From mboxrd@z Thu Jan 1 00:00:00 1970 From: Dan Davison Subject: Re: Org babel R Help Date: Fri, 19 Mar 2010 10:30:30 -0400 Message-ID: <87mxy4wfi1.fsf@stats.ox.ac.uk> References: <20100319210128.15640tev1fryn3h4@www.studentmail.otago.ac.nz> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from mailman by lists.gnu.org with tmda-scanned (Exim 4.43) id 1NsdDn-00010d-AH for emacs-orgmode@gnu.org; Fri, 19 Mar 2010 10:30:43 -0400 Received: from [140.186.70.92] (port=49970 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1NsdDi-000107-Rp for emacs-orgmode@gnu.org; Fri, 19 Mar 2010 10:30:40 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1NsdDf-00080K-V8 for emacs-orgmode@gnu.org; Fri, 19 Mar 2010 10:30:38 -0400 Received: from markov.stats.ox.ac.uk ([163.1.210.1]:58018) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1NsdDf-0007zt-OL for emacs-orgmode@gnu.org; Fri, 19 Mar 2010 10:30:35 -0400 In-Reply-To: <20100319210128.15640tev1fryn3h4@www.studentmail.otago.ac.nz> (Joseph Cole's message of "Fri, 19 Mar 2010 21:01:28 +1300") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Joseph Cole Cc: emacs-orgmode@gnu.org Joseph Cole writes: > I've been struggling with a few aspects of org babel R: > > 1) src_R surrounds output with ==. > > E.g. src_R{1+1} gives =2= > > I would expect it to just give 2. Because it surrounds the output with > equals signs, this means you are unable to use the output in latex > equations, general text or tables as it's ugly. Hi Joseph, If you use ':results raw', then the results will be inserted without the surrounding '='. You will need to pull the latest git head as I just fixed a bug regarding that. So you could use src_R[:results raw]{1+1} but to make it less clumsy you could configure org-babel-default-inline-header-args, e.g. (setq org-babel-default-inline-header-args (org-babel-merge-params org-babel-default-inline-header-args '((:results . "raw")))) after which \begin{equation} 1 + src_R{1+1} = 3 \end{equation} exports to latex as \begin{equation} 1 + 2 = 3 \end{equation} As for the default behaviour, the == declares that the contents should be formatted fixed-width on export. Normally in latex export that results in \texttt{}, but I see that inside a begin_equation the == remain. I wonder whether that could be argued to be an org-mode latex exporter bug? > > Where should I start looking to fix this? I'm a lisp novice but happy > to learn. org-babel-exp.el > > 2) Width/Height exports for R graphics output. Do they work? > > I've tried a lot of combinations of :width and :height as exports, and > they don't seem to work at all. I've tried small numbers (1-10), large > numbers (100-2000) and numbers prefixed by "cm" with no luck. Hmm, I'm not seeing a problem here. It works for me with both png and pdf output. E.g. #+begin_src R :file z.pdf :width 20 :height 40 :exports both plot(1:10) #+end_src What image format (i.e. R graphics device) are you using? Can you post an example block that is not working? The values for :width and :height will be passed straight on to the graphics device, so their meaning depends on which graphics device is being used in R. > > I know I can use #+attr_latex: width=15cm. > > 3) R-graphics quality > > I can't seem to find any examples of how to set the R graphics output > quality, and nothing I try seems to alter the result (using :quality). I'm not sure what you mean by "R graphics output quality". The section "Graphical output" in http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php describes how to pass arguments to the R graphics devices. In addition to the ones that org-babel knows about like :width, you can pass arbitrary extra arguments to the R device using :R-dev-args. > > Are there any publication quality r-graphics examples I could take a > look at, as I've been unable to find any on google. You mean using org-babel or just using R? Hope that helps. Dan > > > > _______________________________________________ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode