2004

2004

2005

C. P. Van Tassell, G. R. Wiggans, and L. L. M. ThorntonAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, MD

Investigation of Herds Years with Abnormal Distributions

of Calving Ease Scores

2004

2005

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

0

20

40

60

80

100

1 2 3 4 5

Calving Ease Scores - Herd 1

Scor

e by

Her

d (%

)

Parity 1Parity 2

0

20

40

60

80

100

1 2 3 4 5

Calving Ease Scores - Herd 2

Scor

e by

Her

d (%

)

2004

2005

Percentage of Score by Parity In All Herds

0102030405060708090

100

1 2 3 4 5

Calving Ease Score

Cou

nts

by H

erd

-Pari

ty (

%)

Parity 1

Parity 2+

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

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2005

Concept

Identify ‘outlier’ herds

Remove that data

Determine if evaluation is ‘better’

Trade-off between edits for bad data and overall loss of data

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2005

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

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2005

GOF Statistics

Multinomial distribution likelihood ratio with ‘expected’ distribution adjusted for herd size

2N

N

P)),pN,pN,pN,pN,pN,NLog(Multi(

N

P)),n,n,n,n,n,NLog(Multi(

GOF4

2

1 i i

i,5ii,4ii,3ii,2ii,1ii

2

1 i i

i,5i,4i,3i,2i,1i

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2005

Predictability of Future Evaluations

Compare evaluations from complete data to evaluations from partial data

Partial data truncated by:Date of calvingGoodness of Fit (GOF) exclusion

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2005

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!

2004

2005

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      11997       0      0       0       0       0        0        0      0 224      1       8      233     -1190.18      11998       0      0      34       0       0       34        0      0 304      0       3      307      -866.92      11999       0      0      60       0       4       64        0      0 290      0       3      293      -862.84      12000       0      0       3       0       0        3        0      0 213      0       0      213      -545.39      12002      21      0       0       0       0       21       87      0 150      0       0      237      -241.89      12003     100     15       8       4       1      128      322      6 7      2       0      337       -59.50      02004     148     15      13       3       1      180      273      8 0      0       0      281       -72.15      0

2004

2005

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      01996      98      39       9      2       0      148      425      27 3      0       0       455     -49.103      01997     188      66      64      4       0      322      545     100 38      1       1       685     -41.237      01998     307      66      90     22       0      485     1382     168 113     12       4      1679     -36.192      01999     407     115      97      9       3      631     1597     170 105      8       3      1883     -63.533      02000     372     183     183      4       1      743     1343     258 141      4       8      1754    -110.008      12001     341     293     184      1       7      826     1078     513 198      4       6      1799    -346.880      12002     219     258     171      2       7      657      923     596 162      6       2      1689    -468.204      12003     165     309     183      5       4      666      652     590 242     14       6      1504    -657.263      12004     273     261     126      3       5      668      804     385 181     10       8      1388    -251.784      1

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2005

Percentage of Score by Parity In All (AN) and GOF4 Excluded

(AG) Herds

0102030405060708090

100

1 2 3 4 5

Calving Ease Score

Cou

nts

by H

erd

-Pari

ty (

%)

Parity 1 - AN

Parity 2 - AN

Parity 1 - AG

Parity 2 - AG

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2005

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

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2005

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 discardedWill conduct sensitivity analysis to assess optimal data discard

Current InterBull test run for calving ease

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2005

Frequency of Codes in Combined Interbull File

Code

SourceOfficial Report

Frequency PercentCumulative

Frequency Percent

Sire Calving Ease

CFrom correlation

No 5367 4.77 5367 4.77

D Domestic No 15,073 13.40 20,440 18.17

D Domestic Yes 26,049 23.15 46,489 41.32

I Interbull Yes 22,809 20.27 69,298 61.59

PSire MGS Indices

Yes 43,208 38.41 112,506 100.00

Daughter Calving Ease

CFrom correlation

Yes 10,792 9.59 10,792 9.59

D Domestic No 15,073 13.40 25,865 22.99

D Domestic Yes 26,049 23.15 51,914 46.14

I Interbull Yes 17,384 15.45 69,298 61.59

PSire MGS Indices

Yes 43,208 38.41 112,506 100.00