[R-sig-ME] glmmADMB

[Thierry Onkelinx]

Dear Veronique,

We need more information. How many animals, villages, treatments,
timepoints, ...? How many observations per animal and per village? Can you
post the data or send it offline?

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

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

2015-11-17 10:09 GMT+01:00 Veronique Dermauw <vdermauw op itg.be>:

> Dear Thierry,
>
>
>
> Thank you for your response and advice.
>
> I’ve omitted missing values (94 out of 965), but I am getting another
> error message, see below:
>
> > cambNA<-na.omit(camb)
>
> >
> mod1b<-glmmadmb(GIS~Treatment*Time+(1|Animal)+(1|Village),family="nbinom",data=cambNA)
>
> Parameters were estimated, but standard errors were not: the most likely
> problem is that the curvature at MLE was zero or negative
>
> Error in glmmadmb(GIS ~ Treatment * Time + (1 | Animal) +  :
>
>   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 mode
>
> In addition: Warning message:
>
> running command 'C:\WINDOWS\system32\cmd.exe /c glmmadmb -maxfn 500 -maxph
> 5 -noinit -shess' had status 1
>
>
>
> Thank you for your help,
>
> Best regards,
>
> Veronique Dermauw.
>
>
>
> *From:* Thierry Onkelinx [mailto:thierry.onkelinx op inbo.be]
> *Sent:* donderdag 12 november 2015 17:44
> *To:* Veronique Dermauw
> *Cc:* r-sig-mixed-models op r-project.org
> *Subject:* Re: [R-sig-ME] glmmADMB
>
>
>
> Dear Veronique,
>
>
>
> It looks like your data contains missing values. Try to remove them. Your
> syntax seems to be correct.
>
>
>
> Note that Treatment + Time + Time * Treatment can be abbreviated to Time
> * Treatment
>
>
>
> Best regards,
>
>
>
> Thierry
>
>
> 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
>
> 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
>
>
>
> 2015-11-11 12:17 GMT+01:00 Veronique Dermauw <vdermauw op itg.be>:
>
> Dear,
>
> Recently I have been working on a dataset which seems to require a
> generalized linear mixed model with a negative binomial distribution.
> I came across the glmmADMB package which seems ideal.
> However, I am a bit stuck here (see codes and error message below).
> The dataset I am working on, involves count variables (GIS) from animals
> from different villages who were allocated a treatment (Treatment) and were
> sampled at various Time point (hence Time and Time*Treatment).
> I was wondering if you could assist me with this command?
>
> Many thanks for your response,
> Best regards,
> Veronique Dermauw.
>
>
> mod1b<-glmmadmb(GIS~Treatment+Time+Time*Treatment+(1|Animal)+(1|Village),family="nbinom",data=camb)
> summary(mod1b)
> Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
>   number of items to replace is not a multiple of replacement length
> In addition: Warning messages:
> 1: In glmmadmb(GIS ~ Treatment + Time + Time * Treatment + (1 | Animal) +
> :
>   NAs removed in constructing fixed-effect model frame: you should
> probably remove them manually, e.g. with na.omit()
> 2: In II[, ii] + REmat$codes[[i]] :
>   longer object length is not a multiple of shorter object length
>
>
> Veronique Dermauw
> PhD, MSc Veterinary Medicine
> Institute of Tropical Medicine
> Nationalestraat 155
> 2000 Antwerp
> +32(0)32476447
>
>
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