Nested Mixed Models in lme4

Dear Prof. Bates,

I am trying to use the function lmer from lme4 to
analyse the following nested factorial design.

I have three treatment factors (neighborhood,
initial, k);
I have three group factors crossing (size, dens,
inst).

Did you mean to write (size, dens, type) there?

Also, by "factor" do you mean that you regard all of these variables
as categorical?  If so, you should check the form of the size variable
in the data frame.  It is being stored as a numeric variable, not as a
factor.  If you want to interpret this  variable as a categorical
factor you should convert it to a factor or, as seems likely in this
case, an ordered factor.  (See ?factor and ?ordered)

yes, thank you a lot! All your corrections are 
appropriate! inst should have been type and all 
variables should have been categorical. My mistake.
Also: as you correctly pointed out, the data are 
from a computer experiment and perfectly balanced, 
and by group factors I meant blocking factors.

Your very clear explanation solved my concerns 
about the nesting! Thanks!

I've also redone the comparison with SAS and now 
results correspond.
The reason was mainly that I needed a quite 
different formula:

lmer(err~initial*neighborhood + initial*k + 
initial*type + initial*size + initial*dens + 
neighborhood*k + neighborhood*type + 
neighborhood*size + neighborhood*dens + k*type + 
k*size + k*dens + type*size + type*dens + 
size*dens + initial*neighborhood*k + 
(1|inst),data=Case3)

True also that we were using lsmeans in SAS that 
you discourage.

To me it would remain only to understand how I 
could obtain the results in a cell means format 
like those in SAS. But this seems to be a problem 
also in lm and hence I must probably study better 
how things work to find the way. Trying something 
of the kind:

fmm1 <- 
lmer(err~-1+ordered(size)+dens+type+(k+initial+neighborhood)^3+(1|inst),data=Case3)

does not seem to help much.

I left all the analysis I did, code + results, 
(SAS and R) at:

http://www.imada.sdu.dk/~marco/Mixed/


Thank you a lot very much for the help!

Best regards,

Marco

Marco Chiarandini 
http://www.imada.sdu.dk/~marco
Department of Mathematics	      Email: 
marco at imada.sdu.dk
and Computer Science,		      Phone: +45 6550 4031
University of Southern Denmark        Fax: +45 
6593 2691