Prediction of breeding values with a mixed model with heterogeneous variances for large-scale dairy data

Journal of Agricultural, Biological, and Environmental Statistics

Volumn 4, Issue 2, 1999, Pages 185-201

  Engel, Bas ^a   Meuwissen, Theo ^a   De Jong, Gerben ^b   Buist, Willem ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b Royal Dutch Cattle Syndicate   (Netherlands)

Author keywords

BLUP; Laplace integration

Indexed keywords

BOS TAURUS;

EID: 0041407276     PISSN: 10857117     EISSN: None     Source Type: Journal    
DOI: 10.2307/1400596     Document Type: Article

References (37)

1. Breslow, N. E., and Clayton, D. G. (1993), "Approximate Inference in Generalized Linear Mixed Models," Journal of the American Statistical Association, 88, 9-25.
2. Engel, B. (1990), "The Analysis of Unbalanced Linear Models With Variance Components," Statistica Neerlandica, 44, 195-219.
3. _ (1997), "Extending Generalized Linear Models With Random Effects and Components of Dispersion," Doctoral dissertation, Agricultural University, Wageningen (available from the author).
4. _ (1998), "A Simple Illustration of the Failure of PQL, IRREML and APHL as Approximate ML Methods for Mixed Models for Binary Data," Biometrical Journal, 40, 141-154.
5. Engel, B., and Buist, W. G. (1996), "Analysis of a Generalized Linear Mixed Model: A Case Study and Simulation Results," Biometrical Journal, 38, 61-80.
6. _ (1998), "Bias Reduction of Approximate Maximum Likelihood Estimates for Heritability in Threshold Models," Biometrics, 54, 1155-1164.
7. Engel, B., Buist, W. G., and Visscher, A. (1995). "Inference for Threshold Models With Variance Components From the Generalized Linear Mixed Model Perspective," Genetics Selection Evolution, 27, 15-32.
8. Engel, B., and Keen, A. (1994), "A Simple Approach for the Analysis of Generalized Linear Mixed Models," Statististica Neerlandica, 48, 1-22.
9. _ (1996), "Contribution to the Discussion of Lee and Nelder (1996) Hierarchical Generalized Linear Models," Journal of the Royal Statistical Society, Series B, 58, 656-657.
10. Everett, R. W., Keown, J. F., and Taylor, J. F. (1982). "The Problem of Heterogenous Within Herd Error Variances When Identifying Elite Cows," Journal of Dairy Science, 65(Suppl. 1), 100 (abstract).
11. Foulley, J. L., San Cristobal, M., Gianola, D., and Im, S. (1992), "Marginal Likelihood and Bayesian Approaches to the Analysis of Heterogenous Residual Variances in Mixed Linear Gaussian Models," Computational Statistics and Data Analysis, 13, 291-305.
12. Genstat 5 Committee. (1993), Genstat 5 Release 3 Reference Manual, Oxford: Clarendon Press.
13. Henderson, C. R. (1976), "A Simple Method for Computing the Inverse of a Numerator Relationship Matrix Used in Prediction of Breeding Values," Biometrics, 32, 69-83.
14. _ (1984), Applications of Linear Models in Animal Breeding, Guelph, Ontario: University of Guelph.
15. Henderson, C. R., Kempthorne, O., Searle, S. R., and Von Krosig, C. N. (1959), "Estimation of Environmental and Genetic Trends From Records Subject to Culling," Biometrics, 15, 192-198.
16. Hill, W. G., Edwards, M. R., Ahmed, M. K. A., and Thompson, R. (1983). "Heritability of Milk Yield and Composition at Different Levels and Variability of Production," Animal Production, 36, 59-68.
17. Hoeschele, I., and Gianola, D. (1989), "Bayesian Versus Maximum Quasi-Likelihood Methods for Sire Evaluation With Categorical Data," Journal of Dairy Science, 72, 1569-1577.
18. Hoeschele, I., Gianola, D., and Foulley, J. L. (1987), "Estimation of Variance Components With Quasi-Continuous Data Using Bayesian Methods," Journal of Animal Breeding and Genetics, 104, 334-349.
19. Kachman, S. D., and Everett, R. W. (1993), "A Multiplicative Mixed Model When the Variances Are Heterogeneous," Journal of Dairy Science, 76, 859-867.
20. Lee, Y., and Neider, J. A. (1996), "Hierarchical Generalized Linear Models (with discussion)," Journal of the Royal Statistical Society, Series B, 58, 619-678.
21. Lofgren, D. L., Vinson, W. E., Pearson, R. E., and Powell, R. L. (1985), "Heritability of Milk Yield at Different Herd Means and Variance for Production," Journal of Dairy Science, 68, 2737-2739.
22. Louis, T. A. (1982), "Finding the Observed Information Matrix When Using the EM Algorithm," Journal of the Royal Statistical Society, Series B, 44, 226-233.
23. McCullagh, P., and Nelder, J. A. (1989), Generalized Linear Models (2nd ed.), London: Chapman and Hall.
24. Meinert, T. R., Pearson, R. E., Vinson, W. E., and Cassell, B. G. (1988), "Prediction of Daughter's Performance From Dam's Cow Index Adjusted for Within Herd Variance," Journal of Dairy Science, 71, 2220-2231.
25. Meuwissen, T. H. E., De Jong, G., and Engel, B. (1996), "Joint Estimation of Breeding Values and Heterogeneous Variances in Large Scale Dairy Data," Journal of Dairy Science, 79, 310-316.
26. Palterson, H. D., and Thompson, R. (1971), "Recovery of Inter-block Information When Block Sizes Are Unequal," Biometrika, 58, 545-554.
27. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992), Numerical Recipes in C. The Art of Scientific Computing (2nd ed.), Cambridge University Press.
28. Quaas, R. L. (1976), "Computing the Diagonal Elements and Inverse of a Large Numerator Relationship Matrix," Biometrics, 32, 949-953.
29. _ (1988), "Additive Genetic Models With Groups and Relationships," Journal of Dairy Science, 71, 13-38.
30. Robinson, G. K. (1991), "That BLUP Is a Good Thing: The Estimation of Random Effects," Statistical Science, 6, 15-51.
31. San Cristobal, M., Foulley, J. L., and Manfredi, E. (1993). "Inference About Multiplicative Heteroskedastic Components of Variance in a Mixed Linear Gaussian Model With an Application to Beef Cattle Breeding," Genetics Selection Evolution, 25, 3-30.
32. Schaeffer, L. R., and Kennedy, B. W. (1986), "Computing Solutions to Mixed Model Equations," Proceedings of the 3rd World Congress on Genetics Applied to Livestock Production, 12, 382-393.
33. Schall, R. (1991), "Estimation in Generalized Linear Models With Random Effects," Biometrika, 78, 719-728.
34. Searle, S. R., Casella, G., and McCulloch, C. E. (1992), Variance Components, New York: John Wiley.
35. Simianer, H., and Schaeffer, L. R. (1989), "Estimation of Covariance Components Between One Continuous and One Binary Trait," Genetics Selection Evolution, 40, 961-971.
36. Van der Werf, J. H. J., Meuwissen, T. H. E., and De Jong, G. (1994), "Effects of Correction for Heterogeneity of Variance on Bias and Accuracy of Breeding Value Estimation for Dutch Dairy Cattle," Journal of Dairy Science, 77, 3174-3184.
37. Wade, K. M., Quaas, R. L., and Van Vleck, L. D. (1993), "Estimation of the Parameters Involved in a First-Order Autoregressive Process for Contemporary Groups," Journal of Dairy Science, 76, 3033-3040.