passing variable to formula environment

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