[O] Second session of the Reproducible Research MOOC (using orgmode)
Dear all, The second session of the Reproducible Research MOOC <https://learninglab.inria.fr/en/mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente/> is going to start on April 1st (no joke!). Like for the first session (of October last year), three independent paths can be followed, one using R/Rstudio, one using Python/Jupyter and, of course, one using orgmode with Python and R. The course videos are in French with English subtitles. The course material is available in both English and French. The course is free, you just have to register on the FUN <https://www.fun-mooc.fr/> platform. Nearly a third of the students who followed the first session were orgmode users. Christophe -- Tant que les lapins n'ont pas d'historiens, l'Histoire est racontée par les chasseurs. Le chef d'état-major, l'amiral William Leahy, un partisan du New Deal, écrivit : « Les Japonais étaient déjà battus et prêts à capituler. L'usage de cette arme barbare à Hiroshima et à Nagasaki n'a apporté aucune contribution matérielle à notre combat contre le Japon. » Les États-Unis, poursuivit-il, « en tant que premier pays à utiliser cette bombe ont adopté des normes éthiques semblables à celles des barbares du Haut Moyen Âge ». En revanche, lorsqu'il fut informé de l'holocauste de Nagasaki, en revenant de la conférence de Potsdam, à bord du croiseur Augusta, Truman fit part de sa jubilation au commandant du bâtiment : « C'est la plus grande chose de l'histoire. » -- Christophe Pouzat 64, rue des Blanches 94400 VITRY SUR SEINE tél : +33662941034
[O] A MOOC on reproducible reasearch (using orgmode) is going to start on October 22
Dear all, A MOOC on Reproducible Research <https://learninglab.inria.fr/en/mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente/> prepared by Arnaud Legrand, Konrad Hinsen and myself together with the Learning Lab of the INRIA (the french research institute dedicated to computer sciences) is going to start on October 22. Three independent paths can be followed, one using R/Rstudio, one using Python/Jupyter and, of course, one using orgmode with Python and R. The course videos are in French with English subtitles. The course material is available in both English and French. Christophe PS An announcement in French <https://learninglab.inria.fr/mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente/> is also available. -- Tant que les lapins n'ont pas d'historiens, l'Histoire est racontée par les chasseurs. Le chef d'état-major, l'amiral William Leahy, un partisan du New Deal, écrivit : « Les Japonais étaient déjà battus et prêts à capituler. L'usage de cette arme barbare à Hiroshima et à Nagasaki n'a apporté aucune contribution matérielle à notre combat contre le Japon. » Les États-Unis, poursuivit-il, « en tant que premier pays à utiliser cette bombe ont adopté des normes éthiques semblables à celles des barbares du Haut Moyen Âge ». En revanche, lorsqu'il fut informé de l'holocauste de Nagasaki, en revenant de la conférence de Potsdam, à bord du croiseur Augusta, Truman fit part de sa jubilation au commandant du bâtiment : « C'est la plus grande chose de l'histoire. » -- Christophe Pouzat 64, rue des Blanches 94400 VITRY SUR SEINE tél : +33662941034
[O] Implementing Reproducible Research
Hi All, The book Implementing Reproducible Research edited by V. Stodden, F. Leisch and R. D. Peng came out last month (I don't have a copy) and I just found out that you can get the chapters (in PDF) from the editors' site: https://osf.io/s9tya/ I did not have enough time to go trhough all of it but org is mentioned a couple of times! Christophe -- A Master Carpenter has many tools and is expert with most of them. If you only know how to use a hammer, every problem starts to look like a nail. Stay away from that trap. Richard B Johnson. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://xtof.disque.math.cnrs.fr
[O] Implementing Reproducible Research
Hi all, I've just seen that a book, Implementing Reproducible Researchhttp://www.amazon.com/Implementing-Reproducible-Research-Chapman-Series/dp/1466561599, edited by V. Stodden, F. Leisch and R. Peng is coming out next year from CRC. I was wondering if anyone has written a chapter presenting org for it. Any clue? Christophe -- A Master Carpenter has many tools and is expert with most of them. If you only know how to use a hammer, every problem starts to look like a nail. Stay away from that trap. Richard B Johnson. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://xtof.disque.math.cnrs.fr
