On Mon, May 12, 2008 at 11:22 AM, Federico Calboli <[EMAIL PROTECTED]> wrote: > 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.
As I indicated, the trick is that the interaction of a fixed factor and a random factor can be defined in more than one way. It sounds as if what you want is lmer(y ~ factor1 * factor2 + (1|factor3) + (1|factor1:factor3) + (1|factor2:factor3) + (1|factor1:factor2:factor3), ...) but I'm not sure. >> 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 models >> >> 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). Documentation for lme4 is pretty sketchy at present. I hope to remedy that during our summer break. ______________________________________________ R-help@r-project.org mailing list 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.
