Nothing
paramlinkConditional = function(Nsim = 5, datamatrix, loci, pedigrees,
truePed = 1, ref=NULL, available = NULL, prior=NULL, seed = NULL){
Npeds = length(pedigrees)
Nmark = length(loci)
persons = rownames(datamatrix)
lik = LR = array(1,dim=c(Nmark, Nsim, Npeds))
set.seed(seed)
simData = matrix(ncol=2, nrow=length(persons))
for (s in 1:Nmark){
foo = paramlinkConditionalOne(Nsim = Nsim, mark=s, datamatrix, loci, pedigrees,
truePed = truePed, available = available, seed = NULL, ref=ref)
lik[s,,] = foo$lik*lik[s,,]
LR[s,,] = foo$LR*LR[s,,]
simData = cbind(simData, foo$simDatamatrix[,1:2])
}
LRall = likall = matrix(1, nrow=Nsim, ncol = Npeds)
for (i in 1:Nmark){
LRall = LRall*LR[i,,]
likall = likall*lik[i,,]
}
list(LR.All.Markers = LRall, lik.All.Markers = likall,
LR.Per.Marker = LR, lik.Per.Marker =lik, first.Sim = simData[,-c(1:2)])
}
paramlinkConditionalOne = function(Nsim = 5, mark=1, ref=2, datamatrix,
loci, pedigrees, truePed = 1, available = NULL, prior=NULL, seed = NULL){
# Simulates markerdata for truePed and marker mark
x = Familias2linkdat(pedigrees, datamatrix, loci) #fjernet truePed
target.num = if(is.character(available)) label2num(available,
pedigrees) else available
sim1 = markerSim(x[[truePed]], Nsim, available=target.num, partialmarker=mark, verbose=F, seed=seed) # la til
sim.df = NULL
Npeds = length(pedigrees)
lik = matrix(NA, ncol=Npeds, nrow=Nsim)
for(i in 1:Npeds){
ped = if(inherits(x[[i]], 'linkdat')) removeMarkers(x[[i]]) else
lapply(x[[i]], removeMarkers)
ped = transferMarkerdata(sim1, ped)
lik[,i] = sapply(1:Nsim, function(j) likelihood(ped, j))
}
LR = t(apply(lik,1, function(x, ref) x/x[ref], ref))
list(LR=LR, lik=lik, simData=sim1, simDatamatrix=sim.df)
}
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