[R-sig-ME] Error in glmer fit

Wed Nov 14 18:31:46 CET 2012

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"
 > 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

On 11/14/2012 06:57 AM, Martí Casals wrote:
> Hello,
> I don't know if it is a good idea to include "nAGQ=5 orother points" in
> the options script!
> If you only use a unique random effect you can try to the AGQ method.
>
> glmer(InInt~speciality+position+stkperyr+conf+age+years+risk+stroke_type+(1|pid),data=dord4mod,nAGQ=5,family=binomial,verbose=TRUE)
>
> Best wishes,
>
> Martí
>
> 2012/11/13 ONKELINX, Thierry <Thierry.ONKELINX at inbo.be
> <mailto:Thierry.ONKELINX at inbo.be>>
>
>     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
>     Instituut voor natuur- en bosonderzoek / Research Institute for
>     Nature and Forest
>     team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>     Kliniekstraat 25
>     1070 Anderlecht
>     Belgium
>     + 32 2 525 02 51 <tel:%2B%2032%202%20525%2002%2051>
>     + 32 54 43 61 85 <tel:%2B%2032%2054%2043%2061%2085>
>     Thierry.Onkelinx at inbo.be <mailto:Thierry.Onkelinx at inbo.be>
>     www.inbo.be <http://www.inbo.be>
>
>     To call in the statistician after the experiment is done may be no
>     more than asking him to perform a post-mortem examination: he may be
>     able to say what the experiment died of.
>     ~ Sir Ronald Aylmer Fisher
>
>     The plural of anecdote is not data.
>     ~ Roger Brinner
>
>     The combination of some data and an aching desire for an answer does
>     not ensure that a reasonable answer can be extracted from a given
>     body of data.
>     ~ John Tukey
>
>
>     -----Oorspronkelijk bericht-----
>     Van: r-sig-mixed-models-bounces at r-project.org
>     <mailto:r-sig-mixed-models-bounces at r-project.org>
>     [mailto:r-sig-mixed-models-bounces at r-project.org
>     <mailto:r-sig-mixed-models-bounces at r-project.org>] Namens Kevin E.
>     Thorpe
>     Verzonden: dinsdag 13 november 2012 1:23
>     Aan: r-sig-mixed-models at r-project.org
>     <mailto:r-sig-mixed-models at r-project.org>
>     Onderwerp: [R-sig-ME] Error in glmer fit
>
>     Hello.
>
>     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)
>
>     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] grid      tcltk     splines   stats     graphics  grDevices utils
>        [8] datasets  methods   base
>
>     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
>
>     loaded via a namespace (and not attached):
>     [1] MASS_7.3-16    Rcpp_0.9.10    cluster_1.14.1 minqa_1.1.18
>     nlme_3.1-102
>     [6] tools_2.14.0
>

-- 
Kevin E. Thorpe
Biostatistician/Trialist,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016