[O] Rsquared for reproductible research
Following on from an old thread about self-configuring org files for reproducible research, R users might be interested to see the following web site which is exactly what I was thinking of for org mode (but of course, works only for R packages.) http://rsquared.stat.uni-muenchen.de/index.rhtml Stephen
Re: [O] Rsquared for reproductible research
Wow! http://rsquared.stat.uni-muenchen.de/index.rhtml looks great--very interesting--thanks for the heads-up on that link. Worked with R/S/S-PLUS in grad school--easily my favorite language/system--especially like its ease of extensibility--reminds me of EMACS LISP! I recognized your name, Stephen, as the long-time maintainer of the Emacs Lisp List--thanks for that too. Are you envisioning a repository beyond Emacs Lisp List for OrgMode implementations and/or Babel examples. Or maybe optional extensions to OrgMode itself? Both? Also, I very much agree that a near exact replica of the http://rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Read the 3 papers on the site and came across this reference that may be interesting to OrgMode/R/Literate Programming persons: http://cran.r-project.org/web/packages/roxygen/index.html Maybe that could be a focus of such a site if it were made?: OrgMode = LiterateProgramming = R/Bable/whatever other languages. --where such topics intersect. On Thu, Jan 12, 2012 at 7:38 AM, Stephen Eglen sj...@cam.ac.uk wrote: Following on from an old thread about self-configuring org files for reproducible research, R users might be interested to see the following web site which is exactly what I was thinking of for org mode (but of course, works only for R packages.) http://rsquared.stat.uni-muenchen.de/index.rhtml Stephen
Re: [O] Rsquared for reproductible research
I recognized your name, Stephen, as the long-time maintainer of the Emacs Lisp List--thanks for that too. Are you envisioning a repository beyond Emacs Lisp List for OrgMode implementations and/or Babel examples. I am interested in maintaining a collection of nice org-babel-R examples, given my interest in R and Emacs; I made a small start last year for my tutorial notes on ESS for the useR meeting, but I'd like to update that. The key problem I found with learning org-babel was worked examples, given that the syntax was changing rapidly. I hope that has now stabilised, and I should followup with Eric about this. (I also hope to kill off the Emacs Lisp List once the ELPA has taken off.) Also, I very much agree that a near exact replica of the http:// rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!? http://cran.r-project.org/web/packages/roxygen/index.html Note that ESS has limited support for editing roxygen tags. Stephen
Re: [O] Rsquared for reproductible research
Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: I recognized your name, Stephen, as the long-time maintainer of the Emacs Lisp List--thanks for that too. Are you envisioning a repository beyond Emacs Lisp List for OrgMode implementations and/or Babel examples. I am interested in maintaining a collection of nice org-babel-R examples, given my interest in R and Emacs; I made a small start last year for my tutorial notes on ESS for the useR meeting, but I'd like to update that. The key problem I found with learning org-babel was worked examples, given that the syntax was changing rapidly. I hope that has now stabilised, and I should followup with Eric about this. The syntax is now stabilized (we wanted to get this sorted before the final Emacs24 merge). That which is currently described in the manual is and should remain the proper Org-mode code block syntax. For many small examples, please see [1] which I (unfortunately) haven't been adding to recently, but I will try to once again start using for all of my small generally-mailing-list-inspired Babel one-offs. (I also hope to kill off the Emacs Lisp List once the ELPA has taken off.) Also, I very much agree that a near exact replica of the http:// rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!? From looking at the fairly terse web site for R^2 it is not clear to me exactly what the system includes (I'm sure I'm missing something obvious). It seems to be the addition of a packaging system over-top of R source files. What would a potential Org-mode based system provide which is not already possible with Org-mode text files, Org-mode publishing and a version control repository. Perhaps the benefit would simply be a system which eases the integration of Org, publishing, version control, and possibly automatic Makefile creation with tasks like publish, clean etc... Best, http://cran.r-project.org/web/packages/roxygen/index.html Note that ESS has limited support for editing roxygen tags. Stephen Footnotes: [1] http://eschulte.me/org-scraps/ -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] Rsquared for reproductible research
Eric Schulte eric.schu...@gmx.com writes: Stephen Eglen s.j.eg...@damtp.cam.ac.uk writes: I recognized your name, Stephen, as the long-time maintainer of the Emacs Lisp List--thanks for that too. Are you envisioning a repository beyond Emacs Lisp List for OrgMode implementations and/or Babel examples. I am interested in maintaining a collection of nice org-babel-R examples, given my interest in R and Emacs; I made a small start last year for my tutorial notes on ESS for the useR meeting, but I'd like to update that. The key problem I found with learning org-babel was worked examples, given that the syntax was changing rapidly. I hope that has now stabilised, and I should followup with Eric about this. The syntax is now stabilized (we wanted to get this sorted before the final Emacs24 merge). That which is currently described in the manual is and should remain the proper Org-mode code block syntax. For many small examples, please see [1] which I (unfortunately) haven't been adding to recently, but I will try to once again start using for all of my small generally-mailing-list-inspired Babel one-offs. (I also hope to kill off the Emacs Lisp List once the ELPA has taken off.) Also, I very much agree that a near exact replica of the http:// rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!? From looking at the fairly terse web site for R^2 it is not clear to me exactly what the system includes (I'm sure I'm missing something obvious). It seems to be the addition of a packaging system over-top of R source files. What would a potential Org-mode based system provide which is not already possible with Org-mode text files, Org-mode publishing and a version control repository. One thing that caught my eye was the facility that compared results across operating systems. Tom Perhaps the benefit would simply be a system which eases the integration of Org, publishing, version control, and possibly automatic Makefile creation with tasks like publish, clean etc... Best, http://cran.r-project.org/web/packages/roxygen/index.html Note that ESS has limited support for editing roxygen tags. Stephen Footnotes: [1] http://eschulte.me/org-scraps/ -- Thomas S. Dye http://www.tsdye.com
