[R] Question about linear mixed effects model (nlme)

[Ben Bolker]

Bert Gunter <gunter.berton <at> gene.com> writes:

> 
> Below.
> 
> On Tue, Oct 4, 2011 at 7:34 AM, Panagiotis <pat2 <at> hi.is> wrote:
> 
> > Hi,
> >
> > I applied a linear mixed effect model in my data using the nlme package.
> > lme2<-lme(distance~temperature*condition, random=~+1|trial, data) and then
> > anova.
> > I want to ask if it is posible to get the least squares means for the
> > interaction effect and the corresponding 95%ci. And then plot this values.
> >
> 
> Uh-Oh. You may have unloosed "The Wrath of Khan" -- or at least of Venables.
> (An explanation of this cryptic remark should follow from others, so please
> do not ask me what it means if you do not know).
> 

   You should probably ask (a version of) this question on the
r-sig-mixed-models list instead.
  What do you mean by "the least squares means for the interaction effect"?
How is it different from the estimate of the interaction parameter?
You can use the predict() function if you want to calculate predicted
values for any particular combination of predictors (you probably want
to specify level=0 to get the population-level effects).  Getting 'good'
confidence intervals for mixed-effect models is surprisingly difficult.
If you are willing to ignore the uncertainty of the among-trial variance,
you can use a modification of the recipe found at http://glmm.wikidot.com/faq