nprcgenekeepr (version 2.0.0)

checkParentAge: Check parent ages against a minimum age

Description

Ensure parents are sufficiently older than offspring

Usage

checkParentAge(
  sb,
  minSireAge = NULL,
  minDamAge = NULL,
  minParentAge = lifecycle::deprecated(),
  reportErrors = FALSE
)

Value

A dataframe containing rows for each animal where one or more parent was less than minParentAge. It contains all of the columns in the original sb dataframe with the following added columns:

1. sireBirth -- sire's birth date

2. sireAge -- age of sire in years on the date indicated by birth.

3. damBirth -- dam's birth date

4. damAge -- age of dam in years on the date indicated by birth.

Arguments

sb

A dataframe containing a table of pedigree and demographic information.

minSireAge

numeric minimum age in years for a male to have sired an offspring. NULL (default) looks up the floor for each sire's species via getSpeciesMinBreedingAge (falling back to 2 years when the species is missing or unknown); a supplied value overrides that floor for all sires. The check is not performed for animals with missing birth dates.

minDamAge

numeric minimum age in years for a female to have borne an offspring. NULL (default) looks up the floor for each dam's species via getSpeciesMinBreedingAge (falling back to 2 years when the species is missing or unknown); a supplied value overrides that floor for all dams.

minParentAge

Deprecated scalar minimum parent age. Supplying it sets both minSireAge and minDamAge; use those sex-specific parameters instead.

reportErrors

logical value if TRUE will scan the entire file and make a list of all errors found. The errors will be returned in a list of list where each sublist is a type of error found.

Examples

library(nprcgenekeepr)
qcPed <- nprcgenekeepr::qcPed
checkParentAge(qcPed, minSireAge = 2L, minDamAge = 2L)
checkParentAge(qcPed, minSireAge = 3L, minDamAge = 3L)
checkParentAge(qcPed, minSireAge = 5L, minDamAge = 5L)
checkParentAge(qcPed, minSireAge = 6L, minDamAge = 6L)
head(checkParentAge(qcPed, minSireAge = 10L, minDamAge = 10L))