[ADMB Users] glmmADMB-Function maximizer failed Poisson, ZIPoisson, NB1, ZINB1
Rocio Jana
rcjp14 at gmail.com
Sun Dec 18 18:04:09 PST 2011
Hello Ben
.dat and .pin files attached.
Now I understood what you were saying (I think), thanks. This time I
copied the cmd.exe file to the temporary folder, and run the command.
"C:/Program Files/R/R-2.14.0/library/glmmADMB/bin/wi
ndows32/glmmadmb.exe" -maxfn 500 -noinit
from the terminal window.
Output follows:
Microsoft Windows [Version 6.0.6002]
Copyright (c) 2006 Microsoft Corporation. All rights reserved.
C:\Users\Rocio\Dropbox\Thesis PhD\Results\Pelorus data\in process\R Pelorus\DK\a
nalysis DK\glmmADMB\glmmtmp>"C:/Program Files/R/R-2.14.0/library/glmmADMB/bin/wi
ndows32/glmmadmb.exe" -maxfn 500 -noinit
Initial statistics: 7 variables; iteration 0; function evaluation 0; phase 1
Function value 9.8743298e+02; maximum gradient component mag -6.2270e+00
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 0.00000 1.07650e+00 | 2 0.00000 2.02307e+00 | 3 0.00000 -2.28066e-01
4 0.00000 -6.22700e+00 | 5 0.00000 4.40416e-01 | 6 0.00000 2.35466e+00
7 0.00000 -3.73239e-01 |
Intermediate statistics: 7 variables; iteration 10; function evaluation 13; phas
e 1
Function value 9.3661483e+02; maximum gradient component mag -1.3118e-01
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 -7.16587 9.77975e-02 | 2 -5.89626 -1.18792e-01 | 3 1.65312 -3.34196e-02
4 12.23006 -3.94453e-02 | 5 0.79002 -4.71586e-03 | 6-19.23210 4.09933e-03
7 -2.39234 -1.31184e-01 |
7 variables; iteration 20; function evaluation 23; phase 1
Function value 9.3630673e+02; maximum gradient component mag 1.1224e-04
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 -9.56385 1.12240e-04 | 2 -4.20424 -1.73660e-05 | 3 2.54873 -5.19771e-05
4 13.79312 -3.84108e-05 | 5 2.29122 3.12230e-05 | 6-27.30826 -1.53161e-05
7 -1.68819 -8.21997e-05 |
- final statistics:
7 variables; iteration 21; function evaluation 24
Function value 9.3631e+02; maximum gradient component mag 2.4472e-05
Exit code = 1; converg criter 1.0000e-04
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 -9.56580 -2.71265e-06 | 2 -4.20375 -2.00960e-06 | 3 2.54936 -1.24119e-05
4 13.79420 -2.47582e-06 | 5 2.29220 2.44725e-05 | 6-27.31371 5.52717e-06
7 -1.68800 6.91965e-06 |
Initial statistics: 8 variables; iteration 0; function evaluation 0; phase 2
Function value 2.5317989e+03; maximum gradient component mag -1.5770e+04
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 -9.56580 -3.34574e+00 | 2 -4.20375 5.64782e-01 | 3 2.54936 4.67688e-01
4 13.79420 -1.97624e+00 | 5 2.29220 2.09047e-01 | 6-27.31371 -2.51638e-01
7 -1.68800 6.99966e-02 | 8 0.05795 -1.57700e+04 |
Intermediate statistics: 8 variables; iteration 10; function evaluation 14; phas
e 2
Function value 1.2108985e+03; maximum gradient component mag -2.3990e+01
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 48.11251 4.36815e-01 | 2 -1.70464 1.01715e-01 | 3 0.08195 3.06426e-02
4 5.08995 1.61697e-01 | 5 0.63700 9.17857e-02 | 6 -9.14759 -4.76702e-01
7 -0.52802 -1.14350e-02 | 8 0.49487 -2.39897e+01 |
8 variables; iteration 20; function evaluation 24; phase 2
Function value 1.2094768e+03; maximum gradient component mag -1.3742e-01
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 45.45399 2.05442e-03 | 2 -2.40041 -7.84976e-04 | 3 -0.23354 2.10991e-03
4 4.46732 -4.20901e-03 | 5 -0.03951 5.50287e-04 | 6 -5.52707 -9.91974e-04
7 -0.41976 -3.00801e-03 | 8 0.47819 -1.37424e-01 |
- final statistics:
8 variables; iteration 28; function evaluation 32
Function value 1.2095e+03; maximum gradient component mag -3.6290e-05
Exit code = 1; converg criter 1.0000e-04
Var Value Gradient |Var Value Gradient |Var Value Gradient
1 45.43909 3.33461e-07 | 2 -2.39643 -8.71364e-07 | 3 -0.24019 1.08903e-06
4 4.47829 -8.06363e-07 | 5 -0.04157 -1.52222e-06 | 6 -5.52336 -5.95947e-07
7 -0.40882 1.30698e-06 | 8 0.47812 -3.62897e-05 |
Hessian type 4
inner maxg = -0.0006781 Inner second time = -0.0006781 Inner f = 1191
f = 1190.630581903202 max g = 0.0006781269614516524
Newton raphson 1
C:\Users\Rocio\Dropbox\Thesis PhD\Results\Pelorus data\in process\R Pelorus\DK\a
nalysis DK\glmmADMB\glmmtmp>
I hope it helps.
I'll email you the data and R code now.
Thanks again
Rocio
2011/12/19 Ben Bolker <bbolker at gmail.com>:
> 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
>
--
Rocio C. Jaña Prado
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