[R] How to have NLME return when convergence not reached

Bert Gunter gunter.berton at gene.com
Tue Dec 2 23:03:44 CET 2014

Yes, Bill almost always has helpful ideas.

Just a comment: If indeed the process is gobbling up too much memory,
that might indicate a problem with your function or implementation. I
defer to real experts on this, however.


Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll

On Tue, Dec 2, 2014 at 1:59 PM, Ramiro Barrantes
<ramiro at precisionbioassay.com> wrote:
> Thanks so much for your reply.  I am using try but nlme never returns!!  and I think the process is getting killed by the system as it is taking over all the memory.  However, I do like William Dunlap's idea of using R.utils::withTimeout to limit the time.
> Thanks again for your help!
> ________________________________________
> From: Bert Gunter [gunter.berton at gene.com]
> Sent: Tuesday, December 02, 2014 4:30 PM
> To: Ramiro Barrantes
> Cc: r-help at r-project.org
> Subject: Re: [R] How to have NLME return when convergence not reached
> ?try
> Or
> ?tryCatch
> Bert
> Sent from my iPhone -- please excuse typos.
>> On Dec 2, 2014, at 12:57 PM, Ramiro Barrantes <ramiro at precisionbioassay.com> wrote:
>> Hello,
>> I am trying to fit many hundreds of simulated datasets using NLME (it's all in a big loop in R).  Some don't seem to converge.  I am working on addressing the issues by perhaps adjusting my simulation, or tweaking iteration steps in nlme, etc.  However, when it doesn't converge, NLME just hangs, and my program either stalls for hours/days or takes over the computer memory and everything crashes eventually.  Is there a way to tell nlme to stop when it doesn't seem to be converging somehow?   I have been looking at the parameters in nlmeControl() but see nothing obvious.
>> Thanks in advance,
>> Ramiro
>>    [[alternative HTML version deleted]]
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