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 <[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