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<h1 class="title">rorg &mdash; R and org-mode</h1>


<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1 Objectives </a>
<ul>
<li><a href="#sec-1.1">1.1 Send data to R from org </a>
<ul>
<li><a href="#sec-1.1.1">1.1.1 Implementations </a></li>
</ul>
</li>
<li><a href="#sec-1.2">1.2 evaluate R code from org and deal with output appropriately </a>
<ul>
<li><a href="#sec-1.2.1">1.2.1 vector output </a></li>
<li><a href="#sec-1.2.2">1.2.2 graphical output </a></li>
</ul></li>
</ul>
</li>
<li><a href="#sec-2">2 Notes </a>
<ul>
<li><a href="#sec-2.1">2.1 Special editing and evaluation of source code in R blocks </a>
<ul>
<li><a href="#sec-2.1.1">2.1.1 Source code blocks </a></li>
<li><a href="#sec-2.1.2">2.1.2 dblocks </a></li>
<li><a href="#sec-2.1.3">2.1.3 R blocks </a></li>
</ul></li>
</ul>
</li>
<li><a href="#sec-3">3 tasks </a></li>
<li><a href="#sec-4">4 buffer dictionary </a></li>
</ul>
</div>
</div>

<div id="outline-container-1" class="outline-2">
<h2 id="sec-1">1 Objectives </h2>
<div id="text-1">


</div>

<div id="outline-container-1.1" class="outline-3">
<h3 id="sec-1.1">1.1 Send data to R from org </h3>
<div id="text-1.1">

<p>Org-mode includes orgtbl-mode, an extremely convenient way of using
tabular data in a plain text file.  Currently, spreadsheet
functionality is available in org tables using the emacs package
calc.  It would be a boon both to org users and R users to allow
org tables to be manipulated with the R programming language.  Org
tables give R users an easy way to enter and display data; R gives
org users a powerful way to perform vector operations, statistical
tests, and visualization on their tables.
</p>

</div>

<div id="outline-container-1.1.1" class="outline-4">
<h4 id="sec-1.1.1">1.1.1 Implementations </h4>
<div id="text-1.1.1">

<ul>
<li id="sec-1.1.1.1">naive <br/>
Naive implementation would be to use <code>(org-export-table "tmp.csv")</code>
and <code>(ess-execute "read.csv('tmp.csv')")</code>.  
</li>
<li id="sec-1.1.1.2">org-R <br/>
org-R passes data to R from two sources: org tables, or csv
files. Org tables are first exported to a temporary csv file
using <a href="existing_tools/org-R.el">org-R-export-to-csv</a>.
</li>
<li id="sec-1.1.1.3">org-exp-blocks <br/>
</li>
<li id="sec-1.1.1.4">RweaveOrg <br/>
NA

</li>
</ul>
</div>
</div>

</div>

<div id="outline-container-1.2" class="outline-3">
<h3 id="sec-1.2">1.2 evaluate R code from org and deal with output appropriately </h3>
<div id="text-1.2">


</div>

<div id="outline-container-1.2.1" class="outline-4">
<h4 id="sec-1.2.1">1.2.1 vector output </h4>
<div id="text-1.2.1">

<p>When R code evaluation generates vectors and 2-dimensional arrays,
this should be formatted appropriately in org buffers (orgtbl-mode) as well
as in export targets (html, latex)
</p><ul>
<li id="sec-1.2.1.1">Implementations <br/>
<ul>
<li id="sec-1.2.1.1.1">org-R <br/>
org-R converts R output (vectors, or matrices / 2d-arrays) to an
org table and stores it in the org buffer, or in a separate org
file (csv output would also be perfectly possible).
</li>
<li id="sec-1.2.1.1.2">org-exp-blocks <br/>
</li>
<li id="sec-1.2.1.1.3">RweaveOrg <br/>
</li>
</ul>
</li>
</ul>
</div>

</div>

<div id="outline-container-1.2.2" class="outline-4">
<h4 id="sec-1.2.2">1.2.2 graphical output </h4>
<div id="text-1.2.2">

