[ADMB Users] glmm.admb in R

[John Sibert]

Is glimm.ADMB a suitable topic for consideration at the June workshop?

Or more generally ADMB/R interfaces?

Was there a report from the NCEAS workshop?

John

On 02/17/2011 02:13 AM, H. Skaug wrote:
> Hi,
>
> The infinite loop is a well known problem (with ADMB) that we give
> high priority to fix.
> Until that has happened I am not sure what advice to give, because it cannot
> easilty be handled from inside R. I know that this feature causes
> great problems in a simulation loop like yours.
>
> Hans
>
>
>
> On Wed, Feb 16, 2011 at 10:21 AM, Zhanpan Zhang
> <zhanpan.zhang at email.ucr.edu>  wrote:
>> Hi all,
>> Thanks for posting my previous email in this list, Prof. Skaug!
>>
>> For the data I previously mentioned, R keeps displaying the error message
>> "Error matrix not positive definite in choleski_decomp" and it keeps running
>> and won't stop (R code is shown below, and the data has only two columns of
>> "y" being the response and "subject" being the random group factor).
>>> problem=data.class(try(glmm.admb(y~1,random=~1,group="subject",data=data,family="nbinom"),silent=T))=="try-error"
>> This has been solved by adding the option "easyFlag=FALSE". However, I
>> simulated some other data, and the same problem of "Error matrix not
>> positive definite in choleski_decomp" endlessly popping out came back again
>> even with "easyFlag=FLASE".
>> I am actually applying glmm.admb to a number of the simulated data (say
>> 500), and I could accept that some of them would not be fitted very well.
>> But is it possible to let R jump to the next data fitting if the above
>> problem happens for the current data set? (the only thing I can do currently
>> is to force R to stop, so I could never finish this loop of fitting 500 data
>> sets.)
>> Any comments will be appreciated!
>>
>> Zhanpan
>>
>>
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-- 
John Sibert
Emeritus Researcher, SOEST
University of Hawaii at Manoa

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