On Mon, Nov 12, 2007 at 07:36:34AM -0500, Duncan Murdoch wrote:
> On 11/12/2007 6:51 AM, Joerg van den Hoff wrote:
> >I initially thought, this should better be posted to r-devel
> >but alas! no response.
>
> I think the reason there was no response is that your example is too
> complicated. You're doing a lot of strange things (fitfunc as a result
> of deriv, using as.name, as.call, as.formula, etc.) You should simplify
thanks for the feedback.
concerning "lot of strange things": OK. I thought the
context might be important ("why, for heaven's sake do you
want to do this!?"), but, then, maybe not. so the easiest
way to trigger a similar (not the identical) behaviour is
something like
f <- function (n) {
#---------------------------------------------------------
#define n data points for a (hardcoded) model:
#-----------
x <- seq(0, 5, length = n)
y <- 2 * exp(-1*x) + 2;
y <- rnorm(y,y, 0.01*y)
#the model (same as the above hardcoded one):
model <- y ~ a * exp (-b*x) + c
#call nls as usual:
res1 <- try(nls(model, start = c(a=2, b=1, c=2)))
#call it a bit differently:
res2 <- nls(y ~ eval(model[[3]]), start = c(a=2, b=1, c=2))
list(res1 = res1, res2 = res2)
#---------------------------------------------------------
}
this is without all the overhead of my first example and now
(since not quite the same) the problem arises at n == 3
where the fit can't really procede (there are also 3
parameters -- the first example was more relevant in this
respect) but anyway the second nls-call does not procede
beyond the parsing phase of `model.frame'.
so, I can't see room for a real bug in my code, but very
well a chance that I misuse `nls' (i.e. not understanding
what really is tolerable for the `model' argument of `nls').
but if the latter is not the case, I would think there is a
bug in `nls' (or, actually, rather in `model.frame' or
whatever) when parsing the nls call.
> it down to isolate the bug. Thats a lot of work, but you're the one in
> the best position to do it. I'd say there's at least an even chance
> that the bug is in your code rather than in nls().
>
> And 2.5.0 *is* ancient; please confirm the bug exists in R-patched if it
> turns out to be an R bug.
if need be, I'll do that (if I get it compiled under
macosX). but assuming that you have R-patched installed
anyway, I would appreciate if you would copy the new example
above or the old one below to your R- prompt and see,
whether it crashes with the same error message if called
with the special number of data points (3 for the new, 5 for
the old example)? and if so, maybe bring this to the
attention of d. bates?
j. van den hoff
>
> Duncan Murdoch
>
>
>
>
> so I try it here. sory for the
> >lengthy explanation but it seems unavoidable. to quickly see
> >the problem simply copy the litte example below and execute
> >
> >f(n=5)
> >
> >which crashes. called with n != 5 (and of course n>3 since
> >there are 3 parameters in the model...) everything is as it
> >should be.
> >
> >in detail:
> >I stumbled over the follwing _very_ strange behaviour/error
> >when using `nls' which I'm tempted (despite the implied
> >"dangers") to call a bug:
> >
> >I've written a driver for `nls' which allows specifying the
> >model and the data vectors using arbitrary symbols. these
> >are internally mapped to consistent names, which poses a
> >slight complication when using `deriv' to provide analytic
> >derivatives. the following fragment gives the idea:
> >
> >#-----------------------------------------
> >f <- function(n = 4) {
> >
> > x <- seq(0, 5, length = n)
> >
> > y <- 2 * exp(-1*x) + 2;
> > y <- rnorm(y,y, 0.01*y)
> >
> > model <- y ~ a * exp (-b*x) + c
> >
> > fitfunc <- deriv(model[[3]], c("a", "b", "c"), c("a", "b", "c", "x"))
> >
> > #"standard" call of nls:
> > res1 <- nls(y ~ fitfunc(a, b, c, x), start = c(a=1, b=1, c=1))
> >
> > call.fitfunc <-
> > c(list(fitfunc), as.name("a"), as.name("b"), as.name("c"), as.name("x"))
> > call.fitfunc <- as.call(call.fitfunc)
> > frml <- as.formula("y ~ eval(call.fitfunc)")
> >
> > #"computed" call of nls:
> > res2 <- nls(frml, start = c(a=1, b=1, c=1))
> >
> > list(res1 = res1, res2 = res2)
> >}
> >#-----------------------------------------
> >
> >the argument `n' defines the number of (simulated) data
> >points x/y which are going to be fitted by some model ( here
> >y ~ a*exp(-b*x)+c )
> >
> >the first call to `nls' is the standard way of calling `nls'
> >when knowing all the variable and parameter names.
> >
> >the second call (yielding `res2') uses a constructed formula
> >in `frml' (which in this example is of course not necessary,
> >but in the general case 'a,b,c,x,y' are not a priori known
> >names).
> >
> >now, here is the problem: the call
> >
> >f(4)
> >
> >runs fine/consistently, as does every call with n > 5.
> >
> >BUT: for n = 5 (i.e. issuing f(5))
> >
> >the second fit leads to the error message:
> >
> >"Error in model.frame(formula, rownames, variables, varnames, extras,
> >extranames, : invalid type (language) for variable 'call.fitfunc'"
> >
> >I cornered this to a spot in `nls' where a model frame is
> >constructed in variable `mf'. the parsing/constructing here
> >seems simply to be messed up for n = 5: `call.fitfunc' is
> >interpreted as variable.
> >
> >I, moreover, empirically noted that the problem occurs when
> >the total number of parameters plus dependent/independent
> >variables equals the number of data points (in the present
> >example a,b,c,x,y).
> >
> >so it is not the 'magic' number of 5 but rather the identity
> >of data vector length and number of parameters+variables in
> >the model which leads to the problem.
> >
> >this is with 2.5.0 (which hopefully is not considered
> >ancient) and MacOSX 10.4.10.
> >
> >any ideas?
> >
> >thanks
> >
> >joerg
> >
> >______________________________________________
> >R-help@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
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