# Sample data
# Anim = 1:16 # Can be alphanumeric too
# Sire = c(6,6,8,8,0,10,0,13,0,14,14,0,15,0,0,0) # Can be alphanumeric too
# Dam = c(5,5,7,9,0,11,12,0,0,0,0,0,16,0,0,0) # Can be alphanumeric too
# ped = data.frame(anim=Anim, sire=Sire, dam=Dam)


colnames(ped) = c("anim","sire","dam")
ped = data.frame(lapply(ped, as.character), stringsAsFactors=FALSE)
ped.old = ped
gen = 0
animgen = data.frame()

while(nrow(ped) > 0)
{
   tmp = ped[!ped$anim %in% ped$sire & !ped$anim %in% ped$dam,]$anim
   print(paste(length(tmp), 'animals in generation', gen))
   animgen = rbind(animgen, data.frame(anim = tmp, generation = gen))
   ped = ped[!ped$anim %in% tmp,]
   gen = gen - 1
}

animgen = animgen[order(animgen$gen, animgen$anim),]
animgen$newID = 1:nrow(animgen)
ped.new = ped.old

for(i in 1:nrow(animgen)) ped.new[ped.new==as.character(animgen$anim[i])] = paste0("_", animgen$newID[i])
ped.new$anim = as.integer(sub("_", "", ped.new$anim))
ped.new$sire = as.integer(sub("_", "", ped.new$sire))
ped.new$dam  = as.integer(sub("_", "", ped.new$dam))

print('ped.old is the old pedigree, and ped.new is the new pedigree.')