[O] [Babel] Inaccuracy in Sec. 14.8.2.13 `:noweb' of the manual
Hi all, There seems to be a wrong statement in the description of the value 'strip-export' of header :noweb (Sec. 14.8.2.13) of the manual: `strip-export' "Noweb" syntax references in the body of the code block will be expanded before the block is evaluated or tangled. However, "noweb" syntax references will not be removed when the code block is exported. The last phrase states that the noweb reference will not be removed but after trying it out with the last ELPA version of org (July 3rd), it turns out that it is removed (which makes sense given the name). Happy 4th of July to all our friends on the other side of the Atlantic (as well as to the one(s) "lost" in the middle of the Pacific). Christophe -- Programming languages teach you not to want what they cannot provide. You have to think in a language to write programs in it, and it's hard to want something you can't describe. Paul Graham, ANSI Common Lisp. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33183945882 mobile: +33662941034 web: http://xtof.disque.math.cnrs.fr/
[O] [Babel] Complete Reference of Delescluse et al (2012) Making Neurophysiological Data Analysis Reproducible...
Hi everyone, I'm pleased to be able to provide now the full reference of the paper Matthieu Delescluse, Romain Franconville, Sébastien Joucla, Tiffany Lieury and myself published in J Physiol (Paris). The editor, Elsevier, "froze" our accepted manuscript early September last year and it just got published! The full reference is: Matthieu Delescluse, Romain Franconville, Sébastien Joucla, Tiffany Lieury and Christophe Pouzat (2012) Making neurophysiological data analysis reproducible. Why and how? Journal of Physiology (Paris) 106 (3-4): 159-170. You can get the BibTeX file together with Org versions of the paper's toy example (using Python and Octave or using Common Lisp and Gnuplot) from my brand new (Org designed) web site: http://xtof.disque.math.cnrs.fr/. Christophe -- Programming languages teach you not to want what they cannot provide. You have to think in a language to write programs in it, and it's hard to want something you can't describe. Paul Graham, ANSI Common Lisp. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33183945882 mobile: +33662941034 web: http://xtof.disque.math.cnrs.fr/
[O] Meeting on Reproducibility in Computational and Experimental Mathematics
Hi everyone, There's a meeting on Reproducibility in Computational and Experimental Mathematics in Brown University next December. I don't see any "Org/Babel person" in the participants list yet. Is there anyone around Providence who could show our favorite colors there? Christophe -- Programming languages teach you not to want what they cannot provide. You have to think in a language to write programs in it, and it's hard to want something you can't describe. Paul Graham, ANSI Common Lisp. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33183945882 mobile: +33662941034 web: http://xtof.disque.math.cnrs.fr/
Re: [O] latex export R code syntax highlighting with minted
Ista Zahn istaz...@gmail.com writes:
Hi all,
I'm having trouble modifying the example at
http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-12-3
to highlight R code blocks. The trouble seems to be that org-mode
identifies R blocks using uppercase R, while pygments looks for
lowercase r.
For example, org exports
\begin{minted}{R}
2+2
\end{minted}
but pygments doesn't know how to highlight R. If I change to
\begin{minted}{r}
2+2
\end{minted}
(note the lower case r) then it works, but of course I don't want to
have to perform a find-and-replace every time.
Do you know how to either a) make org-mode identify R blocks with a
lowercase r, or b) make pygments recognize uppercase R, or c) some
other solution I've overlooked?
Thanks!
Ista
Hi Ista,
Put the following expression:
(add-to-list 'org-export-latex-minted-langs '(R r))
in an emacs-lisp code block at the beginning of your org file (or in the
*scratch* buffer) and evaluate it.
