Check parent ages against a minimum age

Ensure parents are sufficiently older than offspring

Usage

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

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.

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.

Examples

library(nprcgenekeepr)
qcPed <- nprcgenekeepr::qcPed
checkParentAge(qcPed, minSireAge = 2L, minDamAge = 2L)
#>  [1] dam       sire      id        sex       gen       birth     exit     
#>  [8] age       sireBirth damBirth  sireAge   damAge   
#> <0 rows> (or 0-length row.names)
checkParentAge(qcPed, minSireAge = 3L, minDamAge = 3L)
#>  [1] dam       sire      id        sex       gen       birth     exit     
#>  [8] age       sireBirth damBirth  sireAge   damAge   
#> <0 rows> (or 0-length row.names)
checkParentAge(qcPed, minSireAge = 5L, minDamAge = 5L)
#>       dam   sire     id sex gen      birth       exit  age sireBirth   damBirth
#> 63 EX98QB UAJJG4 L8Q55X   F   2 1993-09-23 2007-05-16 13.6      <NA> 1989-02-18
#>    sireAge damAge
#> 63      NA   4.59
checkParentAge(qcPed, minSireAge = 6L, minDamAge = 6L)
#>        dam   sire     id sex gen      birth       exit  age  sireBirth
#> 63  EX98QB UAJJG4 L8Q55X   F   2 1993-09-23 2007-05-16 13.6       <NA>
#> 90  L42X7I ULYO4W BA0JYM   F   2 2004-02-29       <NA> 15.3       <NA>
#> 98  MRGPPA U7F4QJ JUMNN0   F   3 1993-12-31 2008-04-30 14.3       <NA>
#> 102 O4Z4IB UYLDPW HFEQNK   F   2 1996-03-20 2017-02-04 20.9       <NA>
#> 125 RY6OPR 549AEC 80EOVS   F   3 2005-12-10       <NA> 13.5 1998-09-27
#> 156 ZYTIYY UP4NEJ E5BLUE   F   1 1980-08-22 1998-11-18 18.2       <NA>
#>       damBirth sireAge damAge
#> 63  1989-02-18      NA   4.59
#> 90  1998-09-17      NA   5.45
#> 98  1988-03-19      NA   5.79
#> 102 1990-08-29      NA   5.56
#> 125 2000-02-29     7.2   5.78
#> 156 1974-12-21      NA   5.67
head(checkParentAge(qcPed, minSireAge = 10L, minDamAge = 10L))
#>       dam   sire     id sex gen      birth       exit  age  sireBirth
#> 1  0DXI08 HRQJQR G6P0W4   F   1 1979-02-02 2000-04-15 21.2 1969-12-04
#> 2  0RV8OM QBLTI6 8IJUQO   F   3 1999-02-03 2017-04-27 18.2 1987-12-27
#> 11 3CQZ3E U0M96T MRGPPA   F   2 1988-03-19 2008-03-20 20.0       <NA>
#> 12 3O7TMT 5EP5AL L6D4ZC   M   2 1988-06-25 2009-04-10 20.8 1976-09-30
#> 13 43TUN9 L6D4ZC AXDMJM   F   3 1999-11-09       <NA> 19.6 1988-06-25
#> 15 4WB10I 5EP5AL DO4NKS   M   2 1991-08-04 2013-02-08 21.5 1976-09-30
#>      damBirth sireAge damAge
#> 1  1965-01-04    9.16  14.08
#> 2  1992-06-22   11.10   6.62
#> 11 1981-09-22      NA   6.49
#> 12 1981-09-15   11.73   6.78
#> 13 1990-07-14   11.37   9.32
#> 15 1982-03-30   14.84   9.35