Nothing
add.pedigree <- function(ped, IDadd, add.ancestors=FALSE){
if(!all.equal(class(ped), c("pedigree", "data.frame"))) stop(paste(substitute(ped), "has to be an object generated by create.pedigree()"))
if(!all.equal(class(IDadd), c("pedigree", "data.frame"))) stop(paste(substitute(IDadd), "has to be an object generated by create.pedigree()"))
# only unique IDs
IDped <- unique(rbind(ped[ped$ID %in%IDadd$ID, c("ID", "Par1", "Par2")], IDadd[IDadd$ID %in% ped$ID, c("ID", "Par1", "Par2")]))
if(length(unique(IDped[,"ID"]))!=nrow(IDped)) stop("IDs are not unique, removing duplicated individuals")
if(!is.null(ped$sex)&is.null(IDadd$sex)){
IDadd$sex <- NA
warning("No information on sex in ", substitute(IDadd), ". Values will be set to NA")
}
if(is.null(ped$sex)&!is.null(IDadd$sex)){
ped$sex <- NA
warning("No information on sex in ", substitute(ped), ". Values will be set to NA")
}
ped <- rbind(ped, IDadd[IDadd$gener==0,])
IDadd <- IDadd[!IDadd$ID %in% ped$ID,]
gener <- sort(unique(IDadd$gener))
for(i in gener){
geners <- cbind(ped$gener[match(IDadd$Par1[IDadd$gener==i], ped$ID)],
ped$gener[match(IDadd$Par2[IDadd$gener==i], ped$ID)])
geners <- apply(geners,1,max)+1
ped <- rbind(ped, IDadd[IDadd$gener==i,])
ped$gener[ped$ID %in% IDadd$ID[IDadd$gener==i]] <- geners
}
ped <- ped[order(ped$gener, ped$ID), ]
return(ped)
}
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