Dear Wim,
In principle, you could simply use an unstructured random effect of the mother. I.e., if you had a variable "mum" identifying the mother, you would include the argument `random = ~ mum` in your remlf90() call.
However, be careful in interpreting the results as this effect may be confounded with the additive genetic effect. If you have a full and deep pedigree should work. On the other extreme, if you had a partial pedigree with information only about the mother, there will be identifiability issues.
ƒacu.-
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There is no way to work around unidentifiable models.
As an approximation, you could use the pedigree only, and then summarize the breeding values of the offspring for each mother. The mean of that distribution would be a point estimate of the maternal effect.
For making formal inference on those effects (p-values, CIs, etc.) you would need to use bootstrapping techniques, though.
Hope it helps.
ƒacu.-
Dear Facundo
I do have a partial pedigree, where the father's side contains a full and deep pedigree, but the mother's side is only known up to 1 generation.For the moment, I am using the mother as an unstructured random effect, but because of the confounding issues with the additive genetic effect that you mentioned, I was wondering if there was a way in BreedR to work around this.
Op dinsdag 6 maart 2018 17:02:16 UTC+1 schreef Facundo Muñoz:
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Yes. If you can compute de correlation matrix for the dams, then you can feed it into a generic model.
Best wishes
ƒacu.-
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