[R] trouble with extraction/interpretation of variance structure para meters from a model built using gnls and varConstPower
Rand, Hugh
rand at amgen.com
Mon Jan 9 16:37:51 CET 2006
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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