Eliminates partial parentage situations by adding unique placeholder IDs for the unknown parent.

This must be run prior to addParents since the IDs made herein are used by addParents

Usage

addUIds(ped, format = getAutoIdFormat())

Arguments

ped: datatable that is the Pedigree. It contains pedigree information. The fields sire and dam are required.
format: sprintf template for the generated placeholder IDs; defaults to getAutoIdFormat() ("U%04d").

Value

The updated pedigree with partial parentage removed.

Details

The generated placeholder IDs default to the form Unnnn (a leading "U" plus a zero-padded integer), so they are alphanumeric and never contain a period ("."), honoring the ID rule enforced at data input by qcStudbook. The format is configurable via setAutoIdFormat (default "U%04d").

Examples

pedTwo <- data.frame(
  id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
  sire = c(NA, "s0", "s4", NA, "s1", "s1", "s2", "s2"),
  dam = c("d0", "d0", "d4", NA, "d1", "d2", "d2", "d2"),
  sex = c("M", "F", "M", "F", "F", "F", "F", "M"),
  stringsAsFactors = FALSE
)
newPed <- addUIds(pedTwo)
newPed[newPed$id == "s1", ]
#>   id  sire dam sex
#> 1 s1 U0001  d0   M
pedThree <-
  data.frame(
    id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
    sire = c("s0", "s0", "s4", NA, "s1", "s1", "s2", "s2"),
    dam = c(NA, "d0", "d4", NA, "d1", "d2", "d2", "d2"),
    sex = c("M", "F", "M", "F", "F", "F", "F", "M"),
    stringsAsFactors = FALSE
  )
newPed <- addUIds(pedThree)
newPed[newPed$id == "s1", ]
#>   id sire   dam sex
#> 1 s1   s0 U0001   M