From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Updating the Babel section of Worg Was: Generating plot with org-babel-R Date: Sun, 05 Feb 2012 12:29:29 -0700 Message-ID: <87mx8xyt7q.fsf_-_@gmx.com> References: 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]:41561) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ru7mi-0002Lg-4b for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:30:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ru7mg-0006WU-CK for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:30:00 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:49034 helo=mailout-us.mail.com) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Ru7mg-0006W8-5Z for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:29:58 -0500 In-Reply-To: (Thomas S. Dye's message of "Sun, 05 Feb 2012 06:45:36 -1000") 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org, Riccardo Romoli Thanks for raising this point. The bulk of the content in the Babel portion of worg is fairly old, predating the syntax standardization efforts this fall. I've just pushed some minor updates to the main babel pages, but updating the language-specific tutorials and the individual use cases will be a much larger effort. I'm not sure how to proceed. One option would be to go through and add a [uses deprecated syntax] tag to the top of each such page, which could be removed after the page has been checked and possibly updated to ensure consistency with the latest syntax. Given that the Babel syntax will not be changing significantly moving forward now would be a good time to do such a review. Ideally this could be completed before the release of Emacs 24 in a couple of months. Any other ideas for update/reorganization or volunteers? Cheers, tsd@tsdye.com (Thomas S. Dye) writes: > Hi Riccardo, > > Thanks for the URL. Org mode has evolved since this article was > written. It should probably be revised or taken off Worg. I've copied > Eric Schulte, who is better able than me to determine the correct course > of action here. > > In the meantime, an up-to-date description of how Org mode can be used > to write literate programs has appeared in the Journal of Statistical > Software. You can find it here: http://www.jstatsoft.org/v46/i03 > > Perhaps you could use the examples in the JSS article to get started? > If these don't work for you, or if they raise questions that are difficult > to answer, please do come back to the list with your queries. > > All the best, > Tom > > Riccardo Romoli writes: > >> Hi, this is the URL: >> >> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html >> >> Best >> R >> >> 2012/2/5 Thomas S. Dye >> >>> Hi Riccardo, >>> >>> This code appears to be outdated. I don't recall this code on the org >>> site. Could you send a URL? >>> >>> All the best, >>> Tom >>> >>> Riccardo Romoli writes: >>> >>> > Hi, I'm trying to generate some figure with R, into an org session. >>> Firstly >>> > I use the code in the org site. The problem is that the code do not >>> > generate any figure. >>> > >>> > This is the code: >>> > >>> > #+TITLE:Test >>> > #+AUTHOR: Your Name >>> > #+EMAIL: your-email@server.com >>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>> > both :tangle yes >>> > >>> > * Example of Org-Babel for R Literate Programming >>> > ** R text output >>> > A simple summary. >>> > #+begin_src R >>> > x <- rnorm(10) >>> > summary(x) >>> > #+end_src >>> > >>> > ** R graphics output >>> > Note we use the object =3Dx=3D generated in previous code block, than= ks to >>> > the header option =3D:session *R*=3D. The output graphics file is >>> > =3Da.png=3D. >>> > >>> > #+begin_src R :file a.png >>> > y <- rnorm(10) >>> > plot(x, y) >>> > #+end_src >>> > >>> > Same plot with larger dimension: >>> > >>> > #+begin_src R :file b.png :width 800 :height 800 >>> > plot(x, y) >>> > #+end_src >>> > >>> > >>> > Where do I wrong? >>> > >>> > Best >>> > Riccardo >>> > Hi, I'm trying to generate some figure with R, into an org sessio= n. >>> Firstly I use the code in the org site. The problem is that the code do= not >>> generate any figure. This is the code: >>> > #+TITLE:Test >>> > #+AUTHOR: Your Name >>> > #+EMAIL: mailto:your-email@server.com >>> > #+BABEL: :session *R* :cache yes :results output graphics :exports bo= th >>> :tangle yes >>> > >>> > * Example of Org-Babel for R Literate Programming >>> > ** R text output >>> > A simple summary. >>> > #+begin_src R >>> > x <- rnorm(10) >>> > summary(x) >>> > #+end_src >>> > >>> > ** R graphics output >>> > Note we use the object =3Dx=3D generated in previous code block, than= ks to >>> > the header option =3D:session *R*=3D. The output graphics file is >>> > =3Da.png=3D. >>> > >>> > #+begin_src R :file a.png >>> > y <- rnorm(10) >>> > plot(x, y) >>> > #+end_src >>> > >>> > Same plot with larger dimension: >>> > >>> > #+begin_src R :file b.png :width 800 :height 800 >>> > plot(x, y) >>> > #+end_src >>> > Where do I wrong?BestRiccardo >>> >>> -- >>> Thomas S. Dye >>> http://www.tsdye.com >>> >> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use= -Org-Babel-for-R.htmlBestR >> 2012/2/5 Thomas S. Dye Hi= Riccardo, >> >> >> This code appears to be outdated. =C2=A0I don't recall this code on = the org >> site. =C2=A0Could you send a URL? >> >> All the best, >> Tom >> >> Riccardo Romoli writes: >> >>> Hi, I'm trying to generate some figure with R, into an org session.= Firstly >>> I use the code in the org site. The problem is that the code do not >>> generate any figure. >>> >>> This is the code: >>> >>> #+TITLE:Test >>> #+AUTHOR: Your Name >>> #+EMAIL: mailto:your-email@server.com >>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>> both :tangle yes >>> >>> * Example of Org-Babel for R Literate Programming >>> ** R text output >>> A simple summary. >>> #+begin_src R >>> =C2=A0 x <- rnorm(10) >>> =C2=A0 summary(x) >>> #+end_src >>> >>> ** R graphics output >>> Note we use the object =3Dx=3D generated in previous code block, thanks= to >>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>> =3Da.png=3D. >>> >>> #+begin_src R =C2=A0:file a.png >>> =C2=A0 y <- rnorm(10) >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> Same plot with larger dimension: >>> >>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> >>> Where do I wrong? >>> >>> Best >>> Riccardo >>> Hi, I'm trying to generate some figure with R, into an org >>> session. Firstly I use the code in the org site. The problem is >>> that the code do not generate any figure. This is the code: >>> #+TITLE:Test >>> #+AUTHOR: Your Name >>> #+EMAIL: mailto:mailto:your-email@server.com >>> #+BABEL: :session *R* :cache yes :results output graphics :exports both= :tangle yes >>> >>> * Example of Org-Babel for R Literate Programming >>> ** R text output >>> A simple summary. >>> #+begin_src R >>> =C2=A0 x <- rnorm(10) >>> =C2=A0 summary(x) >>> #+end_src >>> >>> ** R graphics output >>> Note we use the object =3Dx=3D generated in previous code block, thanks= to >>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>> =3Da.png=3D. >>> >>> #+begin_src R =C2=A0:file a.png >>> =C2=A0 y <- rnorm(10) >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> Same plot with larger dimension: >>> >>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>> =C2=A0 plot(x, y) >>> #+end_src >>> Where do I wrong?BestRiccardo >> >> -- >> Thomas S. Dye >> http://www.tsdye.com >> --=20 Eric Schulte http://cs.unm.edu/~eschulte/