From ripley at stats.ox.ac.uk  Wed May 16 15:32:53 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 16 May 2007 14:32:53 +0100 (BST)
Subject: [Rd] optim non-bug
In-Reply-To: <Pine.LNX.4.64.0705151821490.909@gannet.stats.ox.ac.uk>
References: <20070514181124.4D9602A36F@slim.kubism.ku.dk>
	<Pine.LNX.4.64.0705150748380.12894@auk.stats>
	<Pine.GSO.4.56.0705150857280.20562@durian.statsci.com>
	<Pine.LNX.4.64.0705151821490.909@gannet.stats.ox.ac.uk>
Message-ID: <Pine.LNX.4.64.0705161126430.13764@gannet.stats.ox.ac.uk>

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


[Rd] optim non-bug
Prof Brian Ripley