[R] Doubt about nested aov output

[Christoph Buser]

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 at 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
 > San Jose, CA 95110, USA
 > 
 > spencer.graves at pdf.com
 > www.pdf.com <http://www.pdf.com>
 > Tel:  408-938-4420
 > Fax: 408-280-7915
 > 
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