---------- Forwarded message ----------
From: Marielle Postava-Davig
Date: Sat, Dec 26, 2009 at 1:21 PM
Subject: Re: [R] Multiple CHOLMOD errors when attempting poisson glmm
To: Douglas Bates
Cc: r-help@r-project.org, R-mixed models mailing list <
r-sig-mixed-models@r-project.org>
Thank you so much for replying. The data set I used for this particular
output has 600 entries. The original had 1657 lines so I've already reduced
it considerably. Here is a copy of the entire output with lme4 package
information:
> substrate=read.csv(file.choose(),header=T)
> attach(substrate)
> library(lme4)
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from package:stats :
contr.helmert,
contr.poly,
contr.SAS,
contr.sum,
contr.treatment,
xtabs
The following object(s) are masked from package:base :
rcond
>
model1=lmer(totalcfus~habitat*temp*moisture*light+location+(1|habitat/colony/location),family=poisson,control=list(msVerbose=1))
0: 553377.59: 1.00573 0.620530 0.169516 26.3904 -13.1266 -33.2286
-21.1955 -21.1064 -0.590761 -0.217403 -0.0342272 -0.960593 -0.0962517
0.441626 1.20575 0.718621 0.680580 0.171006 0.403729 0.278822 0.275395
0.00707767 0.0225599 0.0854869 0.0533373 0.0243451 0.00114120 0.000403226
-0.00566960 -0.0143715 -0.00931896 -0.00879323 -0.000753236 -0.00335745
-0.00178054 -0.000788027 -0.000288944 -0.000909455 -0.000839295 -0.000309293
-1.35885e-05 9.76120e-06 3.57035e-05 2.78985e-05 1.01880e-05
CHOLMOD warning: %h
Error in mer_finalize(ans) :
Cholmod error `not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 432
I was actually curious if there was another version of lme4 I could use. I
use a mac laptop that is about 6 years old and runs on the Tiger OS
10.4.11. I found another version of lme4 that would not work on my
operating system.
I had a feeling singularities might be my problem, but had run out of ideas
for eliminating them without losing the majority of my data set. I also
have not determined how to correctly enter year into the model, and I feel
that may be important. I have nests I sampled multiple years that may also
be causing problems. I greatly appreciate any advice you can give me.
Cheers,
Marielle
On Fri, Dec 25, 2009 at 11:24 AM, Douglas Bates wrote:
> On Thu, Dec 24, 2009 at 1:03 PM, postava-davig.m
> wrote:
> >
> > Hello,
>
> > I have been attempting to run a poisson glmm using lme4 for some time now
> > and have had a lot of trouble. I would say 9 times out of 10 I receive
> the
> > following warning:
>
> > CHOLMOD warning: %h
> > Error in mer_finalize(ans) :
> > Cholmod error `not positive definite' at
> > file:../Cholesky/t_cholmod_rowfac.c, line 432
>
> That is an (admittedly obscure) indication that the Cholesky
> factorization of a matrix derived from the random-effects model matrix
> cannot be performed.
>
> > My data are counts of microbe colony forming units (CFUs) collected from
> > termite cuticles and the surrounding environment over a 3 year period. I
> am
> > attempting to analyze the effect of several factors on these counts
> (termite
> > nest volume, temperature, humidity, light, incubation temperature,
> habitat,
> > year, sample location, etc.) to determine which account for the variance
> in
> > microbial communities. These data are observations, so there are many
> > missing values....which may be part of the problem. I've tried many
> > different combinations of variables, and also have tried reducing my data
> > set to remove as many NA's and confounding variables as possible, but I
> > still can't get any models to work consistently. One most recent attempt
> > had the following output:
>
>
> model1=lmer(totalcfus~habitat*temp*moisture*light+location+(1|habitat/colony/location),family=poisson,control=list(msVerbose=1))
> > 0: 553377.59: 1.00573 0.620530 0.169516 26.3904 -13.1266 -33.2286
> > -21.1955 -21.1064 -0.590761 -0.217403 -0.0342272 -0.960593 -0.0962517
> > 0.441626 1.20575 0.718621 0.680580 0.171006 0.403729 0.278822 0.275395
> > 0.00707767 0.0225599 0.0854869 0.0533373 0.0243451 0.00114120 0.000403226
> > -0.00566960 -0.0143715 -0.00931896 -0.00879323 -0.000753236 -0.00335745
> > -0.00178054 -0.000788027 -0.000288944 -0.000909455 -0.000839295
> -0.000309293
> > -1.35885e-05 9.76120e-06 3.57035e-05 2.78985e-05 1.01880e-05
> > CHOLMOD warning: %h
> > Error in mer_finalize(ans) :
> > Cholmod error `not positive definite' at
> > file:../Cholesky/t_cholmod_rowfac.c, line 432
>
> Thank you for including the output from verbose = TRUE. It would also
> help if you included the output from sessionInfo() so we can see which
> version of R you are using and which version of the lme4 package you
> are using.
>
> How many observations are used in this fit? As you can see, the
> number of parameters being fit is very large and encountering
> singularities is not unexpected.
>
> May I suggest that we move this discussion to the
> R-SIG-Mixed-Models@R-project.org mailing list, which I have cc:d on
> this reply? That list is specifically intended for discussions of
> this type.
> > I have to admit that I'm at a loss, and have been unable to determine any
> > pattern to when this error message comes up. I'm hoping that someone can
> > help me eek out what the issue is with my data so that I can eventually
> work
> > out a usable model.
> >
> > Thanks so much, and happy holidays.
> > --
> > View this message in context:
> http://n4.nabble.com/Multiple-CHOLMOD-errors-when-attempting-poisson-glmm-tp978573p978573.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
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