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LRparamlink = function(x, ref, markers) {
st = proc.time()
# get marker names
y = if(is.linkdat(x[[1]])) x[[1]] else x[[1]][[1]]
if(missing(markers)) markers = seq_len(y$nMark)
markernames = sapply(y$markerdata[markers], attr, "name")
# break all loops (NB: would use rapply, but doesnt work since is.list(linkdat) = TRUE
breaklp = function(a) if(class(a)[[1]] == "linkdat")
breakLoops(a,verbose=F) else a # avoid problems with singletons
x_loopfree = lapply(x, function(xx) if(is.linkdat.list(xx))
lapply(xx, breaklp) else breaklp(xx))
# compute likelihoods
liks = lapply(x_loopfree, function(xx) vapply(markers, function(i)
likelihood(xx, locus1=i), FUN.VALUE=1))
likelihoodsPerSystem = do.call(cbind, liks)
# LR per marker and total
LRperMarker = do.call(cbind, lapply(1:length(x), function(j)
liks[[j]]/liks[[ref]]))
LR = apply(LRperMarker,2,prod)
# output
time = proc.time()-st
rownames(likelihoodsPerSystem) = rownames(LRperMarker) = markernames
list(LR=LR, LRperMarker=LRperMarker,
likelihoodsPerSystem=likelihoodsPerSystem, time=time)
}
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