Dear All I am trying to model the burden of fleas on field voles using a GLMM with poisson error and a nested random effect. The random effect is (1|Farm/Margin) I have 7 farms and 14 margins (2 margins per farm) and have sampled each margin 4 times. However, I continually get an error message even when I simplify the model. The model I am trying to run is: bin<-lmer(fleaburden ~ sex + width + month + vole abundance + alternative host abunandance +(1|Farm/Margin), family=poisson, data=flea, REML=FALSE) The error message: CHOLMOD warning: ?e Error in mer_finalize(ans) : Cholmod error `not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 Any help in understanding this error would be much appreciated. Thanks, Anna Anna Renwick Institute of Biological & Environment Sciences University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ The University of Aberdeen is a charity registered in Scotland, No SC013683.
CHOLMOD warning with GLMM
2 messages · Renwick, A. R., Douglas Bates
2009/2/10 Renwick, A. R. <a.renwick at abdn.ac.uk>:
Dear All I am trying to model the burden of fleas on field voles using a GLMM with poisson error and a nested random effect. The random effect is (1|Farm/Margin) I have 7 farms and 14 margins (2 margins per farm) and have sampled each margin 4 times. However, I continually get an error message even when I simplify the model. The model I am trying to run is:
bin<-lmer(fleaburden ~ sex + width + month + vole abundance + alternative host abunandance +(1|Farm/Margin), family=poisson, data=flea, REML=FALSE)
Do you really have variables named 'vole abundance' and 'alternative host abundance' or did you edit that part of the transcript? I would imagine you would get a syntax error reported from something like that because of the embedded blanks without appropriate quoting.
The error message:
CHOLMOD warning: ?e Error in mer_finalize(ans) : Cholmod error `not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432
Any help in understanding this error would be much appreciated.
Usually I suggest using verbose = TRUE to begin looking at the source of the problem. The error message is unexpected. I would have guessed that it couldn't happen in this calculation. It is from the Cholesky factorization of a matrix derived from the model matrix for the random effects and it indicates that the matrix is singular. As I said, I expected that the way the calculation is done that matrix never could be singular. Would you be willing to share your data with me (you can make it anonymous if you wish - I'm not sure if privacy considerations extend to voles but I am willing to have their real names removed, I only need the numbers) so that I can check in more detail what is happening?