[R-sig-ME] p-correction for effects in LMM

[marKo]

On 26. 11. 2021. 08:41, Bojana Dinic wrote:
> Dear colleagues,
> 
>      I use linear mixed models with 1 random effect (subject), 2 fixed
>      factors (one  is between factor and another is repeated) and one 
> covariate, and
>      explore all main effects, 2-way interactions and one 3-way 
> interaction.
>      Regarding of used software, somewhere I get effect of intercept,
>      somewhere not. Reviewer asks to use p-adjustment for these
>      effects. My dilemma is should I apply p-correction for 7 tests or 8 
> (including
>      random intercept for subjects)?
> 
>      The output do not contain F for random effect, but only variance.
>      Also, the output do not contain effect size. CIs are available only 
> for
>      betas as product of specific level of both fixed effects and 
> covariate, but
>      since I have 3 levels for between and 4 for repeated effects, the
>      output is not helpful + there is no possibility to change reference 
> group.
>      Thus, I'm stuck with p-adjustment.
> 
>     Any help is welcomed.
>      Thank you.
> 

As I understand, p-values are somewhat unreliable (In LMM). As a 
sensible alternative maybe you could compute bootstrap CI and use that 
to infer about significance of specific effects (if i have understood 
your problem correctly).
I you use lme4 or nlme, this should not be a problem.

You ca use (for model  m)

confint(m, level=0.95, method="boot", nsim=No.of.SIMULATIONS)

even use some multi-core processing to speed thing up

confint(m, level=0.95, method="boot", parallel = "multicore", ncpus = 
No.of.CORES, nsim=No.of.SIMULATIONS)

change No.of.SIMULATIONS with the desired number of repetitions (1000 or so)
change No.of.CORES with the desired number of cores (depends of your 
machine).

Hope it helps.


-- 
Marko Tončić, PhD
Assistant professor
University of Rijeka
Faculty of Humanities and Social Sciences
Department of Psychology
Sveucilisna avenija 4, 51000 Rijeka, CROATIA
e-mail: mtoncic using ffri.uniri.hr