Christophe
--
Président, Nicolas Sarkozy représente une sorte de triomphe bouffon de
l'égalitarisme français ; pour la première fois de notre histoire, nous avons
un chef de l'État qui se comporte comme s'il ne valait pas mieux que les
citoyens. C'est en réalité toujours le cas, mais cette vérité doit être cachée
pour que les institutions et le système social tournent de façon, si ce n'est
harmonieuse, du moins raisonnable.
E. Todd, Après la démocratie.
--
Christophe Pouzat
MAP5 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France
tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
Re: [O] Selectively export RESULTS
Matthew Landis lan...@isciences.com writes: cberry at tajo.ucsd.edu writes: Eric Schulte eric.schulte at gmx.com writes: Does this do what you want? Have you looked at the :cache header argument [1], from my understanding of your use case it should be exactly what you are after. Its a step in the right direction. It seems I have to set :cache yes on every block I use before I invoke it. My attempt to use a buffer-wide PROPERTY setting for cache did not pan out. I'd like to put in a vote for the kind of functionality that cberry is describing. I have a very similar situation - a large org file that uses R to do a lot of time consuming data manipulation and model fitting, resulting in statistical tables and graphs. I run a lot of the code blocks as I'm writing it, resulting in :results in the org file. In the end, I'd like to export the org file to html or ODT, but I'd like to be able to choose buffer-wide whether to rerun all of the code blocks or just use the results that are already in the buffer. I tried setting #+PROPERTY: eval no at the top of the buffer in the hopes that on export, it would ignore all my code blocks and just incorporate the :results, but this was ignored and my code blocks were rerun. The cache argument only partially deals with the problem, as this example illustrates: #+begin_src R :session :cache yes x - rnorm(100) #+end_src #+begin_src R :session :results graphics :exports results :file hist.png :cache yes hist(x) #+end_src Now after the first export, I change code block 2, but not code block 1. If I understand how cache works correctly, code block 2 will be rerun, but it will fail because code block 1 is not rerun, so x doesn't exist in the R session. For this reason, I'd prefer to be able to decide whether to re-run on a file- wide basis. Many thanks to all of you who have created such an amazing system. M Matthew, I think that you're wrongly expecting babel's cache header argument to behave like the argument of the same name in Sweave code chunks. Babel will cache, in your case, the value of your code block evaluation and there is none in your first code block, therefore nothing gets cached by babel, try that instead: #+name: my-random-vector #+begin_src R :session :cache yes rnorm(100) #+end_src #+headers: :var x=my-random-vector #+headers: :results graphics :exports results :file hist.png #+begin_src R :session :cache yes hist(x) #+end_src Does it work better? In that case you don't even need a session. Christophe -- Président, Nicolas Sarkozy représente une sorte de triomphe bouffon de l'égalitarisme français ; pour la première fois de notre histoire, nous avons un chef de l'État qui se comporte comme s'il ne valait pas mieux que les citoyens. C'est en réalité toujours le cas, mais cette vérité doit être cachée pour que les institutions et le système social tournent de façon, si ce n'est harmonieuse, du moins raisonnable. E. Todd, Après la démocratie. -- Christophe Pouzat MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
Re: [O] A manuscript on reproducible research introducing org-mode
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
Jambunathan K kjambunat...@gmail.com 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.
Do you have any insights on how the Org's ODT exporter performs wrt your
input Org file. Just curious.
