[R-sig-ME] Error in glmer fit
Ben Bolker
bbolker at gmail.com
Thu Nov 15 01:12:32 CET 2012
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
> >
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