Nothing
`nLogLik.trec.A` = function(coef, phi, rc, genei, hessian=FALSE){
index = rc$index
y = rc$y[genei,]
kappas = rc$kappas
out = input.checks.A(coef=coef, phi=phi, index=index, y=y, kappas=kappas, trecase=FALSE)
hess = NULL
twosex = max(index)>4
if(twosex){
ind.lst = lapply(1:8, function(i){which(index %in% i)})
}else{
ind.lst = lapply(1:4, function(i){which(index %in% i)})
}
nsamples = length(index)
intercept = rep(1, nsamples)
dom = as.numeric(index %in% c(1, 2, 5, 6))
poo = rep(0, length(index))
poo[index %in% c(1, 5)] = 1
poo[index %in% c(2, 6)] = -1
if(twosex){
sex.tot = intercept;sex.tot[index>4] = -1
X = cbind(intercept, kappas, sex.tot, dom, dom*sex.tot, poo, poo*sex.tot)
}else{
X = cbind(intercept, kappas, dom, poo)
}
nll = ll.toRCI.A(coef, yi=y, ind.lst=ind.lst, X=X, twosex=twosex, iphi=1/phi)
if(hessian){
tag = tryCatch({
hess = hessian(ll.toRCI.A, x=coef, yi=y, ind.lst=ind.lst, X=X, twosex=twosex, iphi=1/phi)
0
}, error=function(e) {
warning("estimation of hessian failed")
1
})
}
return(list(nll=nll, hess=hess))
}
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