4.3 KiB
rorg — R and org-mode
Objectives
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")
and (ess-execute "read.csv('tmp.csv')").
org-R
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 org-R-export-to-csv.
org-exp-blocks
RweaveOrg
NA
Evaluate R code in org and deal with output appropriately
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). Values assigned to in the global environment should be available to blocks of R code elsewhere in the org buffer.
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:
- output to screen for immediate viewing is possible
- 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).
Implementations
org-R
org-R does (1) if no output file is specified and (2) otherwise
org-exp-blocks
RweaveOrg
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: 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 bufferdblocks
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