From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christophe Pouzat Subject: Re: A manuscript on "reproducible research" introducing org-mode Date: Thu, 16 Feb 2012 10:21:39 +0100 Message-ID: <87pqdf16cc.fsf@xtof-netbook.home> References: <20110905155520.18046s4zu5o3tbwg@www.biomedicale.univ-paris5.fr> <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> <87zkcjn84f.fsf@xtof-netbook.home> <81aa4jupc8.fsf@gmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:32975) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RxxXB-0000T3-Om for emacs-orgmode@gnu.org; Thu, 16 Feb 2012 04:21:57 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RxxX7-0001Wn-1O for emacs-orgmode@gnu.org; Thu, 16 Feb 2012 04:21:49 -0500 Received: from mail-wi0-f169.google.com ([209.85.212.169]:51800) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RxxX6-0001Wb-Nb for emacs-orgmode@gnu.org; Thu, 16 Feb 2012 04:21:44 -0500 Received: by wibhj13 with SMTP id hj13so1421953wib.0 for ; Thu, 16 Feb 2012 01:21:43 -0800 (PST) In-Reply-To: <81aa4jupc8.fsf@gmail.com> (Jambunathan K.'s message of "Thu, 16 Feb 2012 14:28:31 +0530") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Jambunathan K Cc: Christophe Pouzat , emacs-orgmode@gnu.org Hello Jambunathan, The ODT version was prepared "by hand" using LibreOffice. This was written (last May) before your org-odt functions became part of org-mode (if I'm right). I would now also do it with org-mode. Christophe=20 Jambunathan K writes: > Christophe > > I see an ODT file in there - LFPdetection_in.odt > http://hal.archives-ouvertes.fr/hal-00591455/ > > May I ask how the document was produced.=20 > > Do you have any insights on how the Org's ODT exporter performs wrt your > input Org file. Just curious. > >> @article{Delescluse2011, >> title =3D "Making neurophysiological data analysis reproducible: Why and= how?", >> journal =3D "Journal of Physiology-Paris", >> volume =3D "", >> number =3D "0", >> pages =3D " - ", >> year =3D "2011", >> note =3D "", >> issn =3D "0928-4257", >> doi =3D "10.1016/j.jphysparis.2011.09.011", >> url =3D "http://www.sciencedirect.com/science/article/pii/S0928425711000= 374", >> author =3D "Matthieu Delescluse and Romain Franconville and S=C3=A9basti= en Joucla and Tiffany Lieury and Christophe Pouzat", >> keywords =3D "Software", >> keywords =3D "R", >> keywords =3D "Emacs", >> keywords =3D "Matlab", >> keywords =3D "Octave", >> keywords =3D "LATEX", >> keywords =3D "Org-mode", >> keywords =3D "Python", >> abstract =3D "Reproducible data analysis is an approach aiming at comple= menting classical printed scientific articles with everything required to i= ndependently reproduce the results they present. =E2=80=9CEverything=E2=80= =9D covers here: the data, the computer codes and a precise description of = how the code was applied to the data. A brief history of this approach is p= resented first, starting with what economists have been calling replication= since the early eighties to end with what is now called reproducible resea= rch in computational data analysis oriented fields like statistics and sign= al processing. Since efficient tools are instrumental for a routine impleme= ntation of these approaches, a description of some of the available ones is= presented next. A toy example demonstrates then the use of two open source= software programs for reproducible data analysis: the =E2=80=9CSweave fami= ly=E2=80=9D and the org-mode of emacs. The former is bound to R while the l= atter can be used with R, Matlab, Python and many more =E2=80=9Cgeneralist= =E2=80=9D data processing software. Both solutions can be used with Unix-li= ke, Windows and Mac families of operating systems. It is argued that neuros= cientists could communicate much more efficiently their results by adopting= the reproducible research paradigm from their lab books all the way to the= ir articles, thesis and books." >> } --=20 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 MAP5 - Math=C3=A9matiques Appliqu=C3=A9es =C3=A0 Paris 5 CNRS UMR 8145 45, rue des Saints-P=C3=A8res 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html