I am a little bit confused about how to calculate reliability for EBV of each animal using the BLUPF90 program; taking into account repeated measures data, contemporary groups, and removing parent average effects. I think some programs of BLUPF90 family, such as ACCF90 and BLUPF90test, can compute the reliability directly through a few commands. How could I get them? May someone suggest me some ideas in order to create a script for that kind of analysis?
In my opinion the required function can be created by definition of Membership function(s) for any subject in Fuzzy logic method. Even by more functions definition, the uncertainty of your project would be diminished as well.
Most welcome for any further guidance. Best regards.
Help me understant the problem. The 'contemporary' groups are i.i.d., aren't they? They are all drawn from the same Lot or Population? The phrase about 'Parent' is confusing about the samples.
Hello
I am largely ignorant of Fuzzy logic methods. I suppose that might work.
I meant "reliability" as accuracy of the estimated breeding value, using the prediction error variance (PEV). It refers to a parameter in Animal Breeding and Genetics.
I have read in-depth the manual of BLUPF90 by Yukata Matsuda and found further information on the reliability.
http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=tutorial_blupf90.pdf
Also, three articles have helped me to organize ideas on how to calculate reliability taking into account different approaches.
- Garrick, Dorian J., Jeremy F. Taylor, and Rohan L. Fernando. "Deregressing estimated breeding values and weighting information for genomic regression analyses." Genetics Selection Evolution 41.1 (2009): 55.
- Aguilar, Ignacio, et al. "Effects of ignoring inbreeding in model‐based accuracy for BLUP and SSGBLUP." Journal of Animal Breeding and Genetics (2020).
- Koivula, Minna, et al. "Effect of cow reference group on validation reliability of genomic evaluation." Animal 10.6 (2016): 1061-1066.
Thank you for your opinions and suggestions.
Hi B. Samuel Sosa Madrid :
For the BLUPF90 you can include this option "OPTION store_pev_pec" in order to get the prediction error variances and covariances. Thereafter, you can use these values to calculate the accuracies and reliabilities. The ACCF90 gives you the reliabilities directly.
Dr. Yutaka Masuda has a great material that can help you with examples (http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=tutorial_blupf90.pdf ; page 154).
I hope it helps.
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