From: Horacio Montenegro <nepossiver_at_yahoo.com>

Date: Mon 26 Sep 2005 - 07:05:33 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 Mon Sep 26 07:09:53 2005

Date: Mon 26 Sep 2005 - 07:05:33 EST

- 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 Received on Mon Sep 26 07:09:53 2005

*
This archive was generated by hypermail 2.1.8
: Fri 03 Mar 2006 - 03:40:26 EST
*