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Re: [Orgmode] Reproducible Research Template


From: Charles C. Berry
Subject: Re: [Orgmode] Reproducible Research Template
Date: Wed, 5 Jan 2011 08:31:27 -0800

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
address@hidden                      UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901





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