Improving this document noexport

DONE Document slice indexing of tables

DONE Document synonymous alternatives

DONE Describe useful functions

`org-babel-execute-buffer'
`org-babel-execute-subtree'

DONE Language support

DONE Document noweb references

DONE Why is

TODO Developments

org-babel can now cache the results of source block execution to avoid

(setq org-babel-default-header-args (cons '(:cache) (assq-delete-all :nocache org-babel-default-header-args)))

It is now possible to fold results by tabbing on the beginning of the

(add-hook 'org-mode-hook 'org-babel-result-hide-all)

allow header argument values to be lisp forms, for example the

:file (format "%s/images/pca-scatter.png" dir)

DONE Useful variables

TODO Language specific header arguments

# -*- org-src-preserve-indentation: t -*-
org-babel: capture graphical output from R

If a [:file filename.ext] header arg is provided, then all graphical output from the source block is captured on disk, and output of the source block is a link to the resulting file, as with the graphics-only languages such as gnuplot, ditaa, dot, asymptote. An attempt is made to find a graphics device corresponding to the file extension (currently .png, .jpg, .jpeg, .tiff, .bmp, .pdf, .ps, .postscript are recognised); if that fails, png format output is created.

Additionally, values for several arguments to the R graphics device can be passed using header args:

:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal

Arguments to the R graphics device that are not supported as header args can be passed as a string in R argument syntax, using the header arg :R-dev-args

An example block is (although both bg and fg can be passed directly as header args)

\#+begin_src R :file z.pdf :width 8 :height 8 :R-dev-args bg="olivedrab", fg="hotpink" plot(matrix(rnorm(100), ncol=2), type="l") \#+end_src

Yes, I think we do want a version of this for python and ruby et al. In

def savetofile(result, filename): with open(filename, 'w') as f: f.write(str(result)) savetofile(78, 'outfile.txt') 55

This functionality is now available for ruby & python in branch ded-babel of git://orgmode.org/org-mode/babel.git.

So here, if you specify :file ruby/python blindly outputs a link to , regardless of the contents of the code. Responsibility for creating useful contents of lies with the code. Notice that with this you have to specify the output file twice: once as an org-babel directive, and once in the python code. This is in contrast to the graphics languages (dot, ditaa, asymptote), where the results automatically get sent to the file specified by :file. The same is also true now for graphical output from R.

The difference with python, ruby et al is that they might create file output in a variety of ways which we can't anticipate, so we can't automatically send output to the file. In contrast, the graphics language always create file output and always do it in the same way. [And in R it is possible to divert all graphical output to file] A possible extension of the above might be to use a "magic variable" so that a python variable is created e.g. org_babel_output_file that always holds a string corresponding to the file specified by :file. Eric may have further ideas / views here.

DONE What function is bound to C-c '?

Introduction

this document notes two different functions

Babel is about letting work together. Programming languages live in blocks inside natural language Org-mode documents. A piece of data may pass from a table to a Python code block, then maybe move on to an R code block, and finally end up embedded as a value in the middle of a paragraph or possibly pass through a gnuplot code block and end up as a plot embedded in the document.

Through extending Org-mode with several features for editing exporting and executing source code Babel turns Org-mode into a tool for both Literate Programming and Reproducible Research.

Babel augments Org-mode support for code blocks by providing:

interactive and on-export execution of code blocks;
code blocks as functions that can be parameterised, refer to
export to files for literate programming.

Overview

Babel provides new features on a few different fronts, and different people may want to start in different places.

Using 'src' blocks in Org mode ::
Executing code ::
Literate Programming ::

All of these use cases, as well as exhaustive documentation of the features of Babel are covered in the Working with Source Code section of the Org manual.

Initial Configuration

:PROPERTIES: :CUSTOM_ID: getting-started :results: silent :END:

If you have a working Emacs installation, then getting started with Babel is a simple process.

1) If you are running Emacs24 a current version of Org-mode with Babel is already available by default. Otherwise, it is strongly recommended that you update to the latest version of Org-mode by keeping current with Org-mode development. As of Org-mode 7.0, Babel is included as part of Org-mode.

2) Optionally activate the subset of languages that you will want to execute with Babel. See instructions. Emacs Lisp is activated by default so this step can be skipped for now and all emacs-lisp examples will still work as expected.

3) If you have made any changes don't forget to evaluate your modified .emacs.

Code Blocks

:PROPERTIES: :CUSTOM_ID: source-code-blocks :END:

Code Blocks in Org

:PROPERTIES: :CUSTOM_ID: source-code-blocks-org :END:

Babel is all about code blocks in Org-mode. If you are unfamiliar with the notion of a code block in Org-mode, where they are called 'src' blocks, please have a look at the Org-mode manual before proceeding.

