From: "Charles C. Berry" <cberry@tajo.ucsd.edu>
To: Andy Choens <andy.choens@gmail.com>
Cc: Org-mode ml <emacs-orgmode@gnu.org>
Subject: Re: Reproducible Research Template
Date: Wed, 5 Jan 2011 08:31:27 -0800 [thread overview]
Message-ID: <Pine.LNX.4.64.1101050807570.21556@tajo.ucsd.edu> (raw)
In-Reply-To: <1294170927.2599.110.camel@Yates>
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
prev parent reply other threads:[~2011-01-05 16:31 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-01-04 19:55 Reproducible Research Template Andy Choens
2011-01-05 16:24 ` Thomas S. Dye
2011-01-05 17:24 ` Andy Choens
2011-01-05 16:31 ` Charles C. Berry [this message]
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