[Rd] Proposal: 'global' package refactoring

Paul Murrell p.murrell at auckland.ac.nz
Tue Nov 25 00:12:39 MET 2003


I have wanted to figure out a way to do something along these lines for 
the many, widely-scattered plotting functions.  Something that would be 
less invasive (and less useful, but a valid step in the right 
direction), is simply a "directory" for different functional groups.  A 
list of function names, plus descriptions of what they do, plus a 
pointer to the package they are in would I think be really useful.  A 
lot of work to create and maintain, but really useful.  For example, the 
web pages focused on "spatial projects" 
(http://sal.agecon.uiuc.edu/csiss/Rgeo/index.html) has summaries of all 
spatially related packages.
The coordination of the DBMS stuff 
(http://developer.r-project.org/db/index.html) is another example of 
something similar.
Then of course there is the R GUIs pages (http://www.sciviews.org/_rgui/)


Jan de Leeuw wrote:
> This is a good idea, and it would be great to have these
> refactored meta packages. But it actually implies having
> a group similar to R core that does code review of
> existing packages. For example, what happens if
> a function seems to work but is programmed horribly
> inefficiently ? What happens if something exists on both
> the R and C levels ? What happens with packages that
> rely on private versions of BLAS ? Suppose two packages
> provide the same functionality, how does one choose ?
> And can this be done without coding conventions ? Who is
> in charge ?
> On Nov 24, 2003, at 14:12, Warnes, Gregory R wrote:
>> Looking over the contents of various packages, including my own, it 
>> is  clear
>> that lots of things end up 'hidden away' in packages where they don't
>> belong.  My gregmisc package is a particularly egregious example,  
>> containing
>> something from almost every functional category.
>> I propose that from time to time the R community go through the  
>> complete set
>> of packages and 'refactor' the functions and data sets into packages  
>> that
>> have clearly defined goals.   This should make it easier to ensure  
>> that new
>> functions get placed into a location where users can easily find them,
>> reduce the amount of re-implementation/duplication existing  
>> functionality,
>> and assist in ensuring interoperability.
>> It would be worthwhile, for instance, to pull all of the functions  
>> related
>> to contrasts for generalized linear models into a common location,  
>> instead
>> of having them spread between base, Hmisc, MASS, gregmisc, etc.    
>> Similarly,
>> it would be helpful to pull together all of the genetics-computations  
>> into a
>> single location.
>> I recognize that not all package maintainers would be willing to  
>> participate
>> and that not all functions could be easily categorized, but I believe  
>> that
>> this effort would yield significant benefit and is compatible with 
>> the  goal
>> of R-core to streamline the base packages.
>> To put my money where my mouth is, I'll volunteer to organize a group  
>> effort
>> to do such a refactoring in conjunction with the userR! 2004 or the  next
>> DSC, whichever folks agree is better for this purpose.
>> Gregory R. Warnes, Ph.D.
>> Senior Coordinator
>> Groton Non-Clinical Statistics
>> Pfizer Global Research and Development
>>  <<Warnes, Gregory R.vcf>>
>> LEGAL NOTICE\ Unless expressly stated otherwise, this  
>> messag...{{dropped}}
>> ______________________________________________
>> R-devel at stat.math.ethz.ch mailing list
>> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> ===
> Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
> Editor: Journal of Multivariate Analysis, Journal of Statistical  Software
> US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
> phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw at stat.ucla.edu
> homepage: http://gifi.stat.ucla.edu
> ------------------------------------------------------------------------ 
> -------------------------
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Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz

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