[R-sig-ME] [R] lme nesting/interaction advice

Federico Calboli f.calboli at imperial.ac.uk
Mon May 12 18:22:19 CEST 2008

On 12 May 2008, at 17:09, Douglas Bates wrote:

> I'm entering this discussion late so I may be discussing issues that
> have already been addressed.
> As I understand it, Federico, you began by describing a model for data
> in which two factors have a fixed set of levels and one factor has an
> extensible, or "random", set of levels and you wanted to fit a model
> that you described as
> y ~ effect1 * effect2 * effect3
> The problem is that this specification is not complete.

My apologies for that, I thought that the above formula was the  
shorthand for what I would call the 'full' model, i.e. the single  
factors and the 2 and 3 ways interactions.
> An
> interaction of factors with fixed levels and a factor with random
> levels can mean, in the lmer specification,
> lmer(y ~ effect1 * effect2 + (1| effect3) + (1| 
> effect1:effect2:effect3), ...)
> or
> lmer(y ~ effect1 * effect2 + (effect1*effect2 | effect3), ...)
> or other variations.  When you specify a random effect or an random
> interaction term you must, either explicitly or implicitly, specify
> the form of the variance-covariance matrix associated with those
> random effects.

I'll play around with this and see what I can get.
> The "advantage" that other software may provide for you is that it
> chooses the model for you but that, of course, means that you only
> have the one choice.

I'm more than happy to stick to R, and to put more legwork into my  
> If you can describe how many variance components you think should be
> estimated in your model and what they would represent then I think it
> will be easier to describe how to fit the model.

I'll work on that. Incidentally, what/where is the most comprehensive  
and up to date documentation for lme4? the pdfs coming with the  
package? I suspect knowing which are the right docs will help a lot  
in keeping me within the boundaries of civility and prevent me from  
annoying anyone (which is not something I sent forth to do on purpose).

Best regards,


Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

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