Ensure parents are sufficiently older than offspring
checkParentAge(sb, minParentAge = 2, reportErrors = FALSE)
| 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. |
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 by birth.
# \donttest{ library(nprcgenekeepr) qcPed <- nprcgenekeepr::qcPed checkParentAge(qcPed, minParentAge = 2)#> [1] dam sire id sex gen birth exit #> [8] age sireBirth damBirth sireAge damAge #> <0 rows> (or 0-length row.names)checkParentAge(qcPed, minParentAge = 3)#> [1] dam sire id sex gen birth exit #> [8] age sireBirth damBirth sireAge damAge #> <0 rows> (or 0-length row.names)checkParentAge(qcPed, minParentAge = 5)#> 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 4.59checkParentAge(qcPed, minParentAge = 6)#> 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 5.67checkParentAge(qcPed, minParentAge = 10)#> 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 #> 16 596J7E UKK94T 6MIRJI F 1 1977-05-20 1996-05-06 19.0 <NA> #> 17 5I9OO3 MPR81X INGWI7 F 5 2015-10-24 <NA> 3.7 1997-02-17 #> 19 67RZLW HBEMKY KCOUSL F 3 2002-11-12 2017-05-05 14.5 1995-03-21 #> 20 6EBYMM YRCQFO 8KM1MP F 5 2013-05-22 <NA> 6.1 1994-04-30 #> 21 6EJ6RI 0RZ5LL MPAZXU F 1 1978-04-03 2005-06-27 27.2 1971-01-05 #> 23 6IPOZK HRQJQR ZLPSUH M 2 1988-12-06 2008-12-12 20.0 1969-12-04 #> 24 6MIRJI F0YSEE QBLTI6 M 2 1987-12-27 2002-07-15 14.5 1980-10-16 #> 27 6OL4PZ UMSQ78 HN5YTI F 2 1989-11-09 2008-10-26 19.0 <NA> #> 30 80EOVS MPR81X EUG3WE F 4 2015-01-22 <NA> 4.4 1997-02-17 #> 32 82IE3M QBLTI6 CN4GMN M 3 1999-08-24 <NA> 19.8 1987-12-27 #> 36 95U2JO HP3E04 0DAV0I M 4 2014-10-23 <NA> 4.7 2007-03-24 #> 37 9AZMHA 716P7O RJI1ET F 1 1982-03-24 2002-09-19 20.5 1975-01-30 #> 41 9UAWP7 1MDPFZ 309VM2 F 4 2016-05-19 <NA> 3.1 1998-12-12 #> 46 AXDMJM WMUJC5 HLI95R F 4 2015-01-14 <NA> 4.4 2006-07-24 #> 47 BA0JYM BCSR2N 2KULR3 F 3 2013-06-18 <NA> 6.0 1995-06-06 #> 51 BRLQFI DZ3B9K BNMWNZ F 4 1999-10-01 2014-07-25 14.8 1988-10-27 #> 52 BVFJGE UPR4NB V5L8XH F 2 1993-06-06 2008-10-16 15.4 <NA> #> 54 CJ49U3 TNAWBK 1MDPFZ M 3 1998-12-12 <NA> 20.5 1989-03-10 #> 56 CNPGS5 9Z9TIJ L8SZ2V F 1 1979-06-12 1998-10-25 19.4 1965-12-18 #> 58 CV1SHY 4UTH8P 2IXJ2N F 4 2013-05-21 <NA> 6.1 1998-11-15 #> 63 EX98QB UAJJG4 L8Q55X F 2 1993-09-23 2007-05-16 13.6 <NA> #> 64 F50D26 HRQJQR 6IPOZK F 1 1979-02-09 2005-06-03 26.3 1969-12-04 #> 69 GJ39EY QDY8I7 4KWUTK M 2 1986-04-01 2006-06-20 20.2 1979-02-07 #> 70 HAQR9N V8VU31 RI0O7F F 3 2015-01-09 <NA> 4.4 2005-03-27 #> 71 HFEQNK V8VU31 170ZTZ F 3 2015-02-07 <NA> 4.4 2005-03-27 #> 73 HN5YTI U2Y0HA 2ENDCF F 3 1999-05-05 2017-07-28 18.2 <NA> #> 79 JPKPJC UA2A8P HBEMKY M 2 1995-03-21 2013-10-15 18.6 <NA> #> 83 K0M40I QDY8I7 NQ91B2 F 2 1989-09-22 2010-01-11 20.3 1979-02-07 #> 84 K7QBLH ZWBMTP H00H7D M 2 1996-12-03 2011-02-20 14.2 1978-07-11 #> 89 KY0D3C UYNXK3 48YAZ5 M 3 1998-11-29 2008-10-11 9.9 <NA> #> 90 L42X7I ULYO4W BA0JYM F 2 2004-02-29 <NA> 15.3 <NA> #> 95 MBJMH1 UONB0Y 3CQZ3E F 1 1981-09-22 2001-11-04 20.1 <NA> #> 96 MF8X1C WMUJC5 JGPN6K F 4 2013-07-02 <NA> 6.0 2006-07-24 #> 98 MRGPPA U7F4QJ JUMNN0 F 3 1993-12-31 2008-04-30 14.3 <NA> #> 100 NQ91B2 QDY8I7 MPR81X M 3 1997-02-17 2016-08-17 19.5 1979-02-07 #> 101 NY9FEC