[R] trouble with extraction/interpretation of variance struct ure para meters from a model built using gnls and varConstPower

[Rand, Hugh]

Works perfectly. Thank you.
-Hugh Rand

-----Original Message-----
From: Spencer Graves [mailto:spencer.graves at pdf.com]
Sent: Sunday, January 15, 2006 6:41 PM
To: Rand, Hugh
Cc: 'r-help at lists.R-project.org'
Subject: Re: [R] trouble with extraction/interpretation of variance
structure para meters from a model built using gnls and varConstPower


	  How about this:

 > exp(coef(model3$modelStruct$varStruct)["const"])
     const
0.6551298

	  Does that answer the question about not understanding the
connection 
between summary(model3) and coef(model3$modelStruct$varStruct)["const"]?

	  Regarding the question about R not being able to find
'coef.varFunc', 
I tried the following:
 > methods("coef")
<snip>
  coef.varFunc*
[37] coef.varIdent*        coef.varPower*

    Non-visible functions are asterisked	

	  Since "coef.varFunc" is "asterisked", I tried 
'getAnywhere(coef.varFunc)'.  I walked through this code line by line, 
until I found the following:

 > (val <- as.vector(model3$modelStruct$varStruct))
Variance function structure of class varConstPower representing
     const     power
0.6551298 0.8913665

	  Answer the questions?
	  spencer graves

Rand, Hugh wrote:

> I have been using gnls with the weights argument (and varConstPower) to
> specify a variance structure for curve fits. In attempting to extract the
> parameters for the variance model I am seeing results I don't understand.
> When I simply display the model (or use "summary" on the model), I get
what
> seem like reasonable values for both "power" and "const". When I actually
> try to extract the values, I get the same number for the "power", but a
> different (and less sensible) value for "const".
> 
> The simplest example I can come up with that shows the problem is as
> follows: 
> 
> 
> #Set up data
> 
> x    = c(0,0,0,1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6,7,7,7);
> y0   = c(.1,.1,.1, .5,.5,.5, 1,1,1, 2,2,2, 4,4,4, 7,7,7, 9,9,9, 10,10,10);
> yp   = c(0,.03,.05, 0,.05,.01, 0,.07,.03, .1,0,.2, .2,.1,0, .3,0,.1,
> 0,.3,.4, .3,.5,0);
> y    = y0 + 4*yp;
> data = data.frame(x=x,y=y);
> 
> #Run model
> 
> library(nlme)
> model3 = try(gnls(y ~
>
SSfpl(x,A,B,xmid,scal),data=data,weights=varConstPower(const=1,power=0,form=
> ~fitted(.))));
> 
> #Examine results
> 
> model3;                                         #const = .6551298,   power
=
> .8913665
> summary(model3);                                #const = .6551298,   power
=
> .8913665               
> 
> coef(model3$modelStruct$varStruct)["power"];    #                    power
=
> .8913665
> coef(model3$modelStruct$varStruct)["const"];    #const = -0.4229219 
> coef.varFunc(model3$modelStruct$varStruct);     #R can't seem to find this
> function, Splus can
> 
> 
> Any advice on what I am doing wrong would be appreciated.
> 
> Hugh Rand
> Senior Scientist
> Amgen
> rand at amgen.com
> 
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