anova on binomial LMER objects

    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