H00H7D WMUJC5 M 3 2006-07-24 <NA> 12.9 1996-12-03 #> 102 O4Z4IB UYLDPW HFEQNK F 2 1996-03-20 2017-02-04 20.9 <NA> #> 107 OY032S YIAD2N Z4HGIR F 3 1999-05-07 2016-11-01 17.5 1991-03-11 #> 108 P4CQ2T HRBVOE 168Q0A M 1 1978-10-29 1993-09-15 14.9 1970-12-04 #> 111 PU7JEL HRBVOE QR5CMP M 2 1985-02-16 2001-01-13 15.9 1970-12-04 #> 115 Q444GQ MPR81X DD1U77 F 4 2014-03-31 <NA> 5.2 1997-02-17 #> 117 R34BVI 48YAZ5 6EBYMM F 4 2005-12-26 <NA> 13.5 1998-11-29 #> 118 RD6KMA HRBVOE OTAC9O F 1 1979-12-18 2002-01-25 22.1 1970-12-04 #> 119 RD6KMA HRBVOE ZWBMTP M 1 1978-07-11 1999-02-23 20.6 1970-12-04 #> 121 RRWDL5 V8VU31 7M51X5 F 3 2015-01-30 <NA> 4.4 2005-03-27 #> 123 RTTX6H YIAD2N J3D3N5 M 3 2001-01-25 <NA> 18.4 1991-03-11 #> 124 RX08B3 CQMWGX DZ3B9K M 3 1988-10-27 2007-06-30 18.7 1979-05-15 #> 125 RY6OPR 549AEC 80EOVS F 3 2005-12-10 <NA> 13.5 1998-09-27 #> 126 S8IEHH H0UP6R 2YGWN0 M 3 1998-03-03 2017-06-15 19.3 1989-01-08 #> 127 SAAU6D V8VU31 DR5GXB F 4 2015-02-23 <NA> 4.3 2005-03-27 #> 133 TWWT1N ODSV6N QDY8I7 M 1 1979-02-07 1999-01-04 19.9 1970-01-08 #> 138 WHKS5E IZ0ELE CV1SHY F 3 2006-04-24 <NA> 13.2 1999-05-30 #> 141 XHP9KQ HRQJQR AD0UE1 F 1 1978-12-12 2005-03-15 26.3 1969-12-04 #> 144 Y5QZ1U UHR4CA 8Q43EX F 1 1990-02-04 2004-07-02 14.4 <NA> #> 146 YHI773 C09A7K TNAWBK M 2 1989-03-10 2006-07-26 17.4 1972-12-25 #> 152 ZQ0DRX ONA6E5 GJ39EY F 1 1977-05-02 2003-02-11 25.8 1964-12-05 #> 155 ZXJQQ5 MQB1AE JNWPY2 F 1 1979-09-24 2002-09-03 22.9 1969-01-30 #> 156 ZYTIYY UP4NEJ E5BLUE F 1 1980-08-22 1998-11-18 18.2 <NA> #> 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 #> 16 1968-12-21 NA 8.41 #> 17 2007-10-21 18.68 8.01 #> 19 1990-07-21 7.65 12.31 #> 20 2005-12-26 19.06 7.40 #> 21 1964-12-02 7.24 13.33 #> 23 1979-02-09 19.01 9.82 #> 24 1977-05-20 7.20 10.60 #> 27 1982-07-13 NA 7.33 #> 30 2005-12-10 17.93 9.12 #> 32 1991-01-15 11.66 8.61 #> 36 2002-12-10 7.58 11.87 #> 37 1970-01-15 7.15 12.19 #> 41 2006-05-23 17.43 9.99 #> 46 1999-11-09 8.48 15.18 #> 47 2004-02-29 18.03 9.30 #> 51 1991-12-31 10.93 7.75 #> 52 1986-12-08 NA 6.49 #> 54 1987-04-06 9.76 11.69 #> 56 1969-12-11 13.48 9.50 #> 58 2006-04-24 14.51 7.07 #> 63 1989-02-18 NA 4.59 #> 64 1969-01-21 9.18 10.05 #> 69 1977-05-02 7.15 8.91 #> 70 1999-10-12 9.79 15.24 #> 71 1996-03-20 9.87 18.89 #> 73 1989-11-09 NA 9.48 #> 79 1986-03-07 NA 9.04 #> 83 1979-11-17 10.62 9.85 #> 84 1989-03-06 18.40 7.75 #> 89 1992-09-14 NA 6.21 #> 90 1998-09-17 NA 5.45 #> 95 1975-01-23 NA 6.66 #> 96 2000-02-08 6.94 13.40 #> 98 1988-03-19 NA 5.79 #> 100 1989-09-22 18.03 7.41 #> 101 1995-02-06 9.64 11.46 #> 102 1990-08-29 NA 5.56 #> 107 1984-09-27 8.16 14.61 #> 108 1968-01-20 7.90 10.77 #> 111 1978-03-04 14.20 6.96 #> 115 2004-10-08 17.11 9.48 #> 117 1992-12-12 7.07 13.04 #> 118 1968-12-13 9.04 11.01 #> 119 1968-12-13 7.60 9.57 #> 121 1994-12-25 9.85 20.10 #> 123 1989-01-23 9.88 12.01 #> 124 1980-07-11 9.45 8.30 #> 125 2000-02-29 7.20 5.78 #> 126 1989-11-24 9.15 8.27 #> 127 2005-02-15 9.91 10.02 #> 133 <NA> 9.08 NA #> 138 1990-11-24 6.90 15.41 #> 141 1970-01-04 9.02 8.94 #> 144 1983-12-11 NA 6.15 #> 146 1980-03-18 16.21 8.98 #> 152 1968-01-09 12.41 9.31 #> 155 1970-01-03 10.65 9.72 #> 156 1974-12-21 NA 5.67# }