@article{Delescluse2011,
title = Making neurophysiological data analysis reproducible: Why and how?,
journal = Journal of Physiology-Paris,
volume = ,
number = 0,
pages = - ,
year = 2011,
note = ,
issn = 0928-4257,
doi = 10.1016/j.jphysparis.2011.09.011,
url = http://www.sciencedirect.com/science/article/pii/S0928425711000374;,
author = Matthieu Delescluse and Romain Franconville and Sébastien Joucla
and Tiffany Lieury and Christophe Pouzat,
keywords = Software,
keywords = R,
keywords = Emacs,
keywords = Matlab,
keywords = Octave,
keywords = LATEX,
keywords = Org-mode,
keywords = Python,
abstract = Reproducible data analysis is an approach aiming at
complementing classical printed scientific articles with everything required
to independently reproduce the results they present. “Everything” 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 presented
first, starting with what economists have been calling replication since the
early eighties to end with what is now called reproducible research in
computational data analysis oriented fields like statistics and signal
processing. Since efficient tools are instrumental for a routine
implementation 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 “Sweave family”
and the org-mode of emacs. The former is bound to R while the latter can be
used with R, Matlab, Python and many more “generalist” data processing
software. Both solutions can be used with Unix-like, Windows and Mac
families of operating systems. It is argued that neuroscientists could
communicate much more efficiently their results by adopting the reproducible
research paradigm from their lab books all the way to their articles, thesis
and books.
}
--
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 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France
tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
Re: [O] A manuscript on reproducible research introducing org-mode
Aloha Tom,
Not yet in print, still on the accepted papers list
(http://www.sciencedirect.com/science/journal/aip/09284257), sorry. It
seems that I chose the slowest neuroscience journal!
Your JSS paper of last month (with Eric, Dan and Carsten) is great by
the way. It seems that I missed the announcements on the list when the
pre-print was posted, otherwise I would have managed to cite it in mine.
The bibtex entry for my paper (just downloaded from Elsevier site) is:
@article{Delescluse2011,
title = Making neurophysiological data analysis reproducible: Why and how?,
journal = Journal of Physiology-Paris,
volume = ,
number = 0,
pages = - ,
year = 2011,
note = ,
issn = 0928-4257,
doi = 10.1016/j.jphysparis.2011.09.011,
url = http://www.sciencedirect.com/science/article/pii/S0928425711000374;,
author = Matthieu Delescluse and Romain Franconville and Sébastien Joucla and Tiffany Lieury and Christophe Pouzat,
keywords = Software,
keywords = R,
keywords = Emacs,
keywords = Matlab,
keywords = Octave,
keywords = LATEX,
keywords = Org-mode,
keywords = Python,
abstract = Reproducible data analysis is an approach aiming at complementing classical printed scientific articles with everything required to independently reproduce the results they present. “Everything” 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 presented first, starting with what economists have been calling replication since the early eighties to end with what is now called reproducible research in computational data analysis oriented fields like statistics and signal processing. Since efficient tools are instrumental for a routine implementation 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 “Sweave family” and the org-mode of emacs. The former is bound to R while the latter can be used with R, Matlab, Python and many more “generalist” data processing software. Both solutions can be used with Unix-like, Windows and Mac families of operating systems. It is argued that neuroscientists could communicate much more efficiently their results by adopting the reproducible research paradigm from their lab books all the way to their articles, thesis and books.
}
I will post on the list the official bibliographic reference as soon
as the paper is in print.
Take care,
Christophe
t...@tsdye.com (Thomas S. Dye) writes:
Aloha Christophe,
Has this article appeared in print? If so, can you forward publication
details?
All the best,
Tom
Christophe Pouzat christophe.pou...@parisdescartes.fr writes:
Thomas S. Dye t...@tsdye.com a écritnbsp;:
Christophe Pouzat christophe.pou...@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
Re: [O] org-babel export table from R to LaTeX
Sorry,
Checking foo.org
(http://orgmode.org/w/?p=worg.git;a=blob_plain;f=org-contrib/babel/examples/foo.org;hb=HEAD)
I got the correct way to do it:
#+begin_src R :results output latex :exports results
library(xtable)
xtable(foo, caption = ANOVA Table, label = tab:one,
digits = c(0, 0, 2, 0, 2, 3, 3))
#+end_src
Does it solve your problem?
Christophe
Riccardo Romoli ric.rom...@gmail.com writes:
If I set :export latex when I exports to LaTeX I have only the R code, not the
table.
Best
2012/2/14 Christophe Pouzat christophe.pou...@gmail.com
Riccardo Romoli ric.rom...@gmail.com writes:
Hi, I work with org-babel and R.
