From pgilbert at bank-banque-canada.ca  Fri Dec  3 20:35:35 2010
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Fri, 3 Dec 2010 19:35:35 +0000
Subject: [Rd] Competing with one's own work
In-Reply-To: <AANLkTimZRyzWACEtoHUzu9VtusugjtO4p1sqnRxSqkfr@mail.gmail.com>
References: <4CF91361.7090005@uottawa.ca> <4CF91704.7070605@gmail.com>
	<003601cb930b$b28205a0$178610e0$@edu>
	<AANLkTimZRyzWACEtoHUzu9VtusugjtO4p1sqnRxSqkfr@mail.gmail.com>
Message-ID: <6441154A9FF1CD4386AF4ABF141A056D01691F@WMEXOSCD2-N1.bocad.bank-banque-canada.ca>

At one time I lobbied for putting something in base or a required package, and it was suggested that the idea at the time was to remove things rather than add them. Generally, I agree that is a good idea, so I did not lobby more. 

When this question comes up it is always asked, and answered, in terms of putting things in. However, is there a process for moving things out to normal packages rather than keeping them in required packages or base?

Paul

>-----Original Message-----
>From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
>project.org] On Behalf Of Douglas Bates
>Sent: December 3, 2010 1:28 PM
>To: Ravi Varadhan
>Cc: r-devel at r-project.org; nashjc at uottawa.ca
>Subject: Re: [Rd] Competing with one's own work
>
>On Fri, Dec 3, 2010 at 11:01 AM, Ravi Varadhan <rvaradhan at jhmi.edu>
>wrote:
>> Dear Duncan,
>
>> What constitutes a convincing argument for making significant changes?
>> Taking the example of optimization algorithms (say, for smooth
>objective
>> functions), how does one make a convincing argument that a particular
>class
>> of algorithms are "better" than another class? This can be a difficult
>task,
>> but quite doable with good benchmarking practices.
>
>> Supposing for the moment that such a convincing argument has been
>made, is
>> that sufficient to get the R-core to act upon it? ?Are there
>compelling
>> factors other than just "algorithm A is better than algorithm B"?
>
>> I'd think that the argument is relatively easy if the need for the
>change is
>> driven by consumer demand. But, even here I am not sure how to make an
>> argument to the R-core to consider the big changes. ?For example,
>there is a
>> reasonable demand for constrained (smooth) optimization algorithms in
>R
>> (based on R-help queries). ?Currently, there are only 3 packages that
>can
>> handle this. ?However, in the base distribution only `constrOptim'
>function
>> is provided, which cannot handle anything more than linear, inequality
>> constraints. ?I think that the base distribution needs to have a
>package for
>> constrained optimization that can handle linear/nonlinear and
>> equality/inequality constraints.
>
>constrOptim is in the stats package, not the base package.  Functions
>that are already in the required packages are maintained by R core.
>If you know of bugs in such functions you should report them.  Because
>there is a heavy burden in maintaining the large corpus of software in
>R and its required packages, additions are viewed skeptically,
>Adopting new capabilities and new code in a required package like
>stats means that some member of R core has to be willing to maintain
>it.  If the capabilities can be incorporated in a contributed package
>then that is the preferred method of extending R. The burden of
>maintaining the code, fixing bugs or other infelicities, etc. is on
>the package maintainer.
>
>I don't see anything in what you are proposing that could not be
>incorporated in a contributed package.
>
>> John, thanks for raising an important issue.
>>
>> Thanks & Best,
>> Ravi.
>>
>> -------------------------------------------------------
>> Ravi Varadhan, Ph.D.
>> Assistant Professor,
>> Division of Geriatric Medicine and Gerontology School of Medicine
>Johns
>> Hopkins University
>>
>> Ph. (410) 502-2619
>> email: rvaradhan at jhmi.edu
>>
>>
>> -----Original Message-----
>> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
>project.org]
>> On Behalf Of Duncan Murdoch
>> Sent: Friday, December 03, 2010 11:13 AM
>> To: nashjc at uottawa.ca
>> Cc: r-devel at r-project.org
>> Subject: Re: [Rd] Competing with one's own work
>>
>> On 03/12/2010 10:57 AM, Prof. John C Nash wrote:
>>> No, this is not about Rcpp, but a comment in that overly long
>discussion
>> raised a question
>>> that has been in my mind for a while.
>>>
>>> This is that one may have work that is used in R in the base
>functionality
>> and there are
>>> improvements that should be incorporated.
>>>
>>> For me, this concerns the BFGS, Nelder-Mead and CG options of
>optim(),
>> which are based on
>>> the 1990 edition (Pascal codes) of my 1979 book "Compact numerical
>> methods...", which were
>>> themselves derived from other people's work. By the time Brian Ripley
>took
>> that work (with
>>> permission, even though not strictly required. Thanks!) there were
>already
>> some
>>> improvements to these same algorithms (mainly bounds and masks) in
>the
>> BASIC codes of the
>>> 1987 book by Mary Walker-Smith and I. However, BASIC to R is not
>something
>> I'd wish on
>>> anyone.
>>>
>>> Now there are some R packages, including some I've been working on,
>that
>> do offer
>>> improvements on the optim() offerings. I would not say mine are yet
>fully
>> ready for
>>> incorporation into the base, but they are pretty close. Equally I
>think
>> some of the tools
>>> in the base should be deprecated and users encouraged to try other
>> routines. It is also
>>> getting more and more important that novice users be provided with
>> sensible guidance and
>>> robust default settings and choices. In many areas, users are faced
>with
>> more choice than
>>> is efficient for the majority of problems.
>>>
>>> My question is: How should such changes be suggested / assisted? It
>seems
>> to me that this
>>> is beyond a simple feature request. Some discussion on pros and cons
>would
>> be appropriate,
>>> and those like myself who are familiar with particular tools can and
>> should offer help.
>>>
>>> Alternatively, is there a document available in the style "Writing R
>> Extensions" that has
>>> a title like "How the R Base Packages are Updated"? A brief search
>was
>> negative.
>>>
>>> I'm happy to compete with my own prior work to provide improvements.
>It
>> would be nice to
>>> see some of those improvements become the benchmark for further
>progress.
>>
>>
>> There are answers at many different levels to your questions. ?The
>> simplest is that base packages are part of R, so they get updated when
>a
>> member of R Core updates them, and the updates get released when a new
>> version of R is released.
>>
>> So if you want a change, you need to convince a member of the core to
>> make it. ?Pointing out a bug is the easiest way to do this: ?bugs
>> usually get fixed quickly, if they are clearly demonstrated.
>>
>> If you want a bigger change, you need to make a convincing argument in
>> favour of it. ?If you pick a topic that is of particular interest to
>one
>> core member, and you can convince him to make the change, then it will
>> happen. ?If pick some obscure topic that's not of interest to anyone,
>> you'll need a very strong argument to make it interesting. ?Part of
>any
>> of these arguments is explaining why the change needs to be made to
>the
>> base, why it can't just be published in a contributed package.
>?(That's
>> why bug fixes are easy, and big additions to the base packages are
>not.)
>>
>> Duncan Murdoch
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>______________________________________________
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>https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Competing with one's own work
Paul Gilbert