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

[Ramiro Barrantes]

Ok.  I am trying to figure out if it's a bug in my code or in nlme, will let you know and send you a reproducible example to you, Martin, if the latter, or apologize profusely for blaming nlme :) if the former.

Thanks again for everyone's input.

________________________________________
From: Martin Maechler [maechler at stat.math.ethz.ch]
Sent: Wednesday, December 03, 2014 3:26 AM
To: Bert Gunter
Cc: Ramiro Barrantes; r-help at r-project.org
Subject: Re: [R] How to have NLME return when convergence not reached

>>>>> Bert Gunter <gunter.berton at gene.com>
>>>>>     on Tue, 2 Dec 2014 14:03:44 -0800 writes:

    > 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.

    > Cheers,
    > Bert

    > Bert Gunter
    > Genentech Nonclinical Biostatistics
    > (650) 467-7374


Yes, thank you Bert, it could be entirely Ramiro's function, but
we don't know as you have not given any indication about what
the non-linear function is in your nlme() formula.

The little you wrote _seems_ to indicate a bug in nlme, and if
that was the case, the bug should be reported and fixed,
and we (R core - the maintainer of the recommended package nlme)
would really like to to get a reproducible example.

If OTOH, it is your nonlinear function that "goes haywire",
the implicit blame on nlme would not be warranted.

Martin Maechler,
ETH Zurich and R Core team


    > 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]]
    >>>
    >>> ______________________________________________
    >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
    >>> https://stat.ethz.ch/mailman/listinfo/r-help
    >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    >>> and provide commented, minimal, self-contained, reproducible code.

    > ______________________________________________
    > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
    > https://stat.ethz.ch/mailman/listinfo/r-help
    > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    > and provide commented, minimal, self-contained, reproducible code.