[R-sig-ME] Residual setting with makeLmer in simR package

[Phillip Alday]

If everything else is standardized, then setting the residual sd to 1
seems acceptable.

That said, there are non trivial issues with fully standardizing effect
sizes in mixed-effects models. Henrik Singmann has a very nice post on this:


https://afex.singmann.science/forums/topic/compute-effect-sizes-for-mixed-objects#post-295

On 3/6/21 7:52 am, Fan, L. via R-sig-mixed-models wrote:
> Hi all,
> 
> I have a doubt about how to set residual sd (sigma) for a PA, using makeLmer function of the simR package.
> 
> When defining the fixed effect, my parameter estimates were all standardized coefficients (i.e., I standardised/z-scored all the variables beforehand). When defining the random structures, since I extracted them from another similar but not same-structured study, I also used the standardized variances (variance divided by sum of variances) for random intercepts and slopes to match them with my manipulation for the fixed parts. 
> 
> When I tried to fill the sigma of makeLmer function, I got a little bit lost. It is said in the manual that I should enter the sd of the residual. However, since I standardized the random effects, I believe the residual sd should also be different than the original unstandardized one. My question is, how should I deal with this sigma part, should I indeed use a standardized residual sd? And if yes, should it be simply valued as 1, or how should I standardize it?
> 
> Thanks!
> 
> Best wishes,
> 
> Lei Fan
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