R help - Nov 2004 - R/S-related projects on Sourceforge? Trove Categorization

Hi R-Users and Developers,

Several months ago I made a request on Sourceforge to add the R/S - 
programming language to the _Trove_ categorization. ("The Trove is a 
means to convey basic metainformation about your project.")

Today I got the following response of one of the sourceforge admins.

<SNIP>

SourceForge.net will consider the inclusion of a programming
language within the Trove system when we host at least 5
projects based on that language.  Please advise: Do you know
of 5 projects hosted on SourceForge.net based on this language?
<SNIP>


If anyone of you knew about R-packages, or projects using the R/S programming
language, which are hosted on sourceforge, please reply to this thread. I hope
that your answers will enable me to give more then 5 examples of R projects
hosted on Sourceforge.

Yours Eryk


Ps.

The ID of my original "feature request"  on Sourceforge is 967697.
https://sourceforge.net/tracker/?func=detail&atid=350001&aid=967697&group_id=1

-- 
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219                 __("<    _
http://www.molgen.mpg.de/~wolski      \__/    'v'
http://r4proteomics.sourceforge.net    ||    /   \
mail: witek96@users.sourceforge.net    ^^     m m
      wolski@molgen.mpg.de

Hi,

I have 2 _small_ projects hosted in sf.net that use R 

FLR :: R for fisheries science (http://flr.sf.net)
fsap: fish stock assessment for R (http://sf.net/projects/fsap)

The first one is getting some hip and the second is dying ...

Hope it helps.

Regards

EJ

On Wed, 2004-11-17 at 09:09, Witold Eryk Wolski wrote:
> Hi R-Users and Developers,
> 
> Several months ago I made a request on Sourceforge to add the R/S - 
> programming language to the _Trove_ categorization. ("The Trove is a 
> means to convey basic metainformation about your project.")
> 
> Today I got the following response of one of the sourceforge admins.
> 
> <SNIP>
> 
> SourceForge.net will consider the inclusion of a programming
> language within the Trove system when we host at least 5
> projects based on that language.  Please advise: Do you know
> of 5 projects hosted on SourceForge.net based on this language?
> <SNIP>
> 
> 
> If anyone of you knew about R-packages, or projects using the R/S
programming language, which are hosted on sourceforge, please reply to this
thread. I hope that your answers will enable me to give more then 5 examples of
R projects hosted on Sourceforge.
> 
> Yours Eryk
> 
> 
> Ps.
> 
> The ID of my original "feature request"  on Sourceforge is
967697.
>
https://sourceforge.net/tracker/?func=detail&atid=350001&aid=967697&group_id=1

> <SNIP>
> SourceForge.net will consider the inclusion of a programming
> language within the Trove system when we host at least 5
> projects based on that language.  Please advise: Do you know
> of 5 projects hosted on SourceForge.net based on this language?
> <SNIP>
Gretl, RPad and RMetrics, plus Ernesto's FLR and  fsap make five.

Gretl           Allin Cottrell, USA
Gnu Regression, Econometrics and Time-series Library
Gretl is hosted on SourceForge.
http://gretl.sourceforge.net/

Gretl is not written in R, but interfaces to  R.
http://gretl.sourceforge.net/gretl_and_R.html
"gretl ... is designed as a very user-friendly econometrics package. While 
it is also reasonably sophisticated, it lacks some of the specialized 
statistical methods that a working econometrician might desire.As a way 
around this limitation, gretl offers an interface to the comprehensive 
free-software statistical package, GNU R."

Both RPAd and RMetrics are open-source projects using (and acknowledging 
using) R.
As far as I know, neither is listed on SourceForge.

RPad            EPRI (Electric Power Research Institute), USA
http://www.Rpad.org/Rpad/ 
"Rpad is an interactive, web-based analysis program. Rpad pages are 
interactive workbook-type sheets based on R, an open-source implementation 
of the S language. Rpad is an analysis package, a web-page designer, and a 
gui designer all wrapped in one. Rpad makes it easy to develop powerful 
data analysis applications that can be shared with others (most likely on 
an intranet). The user doesn't have to install anything--everything's
done
through a browser."

RMetrics        Diethelm Wuertz, ETH Zurich, Switzerland
http://www.itp.phys.ethz.ch/econophysics/R/
"Rmetrics is the premier open source solution for financial market 
analysis and valuation of financial instruments. With hundreds of 
functions build on modern and powerful methods Rmetrics combines 
explorative data analysis and statistical modeling with object oriented 
rapid prototyping. Rmetrics is embedded in R,"
My impression is that many projects "on SourceForge" have links to
home
pages hosted on other sites -- so I suppose
if the project authors are willing -- they could be cross listed on 
SourceForge.

Gretl, RPad and RMetrics, plus Ernesto's FLR and  fsap make five.

On the other hand, SourceForge's criteria for inclusion appears to be very 
arbitrary.

Objective criteria that would be more relevant to R include:
- R has several active mailing lists (archived for verification)
- The R Project is archived on CRAN (Comprehensive R Archive Network) 
which has more than 20 mirrors on 6 continents:
Africa
Asia
Australia
Europe
North America
South America
- More than a dozen books have been published with either "R" or
"S"
mentioned in the title ("R" is an open-source  implementation of
"S"). For
example, "Introductory Statistics with R" is available from major 
booksellers including Amazon.com, BarnesandNoble.com and even 
Wal-mart.com!

