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2009-02-05 23:04:09 +00:00
#+TITLE: rorg --- R and org-mode
#+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE
* Commentary
** Eric <2009-02-06 Fri 15:41>
I think we're getting close to a comprehensive set of objectives
(although since you two are the real R user's I leave that decision up
to you). Once we've agreed on a set of objectives and agreed on at
least to broad strokes of implementation, I think we should start
listing out and assigning tasks.
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* Objectives
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** Send data to R from org
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.
*** Implementations
**** naive
Naive implementation would be to use =(org-export-table "tmp.csv")=
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and =(ess-execute "read.csv('tmp.csv')")=.
**** org-R
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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 [[file:existing_tools/org-R.el::defun%20org%20R%20export%20to%20csv%20csv%20file%20options][org-R-export-to-csv]].
**** org-exp-blocks
org-exp-blocks uses [[org-interblock-R-command-to-string]] to send
commands to an R process running in a comint buffer through ESS.
org-exp-blocks has no support for dumping table data to R process, or
vice versa.
**** RweaveOrg
NA
** Evaluate R code from org and deal with output appropriately
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*** vector output
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)
Agreed, if we can convert the vector data to lists then we can use
the many orgtbl-to-* functions to convert the list to whatever
output format we desire. See `orgtbl-to-orgtbl, `orgtbl-to-latex',
`orgtbl-to-html', `orgtbl-to-csv', etc...
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**** Implementations
***** org-R
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).
***** org-exp-blocks
***** RweaveOrg
*** graphical output
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:
1. output to screen for immediate viewing is possible
2. 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).
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**** Implementations
***** org-R
org-R does (1) if no output file is specified and (2) otherwise
***** org-exp-blocks
org-exp-blocks tries to do 2, but I don't think that part was
every really working
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***** RweaveOrg
** Evaluate R code on export
At first I was leaning towards leaving the exporting to Sweave, but it
seems that once we have evaluation or R working, it will not be
difficult to implement full evaluation of R blocks, one-liners, and
creation of R graphics on export directly in elisp.
I think that this would be worth the effort since it would eliminate
the need for using Sweave, and would allow for exportation to any
target format supported by org-mode.
* Notes
** Special editing and evaluation of source code in R blocks
Unfortunately org-mode how two different block types, both useful.
In developing RweaveOrg, a third was introduced.
Eric is leaning towards using the =#+begin_src= blocks, as that is
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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.
Note that upper and lower case are not relevant in block headings.
*** PROPOSED R-block proposal
I (Eric) propose that we use the syntax of source code blocks as they
currently exist in org-mode with the addition of *evaluation*,
*header-arguments*, *exportation*, *single-line-blocks*, and
*references-to-table-data*.
1) *evaluation*: These blocks can be evaluated through =\C-c\C-c= with
a slight addition to the code already present and working in
[[file:existing_tools/org-eval-light.el][org-eval-light.el]]. All we should need to add for R support would
be an appropriate entry in [[org-eval-light-interpreters]] with a
corresponding evaluation function. For an example usinga
org-eval-light see [[* src block evaluation w/org-eval-light]].
2) *header-arguments*: These can be implemented along the lines of
Austin's header arguments in [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]].
3) *exportation*: Should be as similar as possible to that done by
Sweave, and hopefully can re-use some of the code currently present
in [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]].
4) *single-line-blocks*: It seems that it is useful to be able to
place a single line of R code on a line by itself. Should we add
syntax for this similar to Dan's =#+R:= lines? I would lean
towards something here that can be re-used for any type of source
code in the same manner as the =#+begin_src R= blocks, maybe
=#+src_R=?
5) *references-to-table-data*: I get this impression that this is
vital to the efficient use of R code in an org file, so we should
come up with a way to reference table data from a single-line-block
or from an R source-code block. It looks like Dan has already done
this in [[file:existing_tools/org-R.el][org-R.el]].
What do you think? Does this accomplish everything we want to be able
to do with embedded R source code blocks?
**** src block evaluation w/org-eval-light
here's an example using org-eval-light.el
first load the org-eval-light.el file
[[elisp:(load (expand-file-name "org-eval-light.el" (expand-file-name "existing_tools" (file-name-directory buffer-file-name))))]]
then press =\C-c\C-c= inside of the following src code snippet. The
results should appear in a comment immediately following the source
code block. It shouldn't be too hard to add R support to this
function through the `org-eval-light-interpreters' variable.
#+begin_src shell
date
#+end_src
*** Source code blocks
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.
Source code blocks look like the following and allow for the
special editing of code inside of the block through
`org-edit-special'.
#+BEGIN_SRC r
,## hit C-c ' within this block to enter a temporary buffer in r-mode.
,## while in the temporary buffer, hit C-c C-c on this comment to
,## evaluate this block
a <- 3
a
,## hit C-c ' to exit the temporary buffer
#+END_SRC
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*** dblocks
dblocks are useful because org-mode will automatically call
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`org-dblock-write:dblock-type' where dblock-type is the string
following the =#+BEGIN:= portion of the line.
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dblocks look like the following and allow for evaluation of the
code inside of the block by calling =\C-c\C-c= on the header of
the block.
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#+BEGIN: dblock-type
#+END:
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*** R blocks
In developing RweaveOrg, Austin created [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]]. This
allows for the kind of blocks shown in [[file:existing_tools/RweaveOrg/testing.Rorg][testing.Rorg]]. These blocks
have the advantage of accepting options to the Sweave preprocessor
following the #+BEGIN_R declaration.
** Interaction with the R process
We should take care to implement this in such a way that all of the
different components which have to interactive with R including:
- evaluation of source code blocks
- automatic evaluation on export
- evaluation of \R{} snippets
- evaluation of single source code lines
- sending/recieving vector data
I think we currently have two implementation of interaction with R
processes; [[file:existing_tools/org-R.el][org-R.el]] and [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]]. We should be sure to take
the best of each of these approaches.
* Tasks
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* buffer dictionary
LocalWords: DBlocks dblocks