glmmadmb beta - error
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 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
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
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
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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 [[alternative HTML version deleted]]