[R] Using varPower in gnls, an answer of sorts.
Setzer.Woodrow@epamail.epa.gov
Setzer.Woodrow at epamail.epa.gov
Wed Mar 2 22:02:23 CET 2005
Back on January 16, a message on R-help from Ravi Varadhan described a
problem with gnls using weights=varPower(). The problem was that the
fit failed with error
Error in eval(expr, envir, enclos) : Object "." not found
I can reliably get this error in version 2.0.1-patched 2004-12-09 on
Windows XP and 2.0.1-Patched 2005-01-26 on Linux.
The key feature of that example is that the data are being passed in the
environment. Consider a modification of the example in the man page for
gnls:
First, something that should work:
> gnls(weight ~ Asym/(1 + exp((xmid - Time)/scal)),data=Soybean,
+ start=c(Asym=16,xmid=50,scal=7),weights=varPower())
Generalized nonlinear least squares fit
Model: weight ~ Asym/(1 + exp((xmid - Time)/scal))
Data: Soybean
Log-likelihood: -486.8973
Coefficients:
Asym xmid scal
17.35681 51.87230 7.62052
Variance function:
Structure: Power of variance covariate
Formula: ~fitted(.)
Parameter estimates:
power
0.8815438
Degrees of freedom: 412 total; 409 residual
Residual standard error: 0.3662752
## Now, use with() to pass Soybean in the environment of gnls:
> with(Soybean,gnls(weight ~ Asym/(1 + exp((xmid - Time)/scal)),
+ start=c(Asym=16,xmid=50,scal=7),weights=varPower()))
Error in eval(expr, envir, enclos) : Object "." not found
## drop the weights argument from gnls, and the error message goes away.
The problem is in a call to model.frame. When varPower() (and
presumably other weight functions using '.' to represent a fitted model)
is used, gnls() constructs a formula argument for model.matrix that
looks like:
~.+weight+Time
This works when the data are passed in a data frame, but not when they
are in the environment. Look at the example in the man page for
model.frame
> data.class(model.frame(~.+dist+speed, data=cars))
[1] "data.frame"
> data.class(with(cars,model.frame(~.+dist+speed)))
Error in eval(expr, envir, enclos) : Object "." not found
> data.class(with(cars,model.frame(~dist+speed)))
[1] "data.frame"
> env <- new.env(TRUE,NULL)
> assign("dist",cars$dist,envir=env)
> assign("speed",cars$speed,envir=env)
> data.class(model.frame(~dist+speed,data=env))
[1] "data.frame"
> data.class(model.frame(~.+dist+speed,data=env))
Error in eval(expr, envir, enclos) : Object "." not found
I'm sending this to r-help rather to the authors of nlme because I am
not sure where the bug is: is model.frame misbehaving, or should gnls
not include '.' in its call to model.frame?
R. Woodrow Setzer, Jr. Phone: (919) 541-0128
Experimental Toxicology Division Fax: (919) 541-4284
Pharmacokinetics Branch
NHEERL B143-01; US EPA; RTP, NC 27711
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