Error in glmer fit
Kevin E. Thorpe <kevin.thorpe at ...> writes:
Thank you both for your responses. Unfortunately neither solves the problem. Using nAGQ=5 with lme4 results in the same error as already shown. At Thierry's suggestion, I tried lme4.0 and get a different error. glmer(InInt~speciality+position+stkperyr+conf+ age+years+risk+stktype+(1|pid),data=dord4mod,family=binomial) Error in validObject(.Object) : invalid class "mer" object: invalid object for slot "resid" in class "mer": got class "labelled", should be or extend class "numeric"
This is a pretty weird error. Is this from a clean session? Is there any chance you can provide a reproducible problem? (You could send me your data.) To provide a little bit more context for the general public about lme4 development: at present there are three versions of lme4: stable-CRAN: 0.999999-0 lme4 (R-forge): 0.99999911-0 lme4.0 (R-forge): 0.999999-1 As far as we know, lme4.0 is identical to the stable-CRAN version (if not, please let us know!) lme4 is the development version: it has lots of goodies that stable-lme4 doesn't (profiling, a predict method, a built-in parametric bootstrap method, support for alternative optimizers, ...), but at present it (1) doesn't work with all of the downstream add-on packages (gamm4, blme, etc) and (2) has a somewhat unstable GLMM fitting algorithm. We are working hard to fix #2; once that's done we will work on #1, and then release it (yes, we know you've heard that before). In the meantime, if you can live without the goodies, the stable version represents the best bet. Things are a little more difficult if you don't have the latest version, since install.packages() may not find the right version. You can try downloading the relevant binary or source version from http://cran.r-project.org/web/packages/lme4//index.html or https://r-forge.r-project.org/R/?group_id=60
> sessionInfo()
R version 2.14.0 Patched (2011-11-29 r57769) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US [4] LC_COLLATE=C LC_MONETARY=en_US LC_MESSAGES=en_US [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lme4.0_0.999999-1 Matrix_1.0-2 lattice_0.20-0 rms_3.3-2 [5] Hmisc_3.9-0 survival_2.36-10 loaded via a namespace (and not attached): [1] cluster_1.14.1 grid_2.14.0 nlme_3.1-102 stats4_2.14.0
2012/11/13 ONKELINX, Thierry <Thierry.ONKELINX at ...
<mailto:Thierry.ONKELINX at ...>>
Dear Kevin,
I cannot give you answer on why this happens. You can try the lme4.0
package as a work around. It is an older version of lme4.
Best regards,
ir. Thierry Onkelinx
I attempted the following command and got the resultant error.
glmer(InInt~speciality+position+stkperyr+conf+
age+years+risk+stroke_type+(1|pid),data=dord4mod,
family=binomial,verbose=TRUE)
Error in pwrssUpdate(pp, resp, tolPwrss, GQmat, compDev, fac, verbose) :
PIRLS step failed
It seems to happen right off the bat. Any idea what the source may be?
I don't want to post the data in the open, but will send it
privately if requested. Here also is my sessionInfo()
R version 2.14.0 Patched (2011-11-29 r57769)
Platform: x86_64-unknown-linux-gnu (64-bit)
other attached packages:
[1] lme4_0.999902345-0 Matrix_1.0-2 ResearchMethods_1.4
[4] ellipse_0.3-5 gplots_2.10.1 KernSmooth_2.23-7
[7] caTools_1.12 bitops_1.0-4.1 gdata_2.8.2
[10] gtools_2.6.2 irr_0.83 lpSolve_5.6.6
[13] lattice_0.20-0 rms_3.3-2 Hmisc_3.9-0
[16] survival_2.36-10