[R-sig-ME] significance level in lme4 and lmerTest

John Fox j|ox @end|ng |rom mcm@@ter@c@
Tue Jul 5 15:04:41 CEST 2022

Dear Hasibe,

On 2022-07-05 8:14 a.m., Hasibe Kahraman wrote:
> Hello,
> I used the lme4 package for modelling my data and ANOVA Type III (Version 3.0-12; Fox & Weisberg, 2019). I reported the results of LME analyses in my manuscript (see below):
> The main effects of group and prime type were significant (F(1,139.02)=6.5005, p=.011; F(2,197.66)=8.5271, p<.001, respectively), with a robust two-way interaction between Group and Prime Type (F(2,190.45)=11.9593, p<.0001)
> However, one reviewer asked that I should specify which p-value is my "significance" level. Therefore, could I possibly learn whether it is set to .05 or .01?

This is really a statistical question and not a software question. 
lmerTest::anova() (which you mention in the subject of your message) and 
car::Anova() (which you appear to reference in the body of your message) 
both report p-values. If you have an alpha level for the tests, you 
should simply say what it is. Since you consider p = .011 "significant," 
the alpha level you have in mind is apparently .05.

I hesitate to probe below the surface, for example, to ask whether you 
coded contrasts correctly to get type-III tests from Anova() or whether 
you're really interested in the main effects in light of the interactions.

I hope this helps,

> Thanks,
> Hasibe
> 	[[alternative HTML version deleted]]
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John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

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