[R] passing variable to formula environment

[Gabor Grothendieck]

Note that we can omit the second argument to substitute as
in this case since they will be given by the default.

On 8/3/05, Sundar Dorai-Raj <sundar.dorai-raj at pdf.com> wrote:
> 
> 
> Eric Archer wrote:
> > List gurus,
> >
> > I'm trying to code a Gompertz growth curve function as part of a larger
> > project and have run across a problem due to my ignorance of
> > environments. Some sample data and the function are as follows:
> >
> > growth <- data.frame(age = c(1.92, 3, 5.83, 3.17, 15.5, 1.17, 5.58,
> > 13.33, 14.29, 5.83, 13.79, 6.33, 13.75, 16.83, 13, 11.67, 0.25, 1.73,
> > 9.46, 5.67), length = c(157, 165, 179, 171, 195, 135, 179, 193, 194,
> > 186, 196, 186, 210, 200, 189, 194, 106, 161, 188, 159))
> >
> > # return gompertz fit
> > Gompertz <- function(data,Xintercept,Lzero,start) {
> >   gomp <- formula(length ~ Lzero * exp(k * (1 - exp(-g * (age -
> > Xintercept)))))
> >   nls(formula=gomp,data=data,start=start)
> > }
> >
> > When I run the function, I get the following error:
> >
> >  > Gompertz(growth,0,87,list(k=0.5,g=0.5))
> > Error in eval(expr, envir, enclos) : Object "Lzero" not found
> >
> > After reading through the help files on 'nls', 'formula', 'model.frame',
> > and 'environment', I understand that the formula gets evaluated in the
> > environment in which it is created, and in my case, "Lzero" is not
> > defined in that environment, but I'm still shaky on the environment
> > concept and can't figure out how to pass or include "Lzero" in the
> > environment that nls is evaluating gomp and data in.
> >
> > I have tried redefining "gomp" in the function as:
> >
> > gomp <- as.formula("length ~ Lzero * exp(k * (1 - exp(-g * (age -
> > Xintercept))))",environment())
> > # thinking that 'environment()' refers to environment of Gompertz
> > function where Lzero exists
> >
> > gomp <- as.formula("length ~ Lzero * exp(k * (1 - exp(-g * (age -
> > Xintercept))))",environment(Gompertz))
> > # trying to explicitly force it
> >
> > gomp <- as.formula("length ~ Lzero * exp(k * (1 - exp(-g * (age -
> > Xintercept))))",new.env())
> > # my guess at what formula(x,...) does
> >
> > ...but I get the same error. Since I'm still trying to wrap my head
> > around environments and evaluation in R, the solution to this will be
> > very educational.  Thanks in advance.
> >
> > Cheers,
> > e.
> >
> 
> Hi, Eric,
> 
> I think the easiest way to do this is to use substitute:
> 
> # return gompertz fit
> Gompertz <- function(data, Xintercept, Lzero, start) {
>   gomp <- substitute(length ~ Lzero * exp(k * (1 - exp(-g * (age -
> Xintercept)))),
>                      list(Xintercept = Xintercept, Lzero = Lzero))
>   nls(gomp, data, start)
> }
> 
> Gompertz(growth, 0, 87, list(k = 0.5, g = 0.5))
> 
> HTH,
> 
> --sundar
> 
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