[R] anova on binomial LMER objects

[Martin Henry H. Stevens]

Hello all,
1. Does Matrix 0.98-7 fix any of this?
2. Assuming "no", how does one acquire Matrix 0.95-13?
Cheers, and thank you kindly in advance,
Hank

On Sep 26, 2005, at 9:05 AM, Douglas Bates wrote:

> On 9/25/05, Horacio Montenegro <nepossiver at yahoo.com> wrote:
>
>>
>>     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
>>
>
> I have run into a couple of other things that the "improvements" from
> the 0.95 series to the 0.96 series has made worse.  This may take a
> while to sort out.  Thanks to Robert Bagchi for the very thorough
> error report.
>
>
>
>>
>> --- 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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