R help - Jan 2006 - trouble with extraction/interpretation of variance structure para meters from a model built using gnls and varConstPower

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

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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