From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Charles C. Berry" Subject: Re: Reproducible Research Template Date: Wed, 5 Jan 2011 08:31:27 -0800 Message-ID: References: <1294170927.2599.110.camel@Yates> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Return-path: Received: from [140.186.70.92] (port=33002 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1PaWHC-0008Vr-2w for emacs-orgmode@gnu.org; Wed, 05 Jan 2011 11:31:56 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1PaWH9-0001od-9h for emacs-orgmode@gnu.org; Wed, 05 Jan 2011 11:31:54 -0500 Received: from tajo.ucsd.edu ([137.110.122.165]:53776) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1PaWH9-0001j8-42 for emacs-orgmode@gnu.org; Wed, 05 Jan 2011 11:31:51 -0500 In-Reply-To: <1294170927.2599.110.camel@Yates> 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: Andy Choens Cc: Org-mode ml On Tue, 4 Jan 2011, Andy Choens wrote: > I am developing a reproducible research template for R. I am trying to > implement most of a research "compendium" in org. I say "most" because I > am going to allow the actual data to exist outside of org, simply > because most of the data I work with is relational or very large, which > makes storage in plain text problematic or impossible. > > Has anyone ever implemented a reproducible research template in org that > I can look at? I looked at the stuff on Worg and there are examples of a > project, but not a template. > > In a nutshell, I am trying to do two things. > 1) Provide a structure for reproducible research / programming ; > 2) Provide a small set of helper functions. > > But, I don't want the helper functions to get in the way. I have > considered two options: > 1) Store the example code / template stuff in subheadings > 2) Store the example code / template stuff in an external file. One version of 'store the example code / template stuff' externally is to create an R package that holds the helper functions and whose example()s and/or demo()s show off the capabilities of helper functions. The R package 'inst' directory can hold miscellaneous files including suitable *.org templates, SQL snippets, etc. for different kinds of research projects. Then carrying out the research project would consist of starting R, require()-ing that package, issuing a command like choose.template( my.type.of.project, "myLocalWorkfile.org" , my.options ) (which would generate the starting template as myLocalWortkfile.org), and carrying on. HTH, Chuck p.s. You probably know that you can master the R package in a *.org file, but just in case: http://orgmode.org/worg/org-contrib/babel/examples/Rpackage.html#sec-6_1 > > Using subheadings is tempting, but I'm afraid that > org-babel-execute-buffer would cause problems for users who don't use > all of the template functions. > > Using an external file, similar to the Lobrary of Babel is also > tempting. It would allow me to make a cleaner template for structure and > still allow users to access any helper functions. Is there a way to link > to an external file, other than the Library of Babel? If so, how do I do > this? > > Does anyone have any opinions about hiding/linking/importing example > code in a template? > > I certainly appreciate any thoughts. > > --andy > Charles C. Berry Dept of Family/Preventive Medicine cberry@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901