optim non-bug
On Tue, 15 May 2007, Prof Brian Ripley wrote:
There quite a lot of these: optimize, uniroot, nlm for example. I don't think the problem is large enough to merit another argument. It is tempting to move '...' up the argument list so that partial matching will not occur. I am not sure how far you can go: ?optim has positional matching for 'method', and ?optimize has abbreviations for lower and upper. In R you rarely need to pass additional arguments in programming as lexical scoping can be used to capture them. I'll do some experimenting.
Overnight runs show that if we do this maximally, only a very few packages are affected optim: SoPhy has 'meth', copula has 'hess', MeasurementError.cor (BioC) has unnamed 'method' uniroot: distrDoc has 'low', 'up' in a vignette optimize: qtlDesign, sde, waveslim have 'max' nlm: none integrate: none Doubtless there are scripts that will be affected (but with an error and a clearcut error message), but unless I hear cogent reasons otherwise it seems that the balance is well in favour of making the change. (I have more than once been tempted to knock up a version of R that does not allow partial matching of arguments to see what breaks, but a few are entrenched like 'length.out' and 'along.with' in seq.default and 'all' in ls. Seems someone is fond of 'env' in get/exists/assign.)
On Tue, 15 May 2007, Bill Dunlap wrote:
On Tue, 15 May 2007, Prof Brian Ripley wrote:
This is not a bug, but as documented on the help page:
...: Further arguments to be passed to 'fn' and 'gr'. Beware of
partial matching to earlier arguments.
You have partial matching to 'upper'.
We have this problem in optim(), integrate(),
and probably other functions. These functions
have a lot of arguments before the ..., using
up a lot of partial matching space. Would you consider
adding another argument to the tail end of
their argument lists that would include the
auxillary arguments?
E.g.,
optim <- function(par, fn, gr = NULL,
method = c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SANN"),
lower = -Inf, upper = Inf,
control = list(), hessian = FALSE,
..., aux.args = list(...))
If the user did not supply aux.args this would
act like the old version. If the user did supply
aux.args then the function could check that no
unrecognized arguments were given to optim.
optim might require 2 such arguments,
aux.args.fn = list(...), aux.args.gr=aux.args.fn
(The forces you to know that the objective function
is called 'fn', not integrate's 'f' or apply's 'FUN'.)
I don't know what the best name for such an argument
would be. If we added it, it would nice to make it
the same in R and Splus.
On Mon, 14 May 2007, christina.merz at gmx.de wrote: 'optim' does not accept arguments called 'u'. Here is an example:
R> fun<-function(x,u) (x-u)^2 R> optim(7,fn=fun,u=9) Fehler in fn(par, ...) : Argument "u" fehlt (ohne Standardwert) Zus?tzlich: Warning message: bounds can only be used with method L-BFGS-B in: optim(7, fn = fun, u = 9)
---------------------------------------------------------------------------- Bill Dunlap Insightful Corporation bill at insightful dot com 360-428-8146 "All statements in this message represent the opinions of the author and do not necessarily reflect Insightful Corporation policy or position."
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595