Re: [R] Problems with nlme: Quinidine example

From: Douglas Bates <dmbates_at_gmail.com>
Date: Fri 08 Jul 2005 - 22:01:07 EST

On 7/8/05, Dieter Menne <dieter.menne@menne-biomed.de> wrote:
> <rich <at> mi.fu-berlin.de> writes:
>
> >
> > This concerns the "Clinical Study of Quinidine" example on page 380
> > of the book "Mixed-Effects Models in S and S-PLUS" by Pinheiro and Bates
> (2000).
> >
> > I have tried to reproduce the example, but get an error:
> ......
> > system is computationally singular: reciprocal condition number =
> > 6.61723e-17
> >
>
> In R, the underlying non-linear solver is different from that used in S. In
> general, I found the S-version converged in more cases than the R-version, but
> the opposite may also be true.
>
> Sometimes it helps to fiddle with the control parameters on nlme, for example I
> got around some ping-ponging by setting pnlsTol to a large value, but check the
> sanity of your results. Looks like this will not help in this case, as in
> library\nlme\scripts\ch08.R Douglas Bates has added the following:
>
> ## This fit just ping-pongs.
> #fm1Quin.nlme <-
> # nlme(conc ~ quinModel(Subject, time, conc, dose, interval,
> # lV, lKa, lCl),
>

Thanks for pointing that out Dieter. I would have responded myself except for more urgent matters intervening in the last few days.

The optimizer code that was (and, I imagine, still is) used in S-PLUS will be available starting with R-2.2.0. I have modified the lmer function to use R's nlminb optimizer when available and will do the same for the nlme package. That should improve consistency of results between the S-PLUS and the R versions of nlme.



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