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FamiliasConditional= function(Nsim = 5, datamatrix, loci, pedigrees,
truePed = 1, available = NULL, ref=2, 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 = FamiliasConditionalOne(Nsim = Nsim, mark=s, datamatrix, persons, 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$simDatamatrix[,1:2])
}
LRall = likall = matrix(1, nrow=Nsim, ncol = Npeds)
for (i in 1:Nmark){
LRall = LRall*LR[i,,]
likall = likall*lik[i,,]
}
list(LR.All.Markers = LRall, lik.All.Markers = likall,
LR.Per.Marker = LR, lik.Per.Marker =lik, first.Sim = simData[,-c(1:2)])
}
FamiliasConditionalOne = function(Nsim = 5, mark=1, ref=2, datamatrix, persons,
loci, pedigrees, truePed = 1, available = NULL, prior=NULL, seed = NULL){
# Simulates markerdata for truePed and marker mark
x = Familias2linkdat(pedigrees, datamatrix, loci)
target.num = if(is.character(available)) label2num(available,pedigrees) else available
sim1 = markerSim(x[[truePed]], Nsim, available=target.num,
partialmarker=mark, verbose=FALSE, seed=seed)
# Fills sim.df, datamatrix, for Familias
sim.df = if(inherits(sim1, 'linkdat')) as.data.frame(sim1) else
do.call(rbind, lapply(sim1, as.data.frame))
persons.ordered = if(inherits(sim1, 'linkdat')) sim1$plot.labels else
unlist(lapply(sim1,function(z) z$plot.labels))
rownames(sim.df) = persons.ordered
sim.df = sim.df[intersect(persons.ordered, persons),-c(1:5)]
sim.df[sim.df==0]=NA
#One locus made for each simulation
reploci = rep(loci[mark], Nsim)
repnames = paste(loci[[mark]]$locusname, 1:Nsim, sep="_")
names(reploci) = repnames
for(i in seq_along(reploci)) reploci[[i]]$locusname = repnames[i]
if(is.null(prior)) {
lp = length(pedigrees)
prior = rep(1/lp,lp)
}
res = FamiliasPosterior(pedigrees, reploci, sim.df, ref=ref, prior=prior)
list(LR=res$LRperMarker, lik=res$likelihoodsPerSystem, simData=sim1,
simDatamatrix=sim.df)
}
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