Nothing
compute_bnrf <-
function(mpcross1, mpcross2, r, grid=FALSE)
{
output <- list()
nmrk1 <- ncol(mpcross1$founders)
nmrk2 <- ncol(mpcross2$founders)
n.finals <- length(mpcross1$id)
# pairs of loci
pairs <- expand.grid(1:nmrk1, (nmrk1+1):(nmrk1+nmrk2))
n.pairs <- nrow(pairs)
# order by rows
pairs <- pairs[order(pairs[,1], pairs[,2]), ]
# combine two sets of data
finals <- cbind(mpcross1$id, mpcross1$finals, mpcross2$finals)
founders <- cbind(mpcross1$founders, mpcross2$founders)
pedigree <- mpcross1$pedigree
rpairs <- CR_estrf(finals, founders, pedigree, pairs, r)
if (grid) output$lkhdgrid <- cbind(pairs, rpairs)
maxlkhd <- apply(rpairs, 1, max)
minlkhd <- apply(rpairs, 1, min)
same <- ((maxlkhd-minlkhd)<.000001)
tm <- r[apply(rpairs, 1, which.max)]
tm[which(same==TRUE)] <- NA
output$theta <- matrix(data=tm, nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
theta.5 <- which(r==0.5)
if (grid) output$lodgrid <- cbind(pairs, rpairs-rpairs[,theta.5])
lm <- apply(rpairs, 1, max)
output$lkhd <- matrix(data=lm, nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
lm <- apply(rpairs-rpairs[,theta.5], 1, max)
lm[which(same==TRUE)] <- NA
output$lod <- matrix(data=lm, nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
output$rgrid <- r
return(output)
}
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