[R] 'nls' and its arguments

Thu Oct 30 15:54:51 CET 2003

Dear R experts!

I'd to fit data by 'nls' with me-supplied function 'fcn'.

1) I'd like 'fcn' to accept arbitrary arguments, i.e. I defined it
   as f(...) {<body>}. (Ok, that's not actually impotant).
2) Second, I would NOT like to supply every parameter in the formula.
   To illustrate this, let's look at the last example of 'nls' help
   page:

    ## weighted nonlinear regression
    data(Puromycin)
    Treated <- Puromycin[Puromycin$state == "treated", ]
    weighted.MM <- function(resp, conc, Vm, K)
    {
        ## Purpose: exactly as white book p.451 -- RHS for nls()
        ##  Weighted version of Michaelis-Menten model
        ## ---------------------------------------------------------------
        ## Arguments: `y', `x' and the two parameters (see book)
        ## ---------------------------------------------------------------
        ## Author: Martin Maechler, Date: 23 Mar 2001, 18:48
        print(resp)

        pred <- (Vm * conc)/(K + conc)
        (resp - pred) / sqrt(pred)
    }
    Pur.wt <- nls( ~ weighted.MM(rate, conc, Vm, K), data = Treated,
                  start = list(Vm = 200, K = 0.1))

So, in this example I wouldn't like to write `weighted.MM(rate, conc, Vm, K'),
and `start = list(Vm = 200, K = 0.1)', instead I'd like to supply _lists_.
With the 'start' parameter it's easy - I create list

    p.start <- list(Vm = 200, K = 0.1)

and assign it to 'start' in nls():

    start = p.start

- that works. But, with the formula it's not so simple. Well, I tried
at first to make formula more "list-like":

    Pur.wt <- nls( ~ do.call("weighted.MM", list(rate, conc, Vm, K)),
                  data = Treated,
                  start = p.start)

- that works too. Now, let's try to separate data and parameters:

    Pur.wt <- nls( ~ do.call("weighted.MM", c(list(rate, conc), list(Vm, K))),
                  data = Treated,
                  start = p.start)

- that's right. So, I have a data 'Treated', and a start params list
'p.start'. Now, here is the _point_: I want nls to read names of
variables from the lists and supply it to function in the formula.
In this example 'weighted.MM' has a certain arg list, but my function is
'fcn(...)', and I want supply _all_ these names to the fcn. I tried to
change 'list(Vm, K)' to list(as.name("Vm"), as.name("K")):

    Pur.wt <- nls( ~ do.call("weighted.MM", c(list(rate, conc), list(as.name("Vm"), as.name("K")))),
                  data  = Treated, start = p.start)

- works again! Now,
    p.arg  <- list(as.name("Vm"), as.name("K"))
    Pur.wt <- nls( ~ do.call("weighted.MM", c(list(rate, conc), p.arg)),
                             data  = Treated, start = p.start)
    Error in model.frame(formula, rownames, variables, varnames, extras, extranames,  : 
            invalid variable type

How can I fix this, and supply _lists_ with parameter names (and data names)
to fcn(...) in nls?
Thanks a lot! :-)

--
WBR,
Timur.