Subjective criteria for inclusion on SourceForge
- "R" is an implementation of "S" a language developed at
Bell Labs -- the
organization that developed the C programming language and the Unix 
operating system. Open source implementations of C include the GNU 
Complier Collection (GCC) and open source implementations of Unix include 
GNU Linux. So why not include, the open source implementation of S, GNU R?

- R is respected in the statistical community. There are awards and 
articles that could be cited. A personal story -- in the early 1990s I 
attended an American Statistical Association meeting in San Francisco. I 
saw then that the topnotch statisticians, people like Frank Harrell -- 
whose short course on Regression I attended, were maxing out SAS and 
switching to S. I heard about StatLib at Carnegie Mellon and contributed 
code. At the time, the institution I was working for was committed to SAS 
and SPSS and would not have been open to spending more on S. But, years 
latter I was delighted to learn that there was an open source 
implementation S, R and that it was available at StatLib, which now is a 
mirror for the worldwide CRAN mirror sites.

On Wed, 2004-11-17 at 09:09, Witold Eryk Wolski wrote:
> Hi R-Users and Developers,
> 
> Several months ago I made a request on Sourceforge to add the R/S - 
> programming language to the _Trove_ categorization. ("The Trove is a 
> means to convey basic metainformation about your project.")
> 
> Today I got the following response of one of the sourceforge admins.
> 
> <SNIP>
> 
> SourceForge.net will consider the inclusion of a programming
> language within the Trove system when we host at least 5
> projects based on that language.  Please advise: Do you know
> of 5 projects hosted on SourceForge.net based on this language?
> <SNIP>
> 
> 
> If anyone of you knew about R-packages, or projects using the R/S 
programming language, which are hosted on sourceforge, please reply to 
this thread. I hope that your answers will enable me to give more then 5 
examples of R projects hosted on Sourceforge.
> 
> Yours Eryk
>
Jim Callahan
Management, Budget & Accounting
City of Orlando
(407) 246-3039 office
(407) 234-3744 cell phone
	[[alternative HTML version deleted]]

Witold Eryk Wolski <wolski@...> writes:

: 
: Hi R-Users and Developers,
: 
: Several months ago I made a request on Sourceforge to add the R/S - 
: programming language to the _Trove_ categorization. ("The Trove is a 
: means to convey basic metainformation about your project.")

It might be worthwhile to consider all the possible sourceforge-like
sites in case there is a particular advantage of one over the others.
For example, it might be better to choose one with svn support than
one that only has cvs support. Sites include sourceforge, savannah, 
berlios, seul and a few others, some of which are listed at
http://www.ibiblio.org/fosphost/exhost.htm .

Also some languages have started their own sourceforge-style
project repositories such as luaforge.net and rubyforge.org and one
could conceivably have an Rforge too.

I don't know enough about the above sites to say much more but I think
the key requirements are to provide support to addon packages and
projects to encourage the current explosion of such software.
The idea would be to automate the setup of an infrastructure that
includes such things as:

- X-help and X-devel email distribution lists for project X
- access to svn so developers can coordinate their efforts on a project
- wiki, forums, other groupware
- web space for a home page
- ftp space for archiving old versions and distributing beta versions
- slick package development tools to make it easier to develop packages
- ensure that there are a really good set of base classes in the core
  for projects to leverage off of

Hi,

This are the project which I have extracted from all your mails.
  
1. http://sourceforge.net/projects/rpgsql/      R PostgreSQL Interface
2. http://sourceforge.net/projects/r-spatial/   R package for spatial 
data classes
3. http://sourceforge.net/projects/rpy/         RPy (R from Python)
4. http://sourceforge.net/projects/ep-sf/       Expression Profiler
5. http://sourceforge.net/projects/fsap         fish stock assessment for R
6. http://sourceforge.net/projects/flr/         R packages for use in 
fisheries modelling
7. https://sourceforge.net/projects/runit/      R Unit Test Framework
8. http://sourceforge.net/projects/ep-sf/       Expression Profiler
9. http://sourceforge.net/projects/r-asp/       Analysis of Spatial Data 
in R
10. http://sourceforge.net/projects/r4proteomics/  R Packages for proteomics
11. http://sourceforge.net/projects/rdbi/          R Database Interface
12. http://sourceforge.net/projects/nlmeode/       R package combining 
nlme and odesolve
13. http://sourceforge.net/projects/rarcinfo/      RArcInfo
14. http://sourceforge.net/projects/rgdal          GDAL Package for R
15. http://sourceforge.net/projects/gretl/         GNU Regression, 
Econometrics and Time-series Library
16. ...
 
Sorry if I have missed any. But it is surely more than five.

Thanks all of you for your numerous response and also for some more 
general thoughts concerning
*collaboratory* development using source code repositories:
https://stat.ethz.ch/pipermail/r-devel/2004-November/031398.html.
If I see how R is evolving I believe that this ideas will be realized soon.
Especially that there are already repositories covering some of the 
functionality and dedicated to R --  Bioconductor  with a svn archive. 
Unfortunately, as I was told by Geff Gentry the costs of administering 
the svn, cvs servers are high, hence the number of developers must be 
limited. Also CRAN has some of the functionality but the svn or cvs 
support is missing.
Luckily hosting the sources on e.g. sourceforge and the builds on CRAN 
or Bioconductor gives already some of the essential functionality.

Therefore at this place big thanks to the Bioconductor, CRAN and 
sourceforge people.

/E