[ADMB Users] glmmADMB-Function maximizer failed Poisson, ZIPoisson, NB1, ZINB1

[Ben Bolker]

On 11-12-18 05:36 PM, Rocio Jana wrote:
> Hello Ben
> 
> Thanks for the instructions. I did my homework, and tried to follow
> the instructions you sent. So far:
> 1- latest version downloaded today, reinstalled
> 
> 2- new code run
> 
> pel.mataicl.NBalt<-glmmadmb(mataicl ~ rimuover + kahikover + mataiover
> + miroover + hinauover + tawaover+(year|trapno),
> zeroInflation=FALSE,data=pel.3.dat,family =
> "nbinom1",admb.opts=admbControl(run=FALSE),debug=TRUE,save.dir="glmmtmp")
> 
> Temporary folder created in working directory.

   OK.
> 
> 3- I am not sure what you meant with "copy the glmmadmb binary over to
> that directory (if necessary -- this only happens on MacOS and Linux,
> not on Windows)" as the exe file didn't appear in the temporary
> folder, it was only in the new installed version of the package in the
> library.

   Yes.  The point is that, on Windows, you *don't* have to copy the
executable to the temporary directory.

> 
> So I copied the glmmadmb.exe file from the downloaded binary file into
> the glmmtmp folder. And I ran it. CMD window opened and analysis ran.
> Several files were created (can send you the list if you want me to),
> including glmmadmb.dat and glmmadmb.pin files.

  If you send the .dat and .pin files to the list, that will help.

> I don't find any obvious output telling me what command would be run
> by glmmADMB to run the model, sorry. Should it be one of the newly
> created files in the glmmtmp folder?

  I believe the 'debug' output should have told you (can you post the
output of running the command?), but it will be something like the
"C:\WINDOWS\ ..." command below.
> 
> 4- Step 2
> 
> I couldn't make it work. I am sorry, but I don't understand very well
> the instructions in this step.
> 
>> change to the temporary directory and run the command (which in your
>> case would be
> 
>> C:\WINDOWS\system32\cmd.exe /c "C:/Program
>> Files/R/R-2.14.0/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500
>> -noinit
> 
> When you said "change to the temporary directory" you mean change the
> working directory within R (File, change dir...)?
> and "run the command" in R?
> because I tried it, but R didn't recognize it.

  No, I mean in the terminal window, change to the temporary directory
that was created within your working directory, then run
the command above in the terminal window.
> 
> And finally, even I haven't got to step 3, once I do it, should I
> re-run the whole code from step 1? i.e. re-create the temp folder and
> everything? or re-run the code without the extra bit? Will R find the
> output files even they were created in this temporary folder? As I
> need to run 5 other models with other response variables and same
> predictors, will it work automatically or will I need to run the code
> from outside of R before every new model?

  Well, right now we're just trying to figure out what's wrong. If we
can debug this then you won't need to run the code outside of R.

  The basic idea of what I am trying to get you to do here is:

1. Run glmmADMB with run=FALSE to generate the files necessary to run
the model, and copy them to the temporary working directory

2. Run the binary outside of R.

3. Run glmmADMB with run=FALSE again, this time to read in the *output*
files generated in step 2.

  This is more steps than running everything from within R, but it may
help debug/expose whether there are problems when running from within R.

  Are you willing to send me the original data set and the
self-contained code that reads in the data and leads up to running the
glmmADMB model?

> I apologize if I am asking too much, but I find this package extremely
> useful and complete. So I really want to be able to use it well (and I
> also need to).
> 
> Thank you very much
> Rocio
> 
> 
> 
>> Rocio C. Jaña Prado PhD candidate
>> School of Biological Sciences
>> University of Canterbury Te Whare Wananga o Waitaha
>>  Private Bag 4800, Christchurch 8020
>>  New Zealand
>> Phone: +64 3 3643055 or ext 3055 Fax: +64 3 3642590
> _______________________________________________
> Users mailing list
> Users at admb-project.org
> http://lists.admb-project.org/mailman/listinfo/users