In the R session I create a table that I have to export to LaTeX.
This is the code I use:
#+headers: :results latex
#+begin_src R :session *R* :exports results
.
print(xtable(summary(mypca)))
#+end_src
I do not understand why the exported table is delimited by |:
|% latex table generated in R 2.14.1 by xtable 1.6-0 package |
| % Tue Feb 14 16:21:48 2012 |
| \begin{table}[ht] |
| \begin{center} |
| \begin{tabular}{r} |
| \hline |
| PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
PC11 PC12 PC13 PC14 PC15 PC16 \\ |
| \hline |
| Standard deviation 3.4693 2.8113 2.5561 2.2668
2.0015 1.9236 1.7287 1.6220 1.4288 1.3456 1.2596
1.2195 1.1278 1.0778 0.8390 0. \\ |
| Proportion of Variance 0.2188 0.1437 0.1188 0.0934
0.0728 0.0673 0.0543 0.0478 0.0371 0.0329 0.0289
0.0270 0.0231 0.0211 0.0128 0. \\ |
| Cumulative Proportion 0.2188 0.3625 0.4813 0.5747
0.6476 0.7149 0.7692 0.8170 0.8541 0.8871 0.9159
0.9429 0.9661 0.9872 1. 1. \\ |
| \hline |
| \end{tabular} |
| \end{center} |
| \end{table} |
| |
Should I change some headers settings??
Best
Hi Riccardo,
Try :exports latex instead of :exports results
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
MAP5 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France
tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
--
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 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France
tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
[O] org-babel-expand-src-block
Hi all, Using the last org-mode version from the git repository (7.8.03) I've found a mismatch between the key-chord required to call function =org-babel-expand-src-block= (=C-c C-v v=) and the ones given in the info file: =C-c C-v p= or =C-c C-v C-p=. The same goes for the [[http://orgmode.org/worg/org-contrib/babel/intro.html][Babel: Introduction]] where the given key-chord is =C-c M-b p=. In the same lin,e I have a question concerning the inclusion of the /expanded/ source block in the generated output. Let's assume that I define in my =.org= file a variable containing a file name like: #+name: my-file-name dataFile.mat I want then a code block (using =R= in that case) that checks if dataFile.mat is in the working directory with something like: #+BEGIN_SRC R :var fileName=my-file-name :exports both fileName %in% list.files(pattern=*.mat) #+END_SRC I'm passing the file name as a variable because I want to repeat the same analysis on different data files. But I would like to see in the HTML output the value of the above variable =fileName=. I would like essentially to export the expanded source block. Is there a way to do that? Thanks, 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 MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
[O] Question related to org-babel-expand-src-block
Hi all, Using the last org-mode version from the git repository (7.8.03) I've found a mismatch between the key-chord required to call function =org-babel-expand-src-block= (=C-c C-v v=) and the ones given in the info file: =C-c C-v p= or =C-c C-v C-p=. The same goes for the [[http://orgmode.org/worg/org-contrib/babel/intro.html][Babel: Introduction]] where the given key-chord is =C-c M-b p=. In the same line, I have a question concerning the inclusion of the /expanded/ source block in the generated output. Let's assume that I define in my =.org= file a variable containing a file name like: #+name: my-file-name : dataFile.mat I want then a code block (using =R= in that case) that checks if dataFile.mat is in the working directory with something like: #+BEGIN_SRC R :var fileName=my-file-name :exports both fileName %in% list.files(pattern=*.mat) #+END_SRC I'm passing the file name as a variable because I want to repeat the same analysis on different data files. But I would like to see in the HTML output the value of the above variable =fileName=. I would like essentially to export the expanded source block. Is there a way to do that? Thanks, 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 MAP5 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
Re: [O] A manuscript on reproducible research introducing org-mode
Thomas S. Dye t...@tsdye.com a écritnbsp;:
Christophe Pouzat christophe.pou...@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
[O] A manuscript on reproducible research introducing org-mode
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 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