<p>R can generate graphical output on a screen graphics device
(e.g. X11, quartz), and in various standard image file formats
(png, jpg, ps, pdf, etc). When graphical output is generated by
evaluation of R code in Org, at least the following two things are desirable:
</p><ol>
<li>
output to screen for immediate viewing is possible
</li>
<li>
graphical output to file is linked to appropriately from the
org file This should have the automatic consequence that it is
included appropriately in subsequent export targets (html,
latex).
</li>
</ol>
<ul>
<li id="sec-1.2.2.1">Implementations <br/>
<ul>
<li id="sec-1.2.2.1.1">org-R <br/>
org-R does (1) if no output file is specified and (2) otherwise
</li>
<li id="sec-1.2.2.1.2">org-exp-blocks <br/>
</li>
<li id="sec-1.2.2.1.3">RweaveOrg <br/>


</li>
</ul>
</li>
</ul>
</div>
</div>
</div>

</div>

<div id="outline-container-2" class="outline-2">
<h2 id="sec-2">2 Notes </h2>
<div id="text-2">


</div>

<div id="outline-container-2.1" class="outline-3">
<h3 id="sec-2.1">2.1 Special editing and evaluation of source code in R blocks </h3>
<div id="text-2.1">

<p>Unfortunately org-mode how two different block types, both useful.
In developing RweaveOrg, a third was introduced.
</p>
<p>
Eric is leaning towards using the <code>#+begin_src</code> blocks, as that is
really what these blocks contain: source code.  Austin believes
that specifying export options at the beginning of a block is
useful functionality, to be preserved if possible.
</p>
<p>
Note that upper and lower case are not relevant in block headings.
</p>

</div>

<div id="outline-container-2.1.1" class="outline-4">
<h4 id="sec-2.1.1">2.1.1 Source code blocks </h4>
<div id="text-2.1.1">

<p>Org has an extremely useful method of editing source code and
examples in their native modes.  In the case of R code, we want to
be able to use the full functionality of ESS mode, including
interactive evaluation of code.
</p>
<p>
Source code blocks look like the following and allow for the
special editing of code inside of the block through
`org-edit-special'.
</p>


<pre class="src src-r">

,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">hit C-c ' within this block to enter a temporary buffer in r-mode.
</span>
,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">while in the temporary buffer, hit C-c C-c on this comment to
</span>,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">evaluate this block
</span>a <span style="color: #98fb98;">&lt;-</span> 3
a

,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">hit C-c ' to exit the temporary buffer
</span></pre>


</div>

</div>

<div id="outline-container-2.1.2" class="outline-4">
<h4 id="sec-2.1.2">2.1.2 dblocks </h4>
<div id="text-2.1.2">

<p>dblocks are useful because org-mode will automatically call
`org-dblock-write:dblock-type' where dblock-type is the string
following the <code>#+BEGIN:</code> portion of the line.
</p>
<p>
dblocks look like the following and allow for evaluation of the
code inside of the block by calling <code>\C-c\C-c</code> on the header of
the block.  
</p>

</div>

</div>

<div id="outline-container-2.1.3" class="outline-4">
<h4 id="sec-2.1.3">2.1.3 R blocks </h4>
<div id="text-2.1.3">

<p>In developing RweaveOrg, Austin created <a href="existing_tools/RweaveOrg/org-sweave.el">org-sweave.el</a>.  This
allows for the kind of blocks shown in <a href="existing_tools/RweaveOrg/testing.Rorg">testing.Rorg</a>.  These blocks
have the advantage of accepting options to the Sweave preprocessor
following the #+BEGIN<sub>R</sub> declaration.
</p>

</div>
</div>
</div>

</div>

<div id="outline-container-3" class="outline-2">
<h2 id="sec-3">3 tasks </h2>
<div id="text-3">


</div>

</div>

<div id="outline-container-4" class="outline-2">
<h2 id="sec-4">4 buffer dictionary </h2>
<div id="text-4">

<p>LocalWords:  DBlocks dblocks
</p></div>
</div>
<div id="postamble"><p class="author"> Author: Dan
<a href="mailto:dan@Tichodroma">&lt;dan@Tichodroma&gt;</a>
</p>
<p class="date"> Date: 2009-02-05 21:16:20 EST</p>
<p>HTML generated by org-mode 6.20f in emacs 22</p>
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