[R] FW: Re: Doubt about nested aov output

[Ken Knoblauch]

Thank you for your response.  The single response/observer most probably
explains
the complaints that lmer was giving for my example.  Maybe this small
modification
provides a better example and corrects a more serious error in my previous
post:

library(lme4)
y<-rnorm(30)
cond <- rep(gl(3,5,15), 2)
obs<-rep(gl(15,1), 2)
subj<-rep(gl(5,1,15), 2)
dd<-data.frame(y=y,cond=cond,obs=obs,subj=subj)

l1 <- lmer(y~cond + (1|cond:obs), data=dd)
l2 <- lmer(y~cond + (1|cond:subj), data=dd)
l3 <- lmer(y~cond + (1|obs), dd)

Understanding the notation is often about 99% of the job, and it is
very helpful to see multiple ways to accomplish the same thing.

> Douglas Bates a écrit:
> I prefer to have a grouping factor constructed with unique levels for
> each distinct unit.  The only reason I mention constructions like
> Treatment:Rat in the original part of this thread is that data are
> often provided in that form.
>
> Reusing "subject" labels within another group is awkward and can be
> error prone.  One of the data sets I examine in the MlmSoftRev
> vignette of the mlmRev package is called Exam and has student
> identifiers within schools.  The student identifiers are not unique
> but the school:student combination should be.  It isn't.  These data
> have been analyzed in scores of books and articles and apparently none
> of the other authors bothered to check this.  There are some
> interesting ramifications such as some of the schools that are
> classified as mixed-sex schools are likely single-sex schools because
> the only student of one of the sexes in that school is apparently
> mislabelled.
>
> BTW, in your example you have only one observation per level of 'obs'
> so you can't use obs as a grouping factor as this variance component
> would be completely confounded with the per-observation noise.
>
>>
>> Douglas Bates a écrit:
>>
>> The difference between models like
>>   lmer(Glycogen~Treatment+(1|Rat)+(1|Rat:Liver))
>> and
>>   lmer(Glycogen~Treatment+(1|Treatment:Rat)+(1|Treatment:Rat:Liver))
>>
>> is more about the meaning of the levels of "Rat" than about the
>> meaning of "Treatment".  As I understood it there are three different
>> rats labelled 1.  There is a rat 1 on treatment 1 and a rat 1 on
>> treatment 2 and a rat 1 on treatment 3.  Thus the levels of Rat do not
>> designate the "experimental unit", it is the levels of Treatment:Rat
>> that do this.
>>
>> --
>> Ken Knoblauch
>> Inserm U371
>> Cerveau et Vision
>> Dept. of Cognitive Neuroscience
>> 18 avenue du Doyen Lépine
>> 69500 Bron
>> France
>> tel: +33 (0)4 72 91 34 77
>> fax: +33 (0)4 72 91 34 61
>> portable: +33 (0)6 84 10 64 10
>> http://www.lyon.inserm.fr/371/
>>
>>
>


-- 
Ken Knoblauch
Inserm U371
Cerveau et Vision
Dept. of Cognitive Neuroscience
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.lyon.inserm.fr/371/