[R] anova on binomial LMER objects
Horacio Montenegro
nepossiver at yahoo.com
Sun Sep 25 23:05:33 CEST 2005
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
> >
> >
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