[R] anova on binomial LMER objects

[Horacio Montenegro]

    Hi Spencer and Robert,

    I have found the same behaviour, but only for lme4
and Matrix after the 0.96 release. lme4 0.95-10 and
Matrix 0.95-13 releases gave "sensible" results. This
could be an introduced bug, or a solved bug - you
should ask Prof. Bates.

    hope this helps, cheers,

    Horacio Montenegro

--- Spencer Graves <spencer.graves at pdf.com> wrote:
> 	  I agree:  Something looks strange to me in this
> example also;  I have 
> therefore copied Douglas Bates and  Deepayan Sarkar.
>  You've provided a 
> nice simulation.  If either of them have time to
> look at this, I think 
> they could tell us what is happening here.
> 
> 	  If you need an answer to your particular problem,
> you could run that 
> simulation 1000 or 1,000 times.  That would tell you
> whether to believe 
> the summary or the anova, or neither.  If you want
> to understand the 
> algorithm, you could walk through the code. 
> However, "lmer" is a 
> generic, and I don't have time now to figure out how
> to find the source. 
>   A response from Brian Ripley to a question from me
> a couple of days 
> ago provides a nice summary of how to do that, but I
> don't have time to 
> check that now.
> 
> 	  Sorry I couldn't help more.
> 	  spencer graves
> 
> Robert Bagchi wrote:
> 
> > Dear R users,
> > 
> > I have been having problems getting believable
> estimates from anova on a 
> > model fit from lmer. I get the impression that F
> is being greatly 
> > underestimated, as can be seen by running the
> example I have given below.
> > 
> > First an explanation of what I'm trying to do. I
> am trying to fit a glmm 
> > with binomial errors to some data. The experiment
> involves 10 
> > shadehouses, divided between 2 light treatments
> (high, low). Within each 
> > shadehouse there are 12 seedlings of each of 2
> species (hn & sl). 3 
> > damage treatments (0, 0.1, 0.25 leaf area removal)
> were applied to the 
> > seedlings (at random) so that there are 4
> seedlings of each 
> > species*damage treatment in each shadehouse. 
> There maybe a shadehouse 
> > effect, so I need to include it as a random
> effect. Light is applied to 
> > a shadehouse, so it is outer to shadehouse. The
> other 2 factors are 
> > inner to shadehouse.
> > 
> > We want to assess if light, damage and species
> affect survival of 
> > seedlings. To test this I fitted a binomial mixed
> effects model with 
> > lmer (actually with quasibinomial errors). THe
> summary function suggests 
> > a large effect of both light and species (which
> agrees with graphical 
> > analysis). However, anova produces F values close
> to 0 and p values 
> > close to 1 (see example below).
> > 
> > Is this a bug, or am I doing something
> fundamentally wrong? If anova 
> > doesn't work with lmer is there a way to perform
> hypothesis tests on 
> > fixed effects in an lmer model? I was going to
> just delete terms and 
> > then do liklihood ratio tests, but according to
> Pinheiro & Bates (p. 87) 
> > that's very untrustworthy. Any suggestions?
> > 
> > I'm using R 2.1.1 on windows XP and lme4 0.98-1
> > 
> > Any help will be much appreciated.
> > 
> > many thanks
> > Robert
> > 
> >