[R-sig-ME] Error in glmer fit

[Ben Bolker]

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
> >