Create a colony snapshot row from a genetic value report — createColonySnapshot • nprcgenekeepr

Turns one reportGV result into a one-row data.frame in the 27-column snapshot-history schema (issue #167, schema version 1), ready for appendColonySnapshot. Every metric field is a value the nprcgenekeeprGV object already carries, or a Summary Statistics aggregate (mean/median/calcSkewness/ calcKurtosis, NA removed) of its per-animal indivMeanKin/gu/guSE report columns, stored at full precision — no estimator is recomputed or duplicated.

Usage

createColonySnapshot(
  ped,
  geneticValue,
  membershipRule,
  guIter,
  guThresh,
  snapshotDate = Sys.Date()
)

Arguments

ped: The pedigree data.frame the reportGV analysis was run on, carrying at least an id column (plus the logical population column when membershipRule is "focalPopulation").
geneticValue: An object of class nprcgenekeeprGV as returned by reportGV.
membershipRule: Single string naming how the analysis population was assembled; one of "wholePedigree" or "focalPopulation".
guIter: Single positive whole number: the guIter value the reportGV call used. Required — there is no default.
guThresh: Single positive whole number: the guThresh value the reportGV call used. Required — there is no default.
snapshotDate: The snapshot's date: a Date or an ISO-8601 (YYYY-MM-DD) string. Defaults to Sys.Date().

Value

A one-row data.frame in the 27-column snapshot-history schema; it passes checkSnapshotHistory unchanged.

Details

guIter and guThresh are required because the reportGV return object does not carry them, and they are comparability provenance the snapshot must record truthfully: pass exactly the values the reportGV call used (its defaults are 1000L and 1L).

The claimed membershipRule is verified against ped and the report, and a contradiction stops:

"wholePedigree": the report covers exactly the animals in ped.
"focalPopulation": ped carries the logical population column (see setPopulation) and the report covers exactly ped$id[ped$population]. Pass the same population-designated pedigree the reportGV call analyzed.

Examples

ped <- nprcgenekeepr::qcPed
gv <- reportGV(ped, guIter = 10L)
snapshot <- createColonySnapshot(ped, gv, "wholePedigree",
  guIter = 10L, guThresh = 1L
)
history <- appendColonySnapshot(NULL, snapshot)