Re: [O] Rsquared for reproductible research
Also, I very much agree that a near exact replica of the http:// rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!? ... Eric questioned: From looking at the fairly terse web site for R^2 it is not clear to me exactly what the system includes (I'm sure I'm missing something obvious). It seems to be the addition of a packaging system over-top of R source files. What would a potential Org-mode based system provide which is not already possible with Org-mode text files, Org-mode publishing and a version control repository. ... * I mostly agree with your statements. Good challenges. I did more investigation: This link to the paper that Friedrich Leischa, , Manuel Eugsterb, Torsten Hothornb put together may make things clearer--this paper really seems to be the justification/impetus for the R^2 website--it has made things clearer and more exciting for me: http://www.sciencedirect.com/science/article/pii/S1877050911001232 = Executable Papers for the R Community: The R2 Platform for Reproducible Research ** So papers in R (and maybe other languages--maybe languages run thru Babel in OrgMode) could be executed by people in the community--one could verify research studies and papers interactively, ad hoc. *** They mention in the paper that they use several key tools: R: the lingua franca of statistics and data analysis Sweave: the most popular format for executable papers in the R community CRAN: package building and checking system has been developed for more then a decade and copes successfully with the exponential growth of the number of packages Weave/CWEB/CWEAVE/CTANGLE=NOWEB (Knuth) comes to mind here--i.e. Literate Programming * http://www-cs-staff.stanford.edu/~uno/cweb.html = CTANGLE converts a source file foo.w to a compilable program file foo.c; CWEAVE converts a source file foo.w to a prettily-printable and cross-indexed document file foo.tex. * Exactly the paper can be found at: http://www.sciencedirect.com/science\ ?_ob=MiamiImageURL_cid=280203_user=10_pii=S1877050911001232\ _check=y_origin=article_zone=toolbar_coverDate=\ 31-Dec-2011view=coriginContentFamily=serialwchp=\ dGLbVlS-zSkWbmd5=4681e5babd7822f321d2a0dd3a9f11cf/\ 1-s2.0-S1877050911001232-main.pdf * I agree Eric that the website is a bit terse; but, for the most part I was excited about (and I think Stephen is interested in--he suggested it is something the community might do) the general ideas, the structure of the website's process OrgMode=TeX paper in--...process...--Executable/verifiable code interaction a user might experience/stored on-line for researchers (one thing I always enjoy a lot when working with e.g. R/S-PLUS and PYTHON's interactive CLI, etc.) ** They even publish the minute details of the settings on the machines--the local environment variables, etc.--the devil is in the details! * Thanks for the link Eric to your OrgMode scraps--they could be very useful: http://eschulte.me/org-scraps/ * Lastly, most importantly I'll repeat the link and query to the community: ... Also, I very much agree that a near exact replica of the http://rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!?---(Stephen Eglen)
Re: [O] Rsquared for reproductible research
brian powell briangpowel...@gmail.com writes: Also, I very much agree that a near exact replica of the http:// rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. Yes! Any takers?!? ... Eric questioned: From looking at the fairly terse web site for R^2 it is not clear to me exactly what the system includes (I'm sure I'm missing something obvious). It seems to be the addition of a packaging system over-top of R source files. What would a potential Org-mode based system provide which is not already possible with Org-mode text files, Org-mode publishing and a version control repository. ... * I mostly agree with your statements. Good challenges. I did more investigation: This link to the paper that Friedrich Leischa, , Manuel Eugsterb, Torsten Hothornb put together may make things clearer--this paper really seems to be the justification/impetus for the R^2 website--it has made things clearer and more exciting for me: http://www.sciencedirect.com/science/article/pii/S1877050911001232 Ah, thank you for linking to this paper. It seems I was missing was the package-management aspect provided by R2 through CRAN. The instillation of all software dependencies is a huge benefit exactly as installing software with apt-get or pacman is simpler than running ./configure make and manually resolving dependencies. While such a tool makes sense for a single language system like R, I fear an Org-mode version of such a system would have too wide of a scope. Given that code blocks may contain arbitrary languages, and that sh blocks can freely call any command-line executable such a system would turn into a system-wide package management tool. Perhaps there already exists a portable package management system designed for local installs which could handle most of the heavy lifting. As another option, distributing Virtual Machine images are one solution which I think work well and are increasingly realistic. Or similarly providing the research environment as a cloud server image (e.g., Amazon EC2). Certainly an interesting area for further work! Best, -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] Rsquared for reproductible research
The syntax is now stabilized (we wanted to get this sorted before the final Emacs24 merge). That which is currently described in the manual is and should remain the proper Org-mode code block syntax. Thanks Eric, this is great news. I'll ensure my examples from last year still work with the current org-mode syntax. For many small examples, please see [1] which I (unfortunately) haven't That's a nice site, thanks! From looking at the fairly terse web site for R^2 it is not clear to me exactly what the system includes (I'm sure I'm missing something obvious). It seems to be the addition of a packaging system over-top of R source files. What would a potential Org-mode based system provide which is not already possible with Org-mode text files, Org-mode publishing and a version control repository. The accompanying paper from 2011 goes into detail as to what it does. But in essence, the website is supposed to be 'neutral', in that it is not your local system. A document may compile on my system, but not for others, because it depends on my local configuration. Having a neutral system will avoid such problems. A neutral system could also have support for all babel languages, so that I can use it to compile someone's document without e.g. having a common-lisp compiler on my system. Perhaps the benefit would simply be a system which eases the integration of Org, publishing, version control, and possibly automatic Makefile creation with tasks like publish, clean etc... yes, that too! best wishes, Stephen
