Nothing
setMethod(f = "ILS",signature = "CGHdata",
definition = function(.Object,CGHo,uniKmax,multiKmax){
tol = 1e-2
select.tmp = CGHo["select"]
select(CGHo) = "none"
command = parse(text = "invisible(list(mu = mu, theta = B,loglik = loglik,nbiter = iter))")
nbdata = Reduce("sum",lapply(.Object@Y,FUN = function(y){length(y[!is.na(y)])}) )
M = length(names(.Object@Y))
n.com = length(.Object@Y[[1]])
eps = Inf
iter = 0
mu = multisegmean(.Object,CGHo,uniKmax,multiKmax)$mu
B = list(waveffect = rep(0,n.com), GCeffect = rep(0,n.com))
mu.tmp = mu
while ( (eps > tol) & (iter < CGHo@itermax)){
iter = iter+1
B = getbias(.Object,CGHo,mu,B)
removebias(.Object) = B$waveffect+B$GCeffect
mu = multisegmean(.Object,CGHo,uniKmax,multiKmax)$mu
revertbias(.Object) = B$waveffect+B$GCeffect
eps = max(sapply(names(.Object@Y),FUN=function(m,x,y){
xk = rep(x[[m]]$mean,x[[m]]$end-x[[m]]$begin+1);
yk =rep(y[[m]]$mean,y[[m]]$end-y[[m]]$begin+1) ;
return(max(abs((xk-yk)/xk)))},mu.tmp,mu))
mu.tmp = mu
} # end while
out.DP2EM = DP2EM(.Object,mu,theta=Reduce("+",B))
RSS = 0.5*sum(out.DP2EM$nk*(out.DP2EM$x2k-(out.DP2EM$xk)^2))
n = Reduce("sum",lapply(.Object@Y,FUN = function(y){length(y[!is.na(y)])}))
loglik = -(n/2)*(log(2*pi*RSS/n)+1)
select(CGHo) = select.tmp
eval(command)
})
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