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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 >> > > ______________________________________________ > 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 > -- Brian D. Ripley, [EMAIL PROTECTED] 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.html
