addUIds: Add placeholder IDs for unknown parents

In nprcgenekeepr: Genetic Tools for Colony Management

Add placeholder IDs for unknown parents

Description

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").

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").

Value

The updated pedigree with partial parentage removed.

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

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.