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 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html