1. 2004 2005 C. P. Van Tassell, G. R. Wiggans, and L. L. M. Thornton Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Investigation of Herds Years with Abnormal Distributions of Calving Ease Scores

2. 20042005 The Problem  Herds with unusual distributions of data affect evaluations of bulls  Worst case is when large share of records for a bull are in one “bad” herd  Herd reporting changes over time

3. 20042005 Percentage of Score by Parity In All Herds 0 10 20 30 40 50 60 70 80 90 100 12345 Calving Ease Score Counts by Herd-Parity (%) Parity 1 Parity 2+

4. Frequency of CE Scores by herd for HOUSA0000XXXXXXXX Herd 1 2 3 4 5 Total -------- -------- -------- -------- -------- -------- -------- 23050186 2 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 2 ( 1) 23380528 1 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 1 ( 1) 23600003 1 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 1 ( 1) 23600175 1 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 1 ( 1) 32460821 12 ( 18) 0 ( 0) 5 ( 8) 1 ( 2) 48 ( 73) 66 ( 34) ----------------------------------------------------------------------------------------------- 1380 ( 57) 467 ( 19) 410 ( 17) 76 ( 3) 78 ( 3) 2411 ----------------------------------------------------------------------------------------------- 33130011 1 ( 14) 2 ( 29) 4 ( 57) 0 ( 0) 0 ( 0) 7 ( 4) 33130548 4 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 4 ( 2) 33980149 2 ( 67) 1 ( 33) 0 ( 0) 0 ( 0) 0 ( 0) 3 ( 2) 34470727 1 (100) 0 ( 0) 0 ( 0) 0 ( 0) 0 ( 0) 1 ( 1) 35100522 0 ( 0) 1 ( 50) 0 ( 0) 1 ( 50) 0 ( 0) 2 ( 1) 35100639 4 ( 67) 2 ( 33) 0 ( 0) 0 ( 0) 0 ( 0) 6 ( 3)....... Example of a Problem Bull

5. 20042005 Concept  Identify ‘outlier’ herds  Remove that data  Determine if evaluation is ‘better’  Trade-off between edits for bad data and overall loss of data

6. 20042005 Test Edits  Exclude herds with abnormal distributions of scores  Abnormal herds defined by multinomial likelihood  Population frequencies for parity groups (1 vs. 2+) used for expected values  Herd test statistics calculated within parity (1 vs. 2+) and summed

7. 20042005 GOF Statistics  Multinomial distribution likelihood ratio with ‘expected’ distribution adjusted for herd size 

8. 20042005 Predictability of Future Evaluations  Compare evaluations from complete data to evaluations from partial data  Partial data truncated by:  Date of calving  Goodness of Fit (GOF) exclusion

9. 20042005 Strategy for Herd Exclusions  Adjacent herd-years also excluded if exceed a less extreme threshold  5-fold difference in likelihood  A future evaluation could potentially have fewer records than a previous run!

10. 20042005 Example Herd 1 year c1_1 c1_2 c1_3 c1_4 c1_5 sumh1 c2_1 c2_2 c2_3 c2_4 c2_5 sumh2 gof drop 1996 0 0 0 0 1 1 0 1 79 0 2 82 -214.07 1 1997 0 0 0 0 0 0 0 0 224 1 8 233 -1190.18 1 1998 0 0 34 0 0 34 0 0 304 0 3 307 -866.92 1 1999 0 0 60 0 4 64 0 0 290 0 3 293 -862.84 1 2000 0 0 3 0 0 3 0 0 213 0 0 213 -545.39 1 2002 21 0 0 0 0 21 87 0 150 0 0 237 -241.89 1 2003 100 15 8 4 1 128 322 6 7 2 0 337 -59.50 0 2004 148 15 13 3 1 180 273 8 0 0 0 281 -72.15 0

11. 20042005 Example Herd 2 year c1_1 c1_2 c1_3 c1_4 c1_5 sumh1 c2_1 c2_2 c2_3 c2_4 c2_5 sumh2 gof drop 1995 15 1 0 0 0 16 25 1 0 0 0 26 -1.917 0 1996 98 39 9 2 0 148 425 27 3 0 0 455 -49.103 0 1997 188 66 64 4 0 322 545 100 38 1 1 685 -41.237 0 1998 307 66 90 22 0 485 1382 168 113 12 4 1679 -36.192 0 1999 407 115 97 9 3 631 1597 170 105 8 3 1883 -63.533 0 2000 372 183 183 4 1 743 1343 258 141 4 8 1754 -110.008 1 2001 341 293 184 1 7 826 1078 513 198 4 6 1799 -346.880 1 2002 219 258 171 2 7 657 923 596 162 6 2 1689 -468.204 1 2003 165 309 183 5 4 666 652 590 242 14 6 1504 -657.263 1 2004 273 261 126 3 5 668 804 385 181 10 8 1388 -251.784 1

12. 20042005 Percentage of Score by Parity In All (AN) and GOF4 Excluded (AG) Herds 0 10 20 30 40 50 60 70 80 90 100 12345 Calving Ease Score Counts by Herd-Parity (%) Parity 1 - AN Parity 2 - AN Parity 1 - AG Parity 2 - AG

13. 20042005 Conclusions  GOF test excludes herds with poor score distribution uniformly across herd size  Exclusion of herds results in loss of evaluations for some bulls  Exclusion of data is expected to improve run to run stability

14. 20042005 Remaining Issues  Optimum amount of data to exclude  Evaluate different fractions of data removal  Recently submitted test run to InterBull with 1.5% data excluded  Will likely move to 7% data discarded  Will conduct sensitivity analysis to assess optimal data discard  Current InterBull test run for calving ease

15. 20042005 Frequency of Codes in Combined Interbull File CodeSource Official Report FrequencyPercent Cumulative FrequencyPercent Sire Calving Ease CFrom correlationNo53674.7753674.77 DDomesticNo15,07313.4020,44018.17 DDomesticYes26,04923.1546,48941.32 IInterbullYes22,80920.2769,29861.59 PSire MGS IndicesYes43,20838.41112,506100.00 Daughter Calving Ease CFrom correlationYes10,7929.5910,7929.59 DDomesticNo15,07313.4025,86522.99 DDomesticYes26,04923.1551,91446.14 IInterbullYes17,38415.4569,29861.59 PSire MGS IndicesYes43,20838.41112,506100.00