R help - Dec 2017 - Why aov() with Error() gives three strata?

Dear list users,

I am trying to learn Repeated measures ANOVA using the aov() interface, but
I'm struggling to understand its output.

According to tutorials on the web, formula for a repeated measures design
is:

aov(Y ~ IV+ Error(SUBJECT/IV) )

This formula does work but it returns three strata (Error:SUBJECT, Error:
SUBJECT:IV, Error: Within), when I would expect two strata (Within and
Between subjects). I've seems some tutorials  show the exactly same setup,
but returning only the two first strata.

Is it possible to have two or three strata depending on the data?
If there is always three strata, how this would fit the interpretation of
between vs within effects?

Below a reproducible example that gives three strata:

data(beavers)
data=data.frame(id
rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),rbind(beaver1,beaver2))
data$activ=factor(data$activ)
#balance dataset to have 6 samples for every combination of beaver and
activity.
balanced = split(data,interaction(data$id,data$activ))
sizes = sapply(balanced,nrow)
selected = lapply(sizes,sample.int,6)
balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
balanced = do.call(rbind,balanced)
aov(temp~activ+Error(id/activ),data=balanced)

Thanks,
Jorge

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Jorge:

FYI, *generally speaking,* queries that are mostly statistical in
nature, such as yours, are off topic here -- this list is about R
programming help, not statistical help. Having said that, you still
may get a useful response here -- the r-help/statistics intersection
*is* nonempty. However, if not, 2.5 suggestions:

1. Try posting to r-sig-mixed-models instead. Repeated measures are a
type of mixed/multilevel model and you may receive some useful
suggestions there, including alternative R approaches to fitting such
model (e.g. using lme() or lmer() ).

2. Alternatively, try posting to a statistics site like stats.stackexchange.com.

2.5. Or, if you can, the best idea might be to sit down with a local
statistics expert.

Cheers,
Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Dec 28, 2017 at 7:52 AM, Jorge Fernando Saraiva de Menezes
<jorgefernandosaraiva at gmail.com> wrote:
> Dear list users,
>
> I am trying to learn Repeated measures ANOVA using the aov() interface, but
> I'm struggling to understand its output.
>
> According to tutorials on the web, formula for a repeated measures design
> is:
>
> aov(Y ~ IV+ Error(SUBJECT/IV) )
>
> This formula does work but it returns three strata (Error:SUBJECT, Error:
> SUBJECT:IV, Error: Within), when I would expect two strata (Within and
> Between subjects). I've seems some tutorials  show the exactly same
setup,
> but returning only the two first strata.
>
> Is it possible to have two or three strata depending on the data?
> If there is always three strata, how this would fit the interpretation of
> between vs within effects?
>
> Below a reproducible example that gives three strata:
>
> data(beavers)
> data=data.frame(id >
rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),rbind(beaver1,beaver2))
> data$activ=factor(data$activ)
> #balance dataset to have 6 samples for every combination of beaver and
> activity.
> balanced = split(data,interaction(data$id,data$activ))
> sizes = sapply(balanced,nrow)
> selected = lapply(sizes,sample.int,6)
> balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
> balanced = do.call(rbind,balanced)
> aov(temp~activ+Error(id/activ),data=balanced)
>
> Thanks,
> Jorge
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Bert, thanks for the reply but I feel that my question is less about
statistics and more about R interface. Specifically, because the output of
R seems different than other programs (systat, for example, gives a between
and a within table instead of a three level one).

I am familiar with the connection between mixed models and repeated
measures,and how mixed models are essentially replacing the aov models due
to their greater flexibility. But I feel that despite understanding a
little of the logic behind the mixed models that aov error terms seem
completely different to me than lmer randoms.

 I will post in those support lists you pass to me, if nothing comes from
here. However I had little luck in the stats exchange when I tried there.

About a local expert, I am once more in a corner. there are many people in
my department who excel in statistics. But I none use R, drastically
reducing their ability to explain to me the output of aov.

Em 28 de dez de 2017 20:04, "Bert Gunter" <bgunter.4567 at
gmail.com> escreveu:
> Jorge:
>
> FYI, *generally speaking,* queries that are mostly statistical in
> nature, such as yours, are off topic here -- this list is about R
> programming help, not statistical help. Having said that, you still
> may get a useful response here -- the r-help/statistics intersection
> *is* nonempty. However, if not, 2.5 suggestions:
>
> 1. Try posting to r-sig-mixed-models instead. Repeated measures are a
> type of mixed/multilevel model and you may receive some useful
> suggestions there, including alternative R approaches to fitting such
> model (e.g. using lme() or lmer() ).
>
> 2. Alternatively, try posting to a statistics site like
> stats.stackexchange.com.
>
> 2.5. Or, if you can, the best idea might be to sit down with a local
> statistics expert.
>
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip
)
>
>
> On Thu, Dec 28, 2017 at 7:52 AM, Jorge Fernando Saraiva de Menezes
> <jorgefernandosaraiva at gmail.com> wrote:
> > Dear list users,
> >
> > I am trying to learn Repeated measures ANOVA using the aov()
interface,
> but
> > I'm struggling to understand its output.
> >
> > According to tutorials on the web, formula for a repeated measures
design
> > is:
> >
> > aov(Y ~ IV+ Error(SUBJECT/IV) )
> >
> > This formula does work but it returns three strata (Error:SUBJECT,
Error:
> > SUBJECT:IV, Error: Within), when I would expect two strata (Within and
> > Between subjects). I've seems some tutorials  show the exactly
same
> setup,
> > but returning only the two first strata.
> >
> > Is it possible to have two or three strata depending on the data?
> > If there is always three strata, how this would fit the interpretation
of
> > between vs within effects?
> >
> > Below a reproducible example that gives three strata:
> >
> > data(beavers)
> > data=data.frame(id > >
rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),
> rbind(beaver1,beaver2))
> > data$activ=factor(data$activ)
> > #balance dataset to have 6 samples for every combination of beaver and
> > activity.
> > balanced = split(data,interaction(data$id,data$activ))
> > sizes = sapply(balanced,nrow)
> > selected = lapply(sizes,sample.int,6)
> > balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
> > balanced = do.call(rbind,balanced)
> > aov(temp~activ+Error(id/activ),data=balanced)
> >
> > Thanks,
> > Jorge
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
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