Re: [R] Doubt about nested aov output

From: Christoph Buser <buser_at_stat.math.ethz.ch>
Date: Mon 05 Sep 2005 - 19:38:51 EST

Hi

I think the problem is related to specifying "Tratamento" both as a fixed factor and in the error term. I attached a script with a reproducible example that shows a similar output. I do not know the details of the original data and the questions of interest, but maybe a model including "Tratamento" is more what you wanted to implement.

Regards,

Christoph

## R-Script

library(nlme)

## Generating the data
set.seed(1)
ziel <- rep(c(-6,8,20), each = 40) + rep(rnorm(15, 0, 20), each = 4) +   rep(rnorm(60, 0, 10), each = 2) + rnorm(120, 0, 3) dat <- data.frame(y = ziel,

                  fix = factor(rep(1:3, each = 40)),
                  R1 = factor(rep(1:15, each = 8)),
                  R2 = factor(rep(1:60, each = 2)))

## Model including "fix" as fixed and random effect. res2 <- aov(y ~ fix + Error(fix/R1/R2), data = dat) summary(res2)

reslme2 <- lme(y ~ fix , data = dat, random = ~ 1|fix/R1/R2) summary(reslme2)
anova(reslme2)

## Model including "fix" as fixed factor. res1 <- aov(y ~ fix + Error(R1/R2), data = dat) summary(res1)

reslme <- lme(y ~ fix , data = dat, random = ~ 1|R1/R2) summary(reslme)
anova(reslme)



Christoph Buser <buser@stat.math.ethz.ch> Seminar fuer Statistik, LEO C13
ETH (Federal Inst. Technology)	8092 Zurich	 SWITZERLAND
phone: x-41-44-632-4673		fax: 632-1228

http://stat.ethz.ch/~buser/

Spencer Graves writes:
> Others may know the answer to your question, but I don't. However,
> since I have not seen a reply, I will offer a few comments:
>
> 1. What version of R are you using? I just tried superficially
> similar things with the examples in ?aov in R 2.1.1 patched and
> consistently got F and p values.
>
> 2. My preference for this kind of thing is to use lme in
> library(nlme) or lmer in library(lme4). Also, I highly recommend
> Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer).
>
> 3. If still want to use aov and are getting this problem in R 2.1.1,
> could you please provide this list with a small, self contained example
> that displays the symptoms that concern you? And PLEASE do read the
> posting guide! "http://www.R-project.org/posting-guide.html". It might
> increase the speed and utility of replies.
>
> spencer graves
>
> Ronaldo Reis-Jr. wrote:
>
> > Hi,
> >
> > I have two doubts about the nested aov output.
> >
> > 1) I have this:
> >
> >>anova.ratos <- aov(Glicogenio~Tratamento+Error(Tratamento/Rato/Figado))
> >>summary(anova.ratos)
> >
> >
> > Error: Tratamento
> > Df Sum Sq Mean Sq
> > Tratamento 2 1557.56 778.78
> >
> > Error: Tratamento:Rato
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 3 797.67 265.89
> >
> > Error: Tratamento:Rato:Figado
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 12 594.0 49.5
> >
> > Error: Within
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 18 381.00 21.17
> >
> > R dont make the F and P automatically, it is possible?
> >
> > I Like an output like this:
> >
> > Error: Tratamento
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Tratamento 2 1557.56 778.78 2.929 0.197
> >
> > Error: Tratamento:Rato
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 3 797.67 265.89 5.372 0.0141
> >
> > Error: Tratamento:Rato:Figado
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 12 594.0 49.5 2.339 0.0503
> >
> > Error: Within
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 18 381.00 21.17
> >
> > Why it not make automatic calculations? It is possible?
> >
> >
> > 2) I can say that Error: Tratamento:Rato means an interaction between
> > Tratamento and Rato? Normally the : represents an interaction, but in this
> > output I think that it dont mean the interaction.
> >
> > Any explanation are welcome.
> >
> > Thanks
> > Ronaldo
>
> --
> Spencer Graves, PhD
> Senior Development Engineer
> PDF Solutions, Inc.
> 333 West San Carlos Street Suite 700
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>
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Sep 05 19:47:14 2005

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