Re: A manuscript on "reproducible research" introducing org-mode

[Christophe Pouzat <christophe.pouzat@parisdescartes.fr>]

"Thomas S. Dye" <tsd@tsdye.com> a écrit&nbsp;:

> Christophe Pouzat <christophe.pouzat@parisdescartes.fr> writes:
>
>> Dear all,
>>
>> M. Delescluse, R. Franconville, S. Joucla, T. Lieury and myself (C.
>> Pouzat) have just put a manuscript entitled: "Making
>> neurophysiological data analysis reproducible. Why and how?" on a
>> pre-print server: http://hal.archives-ouvertes.fr/hal-00591455/fr/
>> Although the paper has been written for a neurobiological journal, the
>> reader does not have to be a neuroscientist to read and understand it.
>> A toy example illustrating the use of org-mode + Babel (with Python
>> and Octave) takes a fair part of the manuscript. Other tools like R +
>> Sweave are presented and many more are mentioned.
>>
>> I thank Eric Schulte for comments on the manuscript and Eric (again)
>> together with the whole org-mode / Babel community for developing such
>> a great tool.
>>
>> Any comment, remark, suggestion on the manuscript is of course welcome.
>>
>> Christophe
>>

> Aloha Christophe,
>
> Thank you for an interesting and useful paper.  I was happy with the
> distinction you draw between reproducible analysis and reproducible
> research, which certainly applies to my field of archaeology where
> unique sites are typically destroyed by the data collection effort.  I
> also think the emphasis you place on data preprocessing is just the
> right approach; inclusion of the raw data in a reproducible analysis
> opens up many possibilities, which must be a benefit to a scientific
> community's pursuit of knowledge.
>
> May I offer a suggestion?  Carsten Dominik published the Org Mode 7
> Manual last year and it would be nice to see it cited in your paper.
>
> @book{dominik10:_org_mode_refer_manual,
>   author =       {Carsten Dominik},
>   title =        {The Org Mode 7 Reference Manual: Organize Your Life
>   with GNU Emacs},
>   publisher =    {Network Theory Ltd.},
>   year =         2010
> }
>
> All the best,
> Tom
> --
> Thomas S. Dye
> http://www.tsdye.com
>

Dear Tom,

Thanks for these interesting and positive comments. I apologize for  
forgetting the obvious reference to Carsten's reference manual. I will  
definitely include it in the next version.
I hope that people in my field will come to think the way you do about  
sharing their raw data. I'm just afraid that the way is still long…  
but the goal is reachable. Raw data aside, org-mode is surely a tool  
which should help people experimenting with the "reproducible research  
paradigm". As I wrote to Eric (Schulte), M. Delescluse and I wrote a  
first RR manuscript 6 years ago based on R/Sweave. The manuscript  
never got submitted for different reasons, among them, the amount of  
work required to learn R and LaTeX. Learning about org-mode convinced  
me that it would be worth re-activating the project.

Christophe

Most people are not natural-born statisticians. Left to our own  
devices we are not very good at picking out patterns from a sea of  
noisy data. To put it another way, we are all too good at picking out  
non-existent patterns that happen to suit our purposes.
Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap

--

Christophe Pouzat
Laboratoire de Physiologie Cerebrale
CNRS UMR 8118
UFR biomedicale de l'Universite Paris-Descartes
45, rue des Saints Peres
75006 PARIS
France

tel: +33 (0)1 42 86 38 28
fax: +33 (0)1 42 86 38 30
mobile: +33 (0)6 62 94 10 34
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html