From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>

Date: Tue 27 Sep 2005 - 03:57:39 EST

Date: Tue 27 Sep 2005 - 03:57:39 EST

On Mon, 26 Sep 2005, Martin Henry H. Stevens wrote:

> Hello all,

*> 1. Does Matrix 0.98-7 fix any of this?
**> 2. Assuming "no", how does one acquire Matrix 0.95-13?
*

It is in the Archive on CRAN, e.g.

http://cran.r-project.org/src/contrib/Archive/M/Matrix_0.95-13.tar.gz

> 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@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@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
**>>>>>
**>>>>>
**>>>>>
**>>>
**>>> ______________________________________________
**>>> R-help@stat.math.ethz.ch mailing list
**>>> https://stat.ethz.ch/mailman/listinfo/r-help
**>>> PLEASE do read the posting guide! http://www.R-project.org/posting-
**>>> guide.html
**>>>
**>>>
**>>
**>> ______________________________________________
**>> R-help@stat.math.ethz.ch mailing list
**>> https://stat.ethz.ch/mailman/listinfo/r-help
**>> PLEASE do read the posting guide! http://www.R-project.org/posting-
**>> guide.html
**>>
**>
**> ______________________________________________
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**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
**>
*

-- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlReceived on Tue Sep 27 04:01:52 2005

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