[FORGED] Re: Question about gls --- whoops!!!

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

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

_______________________________________________
R-sig-mixed-models at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

[FORGED] Re: Question about gls --- whoops!!!

Thread (3 messages)