[R-sig-ME] glmer and poisson distributions and P values

Tue Mar 17 12:51:42 CET 2009

Dear Emma,

Verbose is just another argument of the glmer function. Just like family is. Hence it does not replace the family argument. Have a look at ?glmer for all its arguments.

Verbose will give you more details on the convergence of the model. It does not make your model converge. I'm still willing to look at your data if you send it in an easy to read format (.Rdata, .csv, .txt).

HTH,

Thierry

----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 
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: Emma Stone [mailto:Emma.Stone at bristol.ac.uk] 
Verzonden: dinsdag 17 maart 2009 11:53
Aan: ONKELINX, Thierry; Emma Stone; Luca Borger
CC: r-sig-mixed-models at r-project.org
Onderwerp: RE: [R-sig-ME] glmer and poisson distributions and P values

Hi Thierry,

Thanks for this, does that mean I add this to the model instead of the 
family = poisson? Is this still applicable for poisson data?

Sorry if I am being stupid, quite new to all this

Emma

--On 17 March 2009 09:23 +0100 "ONKELINX, Thierry" 
<Thierry.ONKELINX at inbo.be> wrote:

> Dear Emma,
>
> As Douglas stated in his post: add verbose = TRUE to your call to glmer.
> Eg glmer(Response ~ Predictor, verbose = TRUE)
>
> Cheers,
>
> Thierry
>
>
> -------------------------------------------------------------------------
> --- ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest Cel biometrie, methodologie en kwaliteitszorg / Section
> biometrics, methodology and quality assurance Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx at inbo.be
> 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] Namens Emma Stone
> Verzonden: dinsdag 17 maart 2009 9:10
> Aan: Luca Borger
> CC: r-sig-mixed-models at r-project.org
> Onderwerp: Re: [R-sig-ME] glmer and poisson distributions and P values
>
> Hi Luca,
>
> Yep had a look on the help archive but this doesn't really help me I'm
> afraid,
>
> There was no fitted model returned and I don't know how to turn on the
> verbose option in the optimizer.
>
> Any ideas?
>
>
>
> --On 16 March 2009 17:52 -0400 Luca Borger <lborger at uoguelph.ca> wrote:
>
>> Hi Emma,
>>
>> (my two cents) It is usually very helpful to do first a search on the
>> mailing list archives. For example, at:
>>
>>
>>############################################################################
>> http://markmail.org/message/oogvmvpxldr5i57q
>>
>> you can find a reply by Prof. Bates:
>>
>> "In mer_finalize(ans) : false convergence (8)
>>
>> That's a warning that the parameter estimates are suspect but it's not
>> an error. I believe that a fitted model would have been returned.
>>
>> I suggest you turn on the verbose option in the optimizer and examine
>> the progress of the iterations.  In the original call to glmer you add
>> verbose = TRUE.  If re-calling "mer_optimize" as above then change the
>> FALSE to TRUE."
>>#############################################################################
>>
>>
>> In addition, more information would be needed about your data etc. For
>> example, in some cases similar convergence problems can be solved by
>> centreing/standardising the predictor variable (but I may get corrected
>> on this by the experts on this list).
>>
>> HTH
>>
>>
>>
>> Cheers,
>>
>> Luca
>>
>>
>>
>> ----- Messaggio originale -----
>> Da: "Emma Stone" <Emma.Stone at bristol.ac.uk>
>> A: r-sig-mixed-models at r-project.org
>> Inviato: Lunedì, 16 marzo 2009 11:21:00 GMT -05:00 U.S.A./Canada, stati
>> orientali Oggetto: [R-sig-ME] glmer and poisson distributions and P
>> values
>>
>>
>> Dear all,
>>
>> I am trying to run a glmer model with count data,with one random factor.
>> When I run it with more than one predictor all is well, but when there is
>> only one predictor in the model I get this warning message, can anyone
>> explain this at all?
>>
>> Warning message: In mer_finalize(ans) : false convergence (8)
>>
>> Also, for other models in the canidate set I am looking at interactions
>> between predictors and I want to get the P values for these interactions,
>> any ideas how I can do this from a glmer model?
>>
>> Thanks
>>
>> Emma
>>
>>
>> --
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
>
> ----------------------
> Emma Stone
> Postgraduate Researcher
> Bat Ecology and Bioacoustics Lab
> & Mammal Research Unit
> School of Biological Sciences,
> University of Bristol, Woodland Road,
> Bristol, BS8 1UG
> Email: emma.stone at bristol.ac.uk
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
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> bevestigd is door een geldig ondertekend document. The views expressed in
> this message  and any annex are purely those of the writer and may not be
> regarded as stating  an official position of INBO, as long as the message
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----------------------
Emma Stone
Postgraduate Researcher
Bat Ecology and Bioacoustics Lab
& Mammal Research Unit
School of Biological Sciences,
University of Bristol, Woodland Road,
Bristol, BS8 1UG
Email: emma.stone at bristol.ac.uk

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
an official position of INBO, as long as the message is not confirmed by a duly 
signed document.