Ensure parents are sufficiently older than offspring
Arguments
- sb
A dataframe containing a table of pedigree and demographic information.
- minParentAge
numeric values to set the minimum age in years for an animal to have an offspring. Defaults to 2 years. The check is not performed for animals with missing birth dates.
- 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:
{sireBirth} {sire's birth date}
{sireAge} {age of sire in years on the date indicated by
birth.}{damBirth} {dam's birth date}
damAge{age of dam in years on the date indicated bybirth.}
Examples
library(nprcgenekeepr)
qcPed <- nprcgenekeepr::qcPed
checkParentAge(qcPed, minParentAge = 2L)
#> [1] dam sire id sex gen birth exit
#> [8] age sireBirth damBirth sireAge damAge
#> <0 rows> (or 0-length row.names)
checkParentAge(qcPed, minParentAge = 3L)
#> [1] dam sire id sex gen birth exit
#> [8] age sireBirth damBirth sireAge damAge
#> <0 rows> (or 0-length row.names)
checkParentAge(qcPed, minParentAge = 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, minParentAge = 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, minParentAge = 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