glmmadmb beta - error - R-SIG-mixed-models

Tue, Feb 23, 2016 3:14 AM #

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

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

Ludovico Frate

Tue, Feb 23, 2016 4:01 AM #

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
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

Highland Statistics Ltd

Tue, Feb 23, 2016 4:08 AM #

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

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


	[[alternative HTML version deleted]]

Ludovico Frate

Tue, Feb 23, 2016 4:43 AM #

Thanks for your reply!I successfully fitted another model with the same number of observation (and structure) and the only difference is that cover values were more centered on the mean values.
I just tried to fit the same model by adding a constant cover value to all observations (+0.20) and the model works
I think that the issue derives from very small cover values...
summary(cover_lf$cover) (divided by 100)
Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 0.0000  0.0050  0.0130  0.0252  0.0385  0.1300 
Call:glmmadmb(formula = cover ~ time + summit + direction + (1 | plot_id),     data = cover_lf, family = "beta")
AIC: -228.7 
Coefficients:            Estimate Std. Error z value Pr(>|z|)    (Intercept)  -1.2241     0.0476  -25.72   <2e-16 ***time2015     -0.0688     0.0337   -2.04   0.0410 *  summitMAC    -0.1407     0.0437   -3.22   0.0013 ** directionN    0.1028     0.0574    1.79   0.0733 .  directionS    0.0760     0.0624    1.22   0.2238    directionW    0.0986     0.0574    1.72   0.0860 .  ---Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
Number of observations: total=50, plot_id=25 Random effect variance(s):Group=plot_id            Variance  StdDev(Intercept) 0.003394 0.05826
Beta dispersion parameter: 403.43 (std. err.: 0.00012419)
Log-likelihood: 122.34

Highland Statistics Ltd

Tue, Feb 23, 2016 4:49 AM #

The fact that the software runs properly, or not, is irrelevant. You 
need to have at least 10 - 15 - 20 observations per regression parameter 
for an ordinary regression model. Using only 50 observations for the 
beta mixed model is not the best thing to do. Maybe this is not what you 
wanted to hear.

Alain

On 23/02/2016 12:43, Ludovico Frate wrote:

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]]