Merge two centers' pedigrees via a curator-confirmed identity link

Collapses a transferred animal's two center-specific records into ONE node with its real parents intact, instead of leaving it as an artificial founder at the receiving center – the failure mode issue #130 names directly (a transferred animal loses its recorded lineage because the two centers use independent id namespaces). Follows the getPedigreeSource() design style (D5): a deterministic, curator-supplied cross-reference table, never coincidental same-string ids, and fail-loud validation on any ambiguity.

Usage

resolveCrossCenterIds(pedA, pedB, mapping)

Arguments

pedA

a pedigree data.frame for the first center, with (at least) columns id, sire, and dam.

pedB

a pedigree data.frame for the second center, with (at least) columns id, sire, and dam.

mapping

a data.frame with columns idA and idB: one row per curator-confirmed cross-center identity link, naming the same physical animal's id in pedA and in pedB. Each id may appear at most once in idA and at most once in idB.

Value

A single merged pedigree data.frame over the union of pedA's and pedB's columns, with one row per distinct animal (mapped pairs collapsed to their canonical idA id).

Details

For each mapping row, the two records collapse into one, keyed by the idA value (the canonical id): every reference to the mapped idB value anywhere in pedB – as that animal's own id or as a sire/dam pointer on any other animal – is rewritten to idA. The merged individual's sire/dam prefer whichever side has a non-NA value (this is what fixes the artificial-founder problem: a center that never knew the animal's real parents recorded NA, and the origin center's real parents win). A mapped pair whose two sides both record a non-NA, different sire or dam is a real data inconsistency, not something to silently pick a side on, so it errors instead. Animals not named in mapping pass through unchanged; an id string present in both pedA and pedB that is not declared in mapping is also an error – per D5, identity is established only by the explicit mapping table, never assumed from a coincidentally matching id string across the two centers' independent namespaces.

See also

getFileDirectRelatives

Examples

library(nprcgenekeepr)
pedA <- data.frame(
  id = c("P1", "P2", "T1"), sire = c(NA, NA, "P1"), dam = c(NA, NA, "P2"),
  stringsAsFactors = FALSE
)
## X9 is the SAME physical animal as T1, but Center B recorded it as an
## artificial founder because it never knew the real parents.
pedB <- data.frame(
  id = c("X9", "O1"), sire = c(NA, "X9"), dam = c(NA, NA),
  stringsAsFactors = FALSE
)
mapping <- data.frame(idA = "T1", idB = "X9", stringsAsFactors = FALSE)
resolveCrossCenterIds(pedA, pedB, mapping)
#>   id sire  dam
#> 1 P1 <NA> <NA>
#> 2 P2 <NA> <NA>
#> 3 T1   P1   P2
#> 4 O1   T1 <NA>