From: Martin Henry H. Stevens <HStevens_at_MUOhio.edu>

Date: Tue 27 Sep 2005 - 03:12:31 EST

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 Received on Tue Sep 27 03:27:54 2005

Date: Tue 27 Sep 2005 - 03:12:31 EST

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@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-
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**>
*

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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 Received on Tue Sep 27 03:27:54 2005

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