[R-sig-ME] Using anova vs. Anova for linear mixed model

[Mitchell Maltenfort]

You may also want to try "drop1" native to the lme4 package for comparison



On Sun, Sep 15, 2019 at 9:38 AM Kevin Chu <kevin.m.chu using duke.edu> wrote:

> Hello Dr. Alday and Dr. Fox,
>
> Thank you for your replies. I am indeed using the anova method from
> lmerTest with the default Satterthwaite method for estimating ddf.
>
> I am not a statistics expert (I am a graduate student in electrical and
> computer engineering), so I do not entirely understand the differences
> between ANOVA types. I ran the anova method using the three ANOVA types,
> but I obtained very similar p-values. The part I am suspicious about is
> that the sum of squares for the STRATEGY factor is exactly equal to 0,
> which I suspect may be due to the missing cells.
>
> My question: Do I need to specify any arguments in the anova method so
> that it can handle missing cells?
>
> Thank you,
> Kevin
>
> On Sep 13, 2019, at 11:08 AM, Alday, Phillip <Phillip.Alday using mpi.nl<mailto:
> Phillip.Alday using mpi.nl>> wrote:
>
> Dear Jon, dear Kevin,
>
> I suspect Kevin is using lmerTest and not lme4 directly. lmerTest does
> have a type argument for anova()  and defaults to the Satterthwaite ddf
> approximation.
>
> Phillip
>
> Sent from my mobile, please excuse the brevity.
> ________________________________
> Von: "Fox, John" <jfox using mcmaster.ca<mailto:jfox using mcmaster.ca>>
> Gesendet: Freitag, 13. September 2019 17:06
> An: Kevin Chu
> Cc: r-sig-mixed-models using r-project.org<mailto:
> r-sig-mixed-models using r-project.org>
> Betreff: Re: [R-sig-ME] Using anova vs. Anova for linear mixed model
>
>
> Dear Kevin,
>
> It's not entirely clear to me what you did, because as far as I know, the
> anova() method for merMod objects supplied by the lme4 package doesn't have
> a type argument and computes sequential ("type-I") tests. (You say that
> you're using anova() in the stats package, but while stats provides the
> anova() generic function, the method is coming from someplace else.)
>
> That said, I suspect that the discrepancy is due to the empty cells in the
> table of the fixed-effects factors. Normally, Anova() will detect the
> resulting aliased coefficients in the model and report an error, but I
> believe that lmer() suppresses the aliased coefficients by removing
> redundant columns of the model matrix. Whatever anova() method you used
> apparently detected the empty cells directly and printed a warning.
>
> Finally, and particularly in light of the empty cells, I wonder why you
> want to compute type-III tests.
>
> I hope that this is of some help,
> John
>
>   -----------------------------
>   John Fox, Professor Emeritus
>   McMaster University
>   Hamilton, Ontario, Canada
>   Web: http::/socserv.mcmaster.ca/jfox<http://socserv.mcmaster.ca/jfox>
>
> > On Sep 12, 2019, at 2:14 PM, Kevin Chu <kevin.m.chu using duke.edu<mailto:
> kevin.m.chu using duke.edu>> wrote:
> >
> > Hello,
> >
> > I built a linear mixed effects model with three fixed factors and one
> random factor. I want to test for statistical significance of the fixed
> effects using F-tests from a type III ANOVA table. Since I am using a type
> III ANOVA, I understand that I need to set the contrasts to contr.sum so
> that the sums of squares are calculated correctly.
> >
> > These are the data types.
> >
> >> str(mydata)
> > 'data.frame': 280 obs. of  5 variables:
> > $ SUBJECT  : Factor w/ 20 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1
> ...
> > $ CONDITION: Factor w/ 4 levels "anechoic","aula",..: 1 1 1 1 2 2 2 2 3
> 3 ...
> > $ CHANNEL  : Factor w/ 2 levels "0","1": 1 1 2 2 1 1 2 2 1 1 ...
> > $ STRATEGY : Factor w/ 2 levels "0","1": 1 2 1 2 1 2 1 2 1 2 ...
> > $ SCORE    : num  107.4 57 90.1 96.1 -16.4 ...
> >
> > Below is the code I used to generated the model.
> >
> > lmm <- lmer(SCORE ~ CONDITION * CHANNEL * STRATEGY + (1 | SUBJECT),
> data=mydata, contrasts=list(CONDITION=contr.sum, CHANNEL=contr.sum,
> STRATEGY=contr.sum))
> >
> > I tried passing lmm through anova from the stats package and Anova from
> the car package, but I obtained different results (screenshots are
> attached).
> >
> > My questions:
> > 1) Why do anova and Anova give different results even though I specified
> type III ANOVA?
> > 2) Why is the Sum Sq equal to 0 in the table produced by anova?
> >
> > I would prefer not to release the data as I plan to publish a paper
> based on my results, but if it helps I can create dummy data.
> >
> > Thank you,
> > Kevin Chu
> >
> <Anova_car.png><anova_stats.png>_______________________________________________
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