Nothing
combine_rf <-
function(mpcross1, mpcross2, r)
{
output <- list()
rfb <- compute_bnrf(mpcross1, mpcross2, r)
# now combine the three pieces
nmrk1 <- ncol(mpcross1$founders)
nmrk2 <- ncol(mpcross2$founders)
ntot <- nmrk1+nmrk2
output$rgrid <- r
output$theta <- matrix(nrow=ntot, ncol=ntot)
output$lod <- matrix(nrow=ntot, ncol=ntot)
output$lkhd <- matrix(nrow=ntot, ncol=ntot)
output$theta[1:nmrk1, 1:nmrk1] <- mpcross1$rf$theta
output$lkhd[1:nmrk1, 1:nmrk1] <- mpcross1$rf$lkhd
output$lod[1:nmrk1, 1:nmrk1] <- mpcross1$rf$lod
output$theta[1:nmrk1, (nmrk1+1):ntot] <- (rfb$theta)
output$lkhd[1:nmrk1, (nmrk1+1):ntot] <- (rfb$lkhd)
output$lod[1:nmrk1, (nmrk1+1):ntot] <- (rfb$lod)
output$theta[(nmrk1+1):ntot, 1:nmrk1] <- t(rfb$theta)
output$lkhd[(nmrk1+1):ntot, 1:nmrk1] <- t(rfb$lkhd)
output$lod[(nmrk1+1):ntot, 1:nmrk1] <- t(rfb$lod)
output$theta[(nmrk1+1):ntot, (nmrk1+1):ntot] <- mpcross2$rf$theta
output$lkhd[(nmrk1+1):ntot, (nmrk1+1):ntot] <- mpcross2$rf$lkhd
output$lod[(nmrk1+1):ntot, (nmrk1+1):ntot] <- mpcross2$rf$lod
# modify the parts corresponding to the second set of data
# mpcross2$rf$lkhdgrid[,1:2] <- mpcross2$rf$lkhdgrid[,1:2]+nmrk1
# mpcross2$rf$lodgrid[,1:2] <- mpcross2$rf$lodgrid[,1:2]+nmrk1
# rfb$lkhdgrid[,2] <- rfb$lkhdgrid[,2]+nmrk1
# rfb$lodgrid[,2] <- rfb$lodgrid[,2]+nmrk1
# not working correctly at this time; need to fix up.
# output$lkhdgrid <- rbind(mpcross1$rf$lkhdgrid, rfb$lkhdgrid, mpcross2$rf$lkhdgrid)
# output$lodgrid <- rbind(mpcross1$rf$lodgrid, rfb$lodgrid, mpcross2$rf$lodgrid)
# output$markers <- c(mpcross1$rf$markers, mpcross2$rf$markers+nmrk1)
# output$mrk.names <- c(mpcross1$rf$mrk.names, mpcross2$rf$mrk.name)
colnames(output$theta) <- rownames(output$theta) <- colnames(output$lod) <- rownames(output$lod) <- colnames(output$lkhd) <- rownames(output$lkhd) <- c(colnames(mpcross1$finals), colnames(mpcross2$finals))
return(output)
}
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