[R-sig-ME] [FORGED] Re: Question about gls --- whoops!!!

[Douglas Bates]

Your comment about S4 classes and methods is misdirected. The gls function
is in the nlme package which uses S3 only.

On Fri, Mar 23, 2018, 17:30 Rolf Turner <r.turner at auckland.ac.nz> wrote:

> On 24/03/18 10:52, Rolf Turner wrote:
> >
> > On 24/03/18 08:58, Andrzej Galecki wrote:
> >
> >> Hi Louise,
> >>
> >> One possible way ...
> >>
> >> mSt <- fit.gls$modelStruct
> >> cSt <- mSt$corStruct
> >> coef(cSt, unconstrained = FALSE)
> >>
> >> #       Phi
> >> # 0.1748786
> >
> > Not exactly obvious, but, is it?  How on earth would one ever figure
> > this out, except by appealing to r-sig-mixed-models?
> >
> > Looking at str(fit.gls) one sees that there is a (list) component
> > "modelStruct" and that this component in turn has a component
> > "corStruct".  If one is an optimist, one might try
> >
> >      fit.gls$modelStruct$corStruct
> >
> > which (mirabile dictu!) gives:
> >
> > Correlation structure of class corAR1 representing
> >        Phi
> > 0.1748786
> >
> > Again if one is an optimist, one might try stripping away all the
> > unwanted baggage by doing
> >
> >      as.vector(fit.gls$modelStruct$corStruct)
> >
> > giving:
> >
> > [1] 0.3533897
> >
> > Bingo.
>
> Nope!  ***NOT*** bingo!!!  Louise just pointed out to me that what I got
> by applying as.vector(), i.e. 0.3533897, is not the same as the number
> one gets by just typing fit.gls$modelStruct$corStruct, which is
> 0.1748786 --- which is what Andrzej's approach gives (and which would
> appear to be the right answer).  Bit of a duhhh on my part.
>
> Setting unconstrained=FALSE as in Andrzej's approach seems to be
> crucial.  I missed that bit ....
>
> But it still mystifies me why as.vector() doesn't give the same numeric
> value as is obtained from just printing the object in question.  Also
> looking at the code of nlme:::coef.corStruct I would have thought that
> this function would simply throw an error when unconstrained is set to
> FALSE.  (Just type "nlme:::coef.corStruct" and you'll see what I mean.)
>
> If I set foo <- nlme:::coef.corStruct and then do
>
>      foo(fit.gls$modelStruct$corStruct)
>
> I do indeed get an error.  WTF?
>
> There would appear to be no way for the results to be different (look
> at the code) --- but different they are.
>
> But that sort of nonsense is to be expected when S4 classes and methods
> are involved in any way.
>
> cheers,
>
> Rolf
>
> --
> Technical Editor ANZJS
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
>
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