Code blocks in supported languages can occur anywhere in an Org-mode file. Code blocks can be entered directly into the Org-mode file, but it is often easier to enter code with the function org-edit-src-code, which is called with the keyboard shortcut, C-c '. This places the code block in a new buffer with the appropriate mode activated.

,#+begin_src language org-switches ,body ,#+end_src

For example, a code block of ruby code looks like this in an Org-mode file:

,#+begin_src ruby ,require 'date' ,"This file was last evaluated on #{Date.today}" ,#+end_src

Code Blocks in Babel

:PROPERTIES: :CUSTOM_ID: source-code-blocks-babel :END:

Babel adds some new elements to code blocks. The basic structure becomes:

,#+begin_src language org-switches header-arguments ,body ,#+end_src

language: The language of the code in the source-code block. Valid
header-arguments: Header arguments control many facets of the
body: The source code to be evaluated. An important key-binding

Source Code Execution

:PROPERTIES: :CUSTOM_ID: source-code-execution :END:

Babel executes code blocks for interpreted languages such as shell, python, R, etc. by passing code to the interpreter, which must be installed on your system. You control what is done with the results of execution.

Ruby

Here are examples of code blocks in three different languages, followed by their output. If you are viewing the Org-mode version of this document in Emacs, place point anywhere inside a block and press C-c C-c to run the code¹ (and feel free to alter it!). In the Org-mode file:

#+begin_src ruby
"This file was last evaluated on #{Date.today}"
#+end_src

HTML export of code:

"This file was last evaluated on #{Date.today}"

HTML export of the resulting string:

This file was last evaluated on 2009-08-09

Shell

In the Org-mode file:

#+begin_src sh
  echo "This file takes up `du -h org-babel.org |sed 's/\([0-9k]*\)[ ]*org-babel.org/\1/'`"
#+end_src

HTML export of code:

echo "This file takes up `du -h org-babel.org |sed 's/$[0-9k]*$[ ]*org-babel.org/\1/'`"

HTML export of the resulting string:

This file takes up  36K

R

What are the most common words in this file? In the Org-mode file:

#+begin_src R :colnames yes
  words <- tolower(scan("intro.org", what="", na.strings=c("|",":")))
  t(sort(table(words[nchar(words) > 3]), decreasing=TRUE)[1:10])
#+end_src

HTML export of code:

words <- tolower(scan("intro.org", what="", na.strings=c("|",":"))) t(sort(table(words[nchar(words) > 3]), decreasing=TRUE)[1:10])

code	org-mode	#+end_src	#+begin_src	block	with	babel	that	#+name:	this
85	60	47	44	40	38	35	34	33	33

ditaa

In the Org-mode file:

#+begin_src ditaa :file blue.png :cmdline -r
+---------+
| cBLU    |
|         |
|    +----+
|    |cPNK|
|    |    |
+----+----+
#+end_src

HTML export of code:

cBLU

+----
	cPNK

HTML export of the resulting image:

Capturing the Results of Code Evaluation

`:results value` (functional mode)

:PROPERTIES: :CUSTOM_ID: results :END: Babel provides two fundamentally different modes for capturing the results of code evaluation: functional mode and scripting mode. The choice of mode is specified by the :results header argument. :PROPERTIES: :CUSTOM_ID: results-value :END: The 'result' of code evaluation is the value of the last statement in the code block. In functional mode, the code block is a function with a return value. The return value of one code block can be used as input for another code block, even one in a different language. In this way, Babel becomes a meta-programming language. If the block returns tabular data (a vector, array or table of some sort) then this will be held as an Org-mode table in the buffer. This setting is the default.

For example, consider the following block of python code and its output.

import time print("Hello, today's date is %s" % time.ctime()) print('Two plus two is') return 2 + 2

Notice that, in functional mode, the output consists of the value of the last statement and nothing else.

`:results output` (scripting mode)

:PROPERTIES: :CUSTOM_ID: results-output :END:

In scripting mode, Babel captures the text output of the code block and places it in the Org-mode buffer. It is called scripting mode because the code block contains a series of commands, and the output of each command is returned. Unlike functional mode, the code block itself has no return value apart from the output of the commands it contains.²

Consider the result of evaluating this code block with scripting mode.

import time print("Hello, today's date is %s" % time.ctime()) print('Two plus two is') 2 + 2

Hello, today's date is Wed Nov 11 18:50:36 2009
Two plus two is

Here, scripting mode returned the text that python sent to stdout. Because the code block doesn't include a print() statement for the last value, (2 + 2), 4 does not appear in the results.

