n_it){ #dist(rbind(x1, x2)) > tol &
if(printpar){
print(pars)
print(paste('iteration #',i,':'))
}
#,'are parameters on iteration',i,'and took',q[3],'segs'))
#x1vector(mode='numeric',length = n_it) = pars
p = proc.time()
trees <- sim_srt(wt=wt, pars=pars, n_trees=n_trees, rec_method=method, parallel = parallel)
pars = subplex(par = pars, fn = llik_st, setoftrees = trees, impsam = impsam)$par
#x2 = pars
Pars[(i+1),] = pars
qt = proc.time()-p
q[i] = qt[3]
i = i+1
}
return(list(pars=Pars, times=q))
}
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