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

marKo mtonc|c @end|ng |rom ||r|@un|r|@hr
Fri Nov 26 20:29:30 CET 2021

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 

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

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