[R-sig-ME] Model comparisons
Yasuaki SHINOHARA
y.shinohara at aoni.waseda.jp
Sat Oct 4 16:54:15 CEST 2014
Dear Thierry,
Thank you very much for your help.
Actually, the first and second questions were not talking about the
same model.
For the first question, the fixed factor of age was just an example,
and the results below are not related to the first question.
I was not sure whether I should include a fixed factor of which I am
not reporting the results in a paper, if the model with the factor
fits significantly better than the model without the factor.
Do you mean that I should include it, if it has a significant effect,
although I am not reporting the result of the factor?
For the second question, the aim of my research is to investigate the
age effects.
I wanted to test how training works for speaker's production, and
whether there is an age effect on it.
So the factor A is "Group" (training group vs. control group), and the
factor B is "Testing Block" (pre-training vs. post-training)
I am trying to find some literature about how the age related to the
improvement made by training, but it is really hard to find.
I am not sure how I can send a figure of the relationship between age
and the response through this emailing list. Sorry.
Anyway, thank you very much for your help.
Best wishes,
Yasu
about whether I should include a fixed factor in a logistic mixed
effects model or not,
On Fri, 3 Oct 2014 08:20:31 +0000
"ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be> wrote:
> Dear Yasu,
>
> It looks like your response is age dependent. Therefore you should
>include age into the model, so the model can take the age effect into
>account.
>
> I prefer to take a look at the functional relationship between age
>and the response (in the logit scale). There is probabily some
>literature on the effect of age on the response. That will give you
>more information on which function to choose: log(age) or poly(age,
>2).
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for
>Nature and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality
>Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
> To call in the statistician after the experiment is done may be no
>more than asking him to perform a post-mortem examination: he may be
>able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does
>not ensure that a reasonable answer can be extracted from a given
>body of data. ~ John Tukey
>
> ________________________________________
> Van: r-sig-mixed-models-bounces at r-project.org
>[r-sig-mixed-models-bounces at r-project.org] namens Yasuaki SHINOHARA
>[y.shinohara at aoni.waseda.jp]
> Verzonden: vrijdag 3 oktober 2014 6:22
> Aan: r-sig-mixed-models at r-project.org
> Onderwerp: [R-sig-ME] Model comparisons
>
> Dear all,
>
> Could I ask a very basic question about glmer?
> I am wondering how important using the best-fitting model is.
>
> (1)
> Please imagine I have three fixed factors "A", "B" and "C" in a
> logistic mixed effects model.
> I want to test these main effects and their all possible
>interactions.
> However, I can include another factor "D" (e.g., age) in which I am
> not interested. If I include the fixed factor "D" in
> the model, the model fits significantly better than the model
> without the factor "D".
> I know I should use the best-fitting model, and report all the
>results
> including the factor "D", although the results are slightly
>different
> from the model which does not include the factor "D".
> However, I also think that including unnecessary factors would
> distract readers from the main point, so it may be good to analyze
> data without the factor "D".
> Could I ask your opinions?
>
> (2)
> Also, I do not understand why the results are so different, if I
> change the relation in one of the factors.
>For example, the model including the fixed factors of "A","B","C" and
> "log(age)" is significantly better than another model including the
> fixed factors of "A","B","C" and "poly(age,2)".
> This difference (log(age) vs. poly(age,2)) affects the results of
> other factors of "A", "B" and "C" as below.
> Could you please explain why?
> In terms of AIC value, MODEL1 is better. However, the results of
> MODEL1 do not look correct.
> Why is it?
>
> MODEL1<-glmer(binomial_response~A*B*log(age)+(1|X)+(1+B|Y)+(1+B|Z),
> family=binomial,
> data=ALLDATA,control=glmerControl(optimizer="bobyqa"))
> MODEL2<-glmer(binomial_response~A*B*poly(age,2)+(1|X)+(1+B|Y)+(1+B|Z),
> family=binomial,
> data=ALLDATA,control=glmerControl(optimizer="bobyqa"))
>
>> Anova(MODEL1,type=3)
> Analysis of Deviance Table (Type III Wald chisquare tests)
>
> Response: prod_corr
> Chisq Df Pr(>Chisq)
> (Intercept) 0.8155 1 0.366503
> A 0.0059 1 0.938896
> B 0.7490 1 0.386791
> log(age) 8.6887 1 0.003202 **
> A:B 0.0044 1 0.947053
> A:log(age) 0.2471 1 0.619110
> B:log(age) 2.5704 1 0.108881
> A:B:log(age) 0.4881 1 0.484767
> ---
> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>> Anova(MODEL2, type=3)
> Analysis of Deviance Table (Type III Wald chisquare tests)
>
> Response: prod_corr
> Chisq Df Pr(>Chisq)
> (Intercept) 41.2696 1 1.326e-10 ***
> A 6.4384 1 0.0111677 *
> B 13.0042 1 0.0003108 ***
> poly(age, 2) 14.2490 2 0.0008051 ***
> A:B 14.2547 1 0.0001597 ***
> A:poly(age, 2) 1.1039 2 0.5758358
> B:poly(age, 2) 3.2066 2 0.2012318
> A:B:poly(age, 2) 0.3203 2 0.8520201
> ---
> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
> Best wishes,
> Yasu
>
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************************************
Yasuaki SHINOHARA, Ph.D.
Assistant Professor
Center for English Language Education (CELESE)
Waseda University Faculty of Science and Engineering
3-4-1 Okubo, Shinjuku-ku, 169-8555, Tokyo JAPAN
email: y.shinohara at aoni.waseda.jp
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