[R] Reproducible Research - Examples

[Jean lobry]

>  Question: Reproducible research is clearly desirable and feasible. Could
>  anyone provide examples (stand-alone URLs or supplementary material in
>  journals) that you would recommend as a models for reproducible research in
>  R?

Here are some attempts based on RWeb, contributed by Jeff Banfield, to allow
for the reproduction of research papers:

http://biomserv.univ-lyon1.fr/~necsulea/repro/
http://pbil.univ-lyon1.fr/members/lobry/repro/gene06/
http://biomserv.univ-lyon1.fr/~palmeira/repro/
http://pbil.univ-lyon1.fr/members/lobry/repro/toxo/
http://pbil.univ-lyon1.fr/datasets/SemonLobryDuret2005/
http://pbil.univ-lyon1.fr/members/lobry/repro/gene05/
http://pbil.univ-lyon1.fr/members/lobry/repro/bioinfo04/
http://pbil.univ-lyon1.fr/members/lobry/repro/lncs04/
http://pbil.univ-lyon1.fr/members/lobry/repro/jag03/
http://pbil.univ-lyon1.fr/members/lobry/repro/jme97/
http://pbil.univ-lyon1.fr/members/lobry/repro/jme95/
http://pbil.univ-lyon1.fr/members/lobry/repro/cabios95/
http://pbil.univ-lyon1.fr/members/lobry/repro/nar94/

I would not recommend these as a "models", but I would like to point out that:

1) If you are already using Sweave (many thanks to Friedrich Leisch) there
    is virtually no extra-cost for the authors of the paper to write the
    corresponding web page.

2) There is no way to be more cristal clear with respect to your reviewers
    during the submission process: data are available online, methods are
    available online, the parameters of the methods are available and
    editable online.

This is good science, but, problem: what would be the equivalent
of JSTOR for this? How people can, say 100 years in the future,
reproduce your results?

Best,

Jean Lobry


P.S. If you want to play with the data used by Student (aka William Sealy
Gosset) for the experimental validation of the famous t-test
(The probable error of a mean. Biometrika, 6:1-25,1908) they are at
your R prompt:
crim<-read.table(file="http://pbil.univ-lyon1.fr/R/donnees/criminals1902.txt")
Can you reproduce Student's results nowadays?

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 12 87     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/