[R-sig-ME] glmmADMB

[Veronique Dermauw]

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 at inbo.be]
Sent: donderdag 12 november 2015 17:44
To: Veronique Dermauw
Cc: r-sig-mixed-models at 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 at itg.be<mailto:vdermauw at 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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