Re: [R] Reproducible Research - Examples

From: Jean lobry <lobry_at_biomserv.univ-lyon1.fr>
Date: Thu 20 Jul 2006 - 03:49:24 EST

> 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@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/

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Received on Thu Jul 20 03:54:02 2006

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