org-mode/rorg.org

rorg — R and org-mode

• Objectives
  • Import data into R from org
    • Implementations
      • naive
      • org-R
      • org-exp-blocks
      • RweaveOrg
  • evaluate R code and make the output available for processing in an org buffer
  • evaluate R code and format the output for export
• Notes
  • Special editing and evaluation of source code in R blocks
    • Source code blocks
    • dblocks
    • R blocks
• tasks
• buffer dictionary

Please feel free to change the layout of this file, I'm just putting this here to get things started.

Objectives

Import data into 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") and (ess-exec "read.csv('tmp.csv')").

org-R

org-R-export-to-csv

org-exp-blocks

RweaveOrg

NA

evaluate R code and make the output available for processing in an org buffer

evaluate R code and format the output for export

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 really what these blocks contain is 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.

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'.

,## 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

dblocks

dblocks are useful because org-mode will automatically call `org-dblock-write:dblock-type' where dblock-type is the string following the #+BEGIN: portion of the line.

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.

R blocks

In developing RweaveOrg, Austin created org-sweave.el. This allows for the kind of blocks shown in testing.Rorg. These blocks have the advantage of accepting options to the Sweave preprocessor following the #+BEGIN_R declaration.

tasks

buffer dictionary

LocalWords: DBlocks dblocks