On Mon, Mar 3, 2008 at 10:16 AM, Douglas Bates <bates at stat.wisc.edu> wrote:
On Mon, Mar 3, 2008 at 6:18 AM, Nick Isaac <njbisaac at googlemail.com> wrote:
> I just installed lme4_0.999375-5 and the problem has disappeared. Thanks!
Hmm - interesting. When I try the example using that version of the lme4 package it segfaults. I'm debugging now. Thanks for the example. I'm pretty sure it has to do with the use of the weights and that should help to isolate the problem.
There were indeed a couple of dumb programming mistakes that caused segfaults when fitting a linear mixed model with weights. After having fixed those I can get your example to run but the results (enclosed) don't look correct. I think the problem is that I am using the penalized, weighted residual sum of squares to evaluate the conditional estimate of the common scale parameter (i.e. sigma) without taking into account the sum of the weights. I already have a FIXME comment in the code that I should evaluate and store sigma in a different way so I will make that change and check on the way that sigma should be estimated at the same time.
> On 20/02/2008, Douglas Bates <bates at stat.wisc.edu> wrote:
> > Thanks for the report Nick and thanks for including the data so that > > we can reproduce the problem. > > > > I don't think I will have time to look at it until next week. I am > > travelling for the rest of the week (and, naturally, still need to > > finish my presentation). > > > > > > On Feb 20, 2008 11:18 AM, Nick Isaac <njbisaac at googlemail.com> wrote:
> > > Dear all, > > > > > > I just installed lme4_0.999375-4 and am sad to report unexpected
> behaviour
> > > the first time I ran lmer. > > >
> > > > sessionInfo()
> > > R version 2.6.2 (2008-02-08)
> > > i386-apple-darwin8.10.1
> > >
> > > locale:
> > > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> > >
> > > attached base packages:
> > > [1] stats graphics grDevices utils datasets methods base
> > >
> > > other attached packages:
> > > [1] lme4_0.999375-4 Matrix_0.999375-4 lattice_0.17-4
> > >
> > > loaded via a namespace (and not attached):
> > > [1] grid_2.6.2
> > >
> > >
> > >
> > > The dataset is attached. A call to:
> > >
> > > data<-read.table("ESW_080220.txt",sep="\t",header=T)
> > > data$W<- 5-log(1+data$CV)
> > > full1.w.mm <- lmer(ESW ~ Wingspan * Dataset * VCS + (1|Site) +
> (1|Species),
> > > data=data, weights=W) > > > > > > > > > > > > Produces a crash with the following message: > > > > > > *** caught bus error *** > > > address 0x0, cause 'non-existent physical address' > > > > > > Traceback: > > > 1: .Call(mer_optimize, ans, verbose) > > > 2: mer_finalize(ans, verbose) > > > 3: lmer(ESW ~ Wingspan * Dataset * VCS + (1 | Site) + (1 | Species), > > > data = data, weights = W) > > > > > > > > > > > > I repeated the exercise on another machine, running the version on
> CRAN:
> > > > > >
> > > > sessionInfo()
> > > R version 2.6.2 (2008-02-08) > > > i386-apple-darwin8.10.1 > > > > > > locale: > > > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > > other attached packages: > > > [1] lme4_0.99875-9 Matrix_0.999375-4 lattice_0.17-4 > > > > > > > > > > > > > > > The lmer fit the model with a warning: > > > > > > Warning message: > > > In .local(x, ..., value) : > > > Estimated variance for factor 'Site' is effectively zero > > > > > > > > > > > > The warning reflects the fact that this model is rather over-specified. > > > However, the behaviour in the development version is rather unexpected. > > > Best wishes, Nick Isaac > > >
> >
> > > _______________________________________________ > > > R-sig-mixed-models at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > > > > > >
> >
> >