[R-sig-ME] glmmadmb beta - error

Tue Feb 23 13:08:29 CET 2016

glmmadmb was just telling you in a nice way to get more data. Normally, 
I would say 'try to simplify your model'....but even then you may have 
problems with such a small data set.

You are having around 6 regression parameters, a beta distribution and a 
random effect that has around 2 observations per level.

Alain

On 23/02/2016 12:01, Ludovico Frate wrote:
> I'm sorry,
> the structure of the data is
>
> data.frame':50 obs. of  5 variables:
> $ plot_id  : Factor w/ 25 levels "FEME11","FEME13",..: 5 6 7 8 1 2 3 4 
> 9 10 ...
>  $ summit   : Factor w/ 2 levels "FEM","MAC": 1 1 1 1 1 1 1 1 1 1 ...
>  $ direction: Factor w/ 4 levels "E","N","S","W": 2 2 2 2 1 1 1 1 3 3 ...
>  $ time     : int  2001 2001 2001 2001 2001 2001 2001 2001 2001 2001 ...
>  $ cover    : num  0.023 0.071 0.063 0.014 0.003 0.035 0.055 0.01 
> 0.065 0.04 ...
>
> Ludovico
> __
> Dott. For. Ludovico Frate, Ph.D.
> University of Molise - Italy
> Environmetrics Lab
> http://www.distat.unimol.it/STAT/environmetrica/organico/collaboratori/ludovico-frate-1
> Department of Biosciences and Territory- DiBT
> Università del Molise.
> Contrada Fonte Lappone,
> 86090 - Pesche (IS)
> ITALIA.
> Cel: ++39 3333767557
> Fax: ++39 (0874) 404123
> E-mail ludovico.frate at unimol.it
> ludovicofrate at hotmail.it
> https://www.researchgate.net/profile/Ludovico_Frate
>
>
> > To: r-sig-mixed-models at r-project.org
> > From: highstat at highstat.com
> > Date: Tue, 23 Feb 2016 11:14:55 +0000
> > Subject: Re: [R-sig-ME] glmmadmb beta - error
> >
> >
> >
> >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Tue, 23 Feb 2016 09:58:39 +0100
> > > From: Ludovico Frate <ludovicofrate at hotmail.it>
> > > To: "r-sig-mixed-models at r-project.org"
> > > <r-sig-mixed-models at r-project.org>
> > > Subject: [R-sig-ME] glmmadmb beta - error
> > > Message-ID: <DUB126-W5256D4E695B95DA5076216D6A40 at phx.gbl>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Dear list,I have got the following error message trying to fit 
> this model:
> > > glmmadmb<-(cover~time+summit+direction+(1|plot_id), family = 
> "beta", data = cover_lf)
> > > Error in glmmadmb(cover~time+summit+direction+(1|plot_id), : The 
> function maximizer failed (couldn't find parameter file) 
> Troubleshooting steps include (1) run with 'save.dir' set and inspect 
> output files; (2) change run parameters: see '?admbControl';(3) re-run 
> with debug=TRUE for more information on failure modeIn addition: 
> Warning message:running command 'C:\Windows\system32\cmd.exe /c 
> glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had status 1
> > > str(cover_lf)'data.frame': 50 obs. of 5 variables: $ plot_id : 
> Factor w/ 48 levels "FEME11","FEME13",..: 5 6 7 8 1 2 3 4 9 10 ... $ 
> summit : Factor w/ 2 levels "FEM","MAC": 1 1 1 1 1 1 1 1 1 1 ... $ 
> direction: Factor w/ 4 levels "E","N","S","W": 2 2 2 2 1 1 1 1 3 3 ... 
> $ time : Factor w/ 2 levels "2001","2015": 1 1 1 1 1 1 1 1 1 1 ... $ 
> cover : num 0.023 0.071 0.063 0.014 0.003 0.035 0.055 0.01 0.065 0.04 ...
> > > cover is the dependent variable that is percentage of cover 
> (0-100) divided by 100 to match the beta distribution. The random 
> effect was included to allow repeated measure on each plot for two 
> time period (time treated as factor).
> > > Thank you in advance,Regards
> > > Ludovico
> >
> > Do I read correctly in the error message the phrase '50 obs. of 5
> > variables"? Does that mean that you only have 50 observations? If that
> > is the case then it is no wonder that a beta model with random effects
> > (48 levels?) and 6 or 7 regressions parameters is crashing.
> >
> > Kind regards,
> >
> > Alain
> > >
> >
> >
> > >
> > > Dott. For. Ludovico
> > > Frate, Ph.D.
> > > University of Molise - Italy
> > > Environmetrics Lab
> > > 
> http://www.distat.unimol.it/STAT/environmetrica/organico/collaboratori/ludovico-frate-1
> > > Department of Biosciences and Territory - DiBT
> > > Universit? del Molise.
> > > Contrada Fonte
> > > Lappone,
> > > 86090 - Pesche (IS)
> > > ITALIA.
> > > Cel: ++39
> > > 3333767557
> > > Fax: ++39 (0874) 404123
> > > E-mail ludovico.frate at unimol.it
> > > ludovicofrate at hotmail.it
> > > https://www.researchgate.net/profile/Ludovico_Frate
> > >
> >
> >
> > >
> >
> > --
> > Dr. Alain F. Zuur
> >
> > First author of:
> > 1. Beginner's Guide to GAMM with R (2014).
> > 2. Beginner's Guide to GLM and GLMM with R (2013).
> > 3. Beginner's Guide to GAM with R (2012).
> > 4. Zero Inflated Models and GLMM with R (2012).
> > 5. A Beginner's Guide to R (2009).
> > 6. Mixed effects models and extensions in ecology with R (2009).
> > 7. Analysing Ecological Data (2007).
> >
> > Highland Statistics Ltd.
> > 9 St Clair Wynd
> > UK - AB41 6DZ Newburgh
> > Tel: 0044 1358 788177
> > Email: highstat at highstat.com
> > URL: www.highstat.com
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

-- 
Dr. Alain F. Zuur

First author of:
1. Beginner's Guide to GAMM with R (2014).
2. Beginner's Guide to GLM and GLMM with R (2013).
3. Beginner's Guide to GAM with R (2012).
4. Zero Inflated Models and GLMM with R (2012).
5. A Beginner's Guide to R (2009).
6. Mixed effects models and extensions in ecology with R (2009).
7. Analysing Ecological Data (2007).

Highland Statistics Ltd.
9 St Clair Wynd
UK - AB41 6DZ Newburgh
Tel:   0044 1358 788177
Email: highstat at highstat.com
URL:   www.highstat.com

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