R help - Apr 2001 - Hmisc and Design libraries

After several nice and informative discussions with Bill Venables,
Duncan Temple Lang, Tony Rossini, Martin Maechler, and Robert
Gentleman, I am pleased to announce that I am becoming an R user
and have begun porting the Hmisc and Design libraries to R. 
I have been very impressed with the maturity of R and with its 
logical design, particularly its online documentation setup and
the way packages are downloaded and installed, not to mention the
scoping rules and other fundamentals.  Another factor that has
influenced me is the excellent book "Rebel Code" by Glyn Moody
which chronicles the open source movement and Linux.  I wish
to especially thank Bill Venables for his friendly wisdom.

My guess is that porting the libraries can be largely
accomplished in the next 4 months (there are about
350 functions), especially if any experienced R programmers
who want to use the libraries would like to help.  I am
in the process of setting up an ssh-accessed CVS repository
for each library so that functions can be checked in and
out.  Anyone wanting to help will of course get plenty
of acknowledgement.  I have already debugged about 1/4
of the Hmisc library under R.

Descriptions of functions in my libraries may be found
at http://hesweb1.med.virginia.edu/biostat/s/splus.html

As I will be maintaining the libraries for S-Plus (both
Windows and Linux/Unix versions, S version 3 and 4
languages) and for R, I would appreciate learning how
other users who do the same set up their directories
to facilitate distributing libraries for both R and
S-Plus in a way that is also consistent with CVS.  In
other words, I would like to be able to construct
distributions suitable for CRAN without making it too
hard to run Unix/Linux shell scripts that also create
S-Plus distributions.  I am using a single code base
for all platforms except for Fortran and C code
where I allow for single precision objects in S-Plus.

As I am now Microsoft-free (one of my colleagues creates
Microsoft Windows files for S-Plus; I have found that
Linux is amazingly more reliable and powerful than
Windows.  I have set up a web page at
http://hesweb1.med.virginia.edu/biostat/s/linux.setup.html
to help Windows users set up Linux) I am honestly not 
motivated to do special work to make a Windows distribution
for R.  If a Windows R user who has suitable Fortran and
C compilers wishes to periodically create a Windows
distribution once the libraries work under R on
Linux/Unix that would be great.

I am very glad to join the talented R community, and look
forward to collaborating with other users.

Sincerely,

Frank Harrell
-- 
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat
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Frank
>As I will be maintaining the libraries for S-Plus (both
>Windows and Linux/Unix versions, S version 3 and 4
>languages) and for R, I would appreciate learning how
>other users who do the same set up their directories
>to facilitate distributing libraries for both R and
>S-Plus in a way that is also consistent with CVS.  In
>other words, I would like to be able to construct
>distributions suitable for CRAN without making it too
>hard to run Unix/Linux shell scripts that also create
>S-Plus distributions.
I have have just completed a multi-year transition from developing my
code in Splus and  wanting it to run also in R, to developing in R and
wanting it to run also in Splus. (I still only use Splus 3.3.) The code
was never a big issue for me as I have been careful to avoid anything
depending on fundamental differences between R and S.

Although I have been using R for many years (mainly to avoid debugging
For loops) the real start of my transition was the remarkable support
for help documentation starting sometime just before R 1.0. The final
act was to move all my test programs from my own ad hoc system to R's
tests directories, so that the tests are run by R CMD check. With a few
scripts and a Makefile I now mimic R's approach to run my tests in Splus
and to generate html help for S. I would be happy to send these if you
are interested. I maintain about 1000 functions in a dozen packages
organized into three bundles (one of which I do not distribute).

There is no problem  using  CVS, but I use it only for co-ordinating my
home version with my work version, so there may be complications I am
not aware of. I don't use Windows and there are undoubtedly
complications, although I think I now have my packages in a state where
there are no serious problems.

Here are a few points you may want to consider.

1/ Up until very recently I tried to mimic a few S functions in R. I
have just converted to mimicking the R conventions in S and I find it
works much better. To do this I have S functions for a few things like
is.R(), Platform(), Sys.info(). This works better, in part because the
cross platform issues are very well thought out in R. (But to be fair,
in S I only try to make it work in Unix and I have not been changing
versions.) I will distribute these functions, but it would make sense to
have a common effort if others are interested.

2/ In the few cases where I need a slightly different definition of
something for S, I keep the functions in an S subdirectory in the R
package structure. I source these first when I build the S version, and
then I use is.R() to avoid redefining them when I source code from the R
subdirectory.

3/ If there is a logical way to divide things up into multiple packages
(and perhaps put them together into a bundle) then it is a good idea. It
is much quicker to build and test changes this way. (At least once you
get the dependencies worked out.)

4/ I keep fortran code in the R package src directory and my Splus
install script compiles it there. For R/S code I essentially build an R
like package for Splus and then have an install script that sources
things from the S and R subdirectories to generate .Data.

Best of luck with your effort, and let me know if you would like my
Makefile or any of my scripts or other code.

Paul Gilbert

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