Re: [Rd] optim non-bug

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Wed, 16 May 2007 14:32:53 +0100 (BST)

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)
>>>> Zusätzlich: 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


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