Re: [R] Multiple CHOLMOD errors when attempting poisson glmm
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 ba...@stat.wisc.edu wrote: On Thu, Dec 24, 2009 at 1:03 PM, postava-davig.m postava-davi...@husky.neu.edu 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 valueswhich 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-mod...@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.
Re: [R] Multiple CHOLMOD errors when attempting poisson glmm
On Sat, Dec 26, 2009 at 1:21 PM, Marielle Postava-Davig postava-davi...@husky.neu.edu wrote: I was actually curious if there was another version of lme4 I could use. You could try glmmPQL in the MASS package. __ 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.
Re: [R] Multiple CHOLMOD errors when attempting poisson glmm
On Thu, Dec 24, 2009 at 1:03 PM, postava-davig.m postava-davi...@husky.neu.edu 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 valueswhich 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-mod...@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. __ 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.
[R] Multiple CHOLMOD errors when attempting poisson glmm
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 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 valueswhich 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 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.
