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I accustomed to lme4 where it would be simply: (1|genotype/root_ID) but it's unclear to me looking through the documentation the appropriate way to do this in sommer.

mod1 <- mmer(Y ~ 1,
            random= ~vsr(genotype,Gu=a) + genotype + genotype:root_ID,
            rcov= ~units, nIters=10,
            data=fold, verbose = FALSE, dateWarning=FALSE)

The results look realistic but I am not entirely sure this is correct and am worried that I will get inflated CV accuracies...

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  • Welcome to SO. This question doesn't really fall under the remit of SO as it's not really a programming question. I would suggest posting on the sister site Cross Validated.
    – dthorbur
    Commented Jul 9 at 9:19
  • @dthorbur you are total right. Thanks for the heads up.
    – bigoof99
    Commented Jul 9 at 13:05
  • @dthorbur "This question appears to be off-topic because it focuses on programming, debugging, or performing routine operations, or it asks about obtaining datasets. You could try the support links we maintain or the Open Data site instead. If you are asking about how to debug some code or carry out a task in a programming language, this is not an on-topic question. If you're asking about how to obtain data, that is not an on-topic question. If you feel your question is truly about statistics as described in the help center, please edit to clarify. Closed 1 hour ago."
    – bigoof99
    Commented Jul 9 at 20:41
  • My apologies, I thought it would get more appropriate attention there. To me your question sounds like you're asking about the differences between the sommer and lme4 packages and how to parameterize the model.
    – dthorbur
    Commented Jul 10 at 8:35
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