Session-based Evaluation

For some languages, such as python, R, ruby and shell, it is possible to run an interactive session as an "inferior process" within Emacs. This means that an environment is created containing data objects that persist between different source code blocks. Babel supports evaluation of code within such sessions with the :session header argument. If the header argument is given a value then that will be used as the name of the session. Thus, it is possible to run separate simultaneous sessions in the same language.

Session-based evaluation is particularly useful for prototyping and debugging. The function org-babel-pop-to-session can be used to switch to the session buffer.

Once a code block is finished, it is often best to execute it outside of a session, so the state of the environment in which it executes will be certain.

With R, the session will be under the control of Emacs Speaks Statistics as usual, and the full power of ESS is thus still available, both in the R session, and when switching to the R code edit buffer with C-c '.

Arguments to Code Blocks

:PROPERTIES: :CUSTOM_ID: arguments-to-source-code-blocks :END: Babel supports parameterisation of code blocks, i.e., arguments can be passed to code blocks, which gives them the status of functions. Arguments can be passed to code blocks in both functional and scripting modes.

Simple example of using a code block as a function

First let's look at a very simple example. The following source code block defines a function, using python, that squares its argument.

return x*x

In the Org-mode file, the function looks like this:

#+name: square
#+header: :var x=0
#+begin_src python
return x*x
#+end_src

Now we use the source block:

#+call: square(x=6)

(for information on the call syntax see Library of Babel)

A more complex example using an Org-mode table as input

In this example we define a function called fibonacci-seq, using Emacs Lisp. The function fibonacci-seq computes a Fibonacci sequence. The function takes a single argument, in this case, a reference to an Org-mode table.

Here is the Org-mode table that is passed to =fibonacci-seq=:

1	2	3	4	5	6	7	8	9	10
2	4	6	8	10	12	14	16	18	20

The table looks like this in the Org-mode buffer:

#+tblname: fibonacci-inputs
| 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
| 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |

The Emacs Lisp source code:

(defun fibonacci (n) (if (or (= n 0) (= n 1)) n (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))

(mapcar (lambda (row) (mapcar #'fibonacci row)) fib-inputs)

In the Org-mode buffer the function looks like this:

#+name: fibonacci-seq
#+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
  (defun fibonacci (n)
    (if (or (= n 0) (= n 1))
        n
      (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))

  (mapcar (lambda (row)
            (mapcar #'fibonacci row)) fib-inputs)
#+end_src

The return value of fibonacci-seq is a table:

1	1	2	3	5	8	13	21	34	55
1	3	8	21	55	144	377	987	2584	6765

In-line Code Blocks

Code can be evaluated in-line using the following syntax:

Without header args: src_lang{code} or with header args: src_lang[args]{code},
for example src_python[:session]{10*x}, where x is a variable existing in the
python session.

Code Block Body Expansion

Babel "expands" code blocks prior to evaluation, i.e., the evaluated code comprises the code block contents augmented with code that assigns referenced data to variables. It is possible to preview expanded contents, and also to expand code during tangling. Expansion takes into account header arguments and variables.

preview: C-c M-b p is bound to org-babel-expand-src-block. It

tangling: The expanded body can be tangled. Tangling this way includes

One possible use for tangling expanded code block is for emacs initialization. Values such as user names and passwords can be stored in headline properties or in tables. The =:no-expand= header argument can be used to inhibit expansion of a code block during tangling.

Here is an example of a code block and its resulting expanded body.

The data are kept in a table:

username	john-doe
password	abc123

The code block refers to the data table:

(setq my-special-username (first (first data))) (setq my-special-password (first (second data)))

With point inside the code block, C-c M-b p expands the contents:

(let ((data (quote (("john-doe") ("abc123"))))) (setq my-special-username (first (first data))) (setq my-special-password (first (second data))) )

A Meta-programming Language for Org-mode

:PROPERTIES: :CUSTOM_ID: meta-programming-language :END:

Because the return value of a function written in one language can be passed to a function written in another language, or to an Org-mode table, which is itself programmable, Babel can be used as a meta-functional programming language. With Babel, functions from many languages can work together. You can mix and match languages, using each language for the tasks to which it is best suited.

For example, let's take some system diagnostics in the shell and graph them with R.

Create a code block, using shell code, to list

#+name: directories

#+begin_src sh :results replace cd ~ && du -sc * |grep -v total #+end_src

72	"Desktop"
12156104	"Documents"
3482440	"Downloads"
2901720	"Library"
57344	"Movies"
16548024	"Music"
120	"News"
7649472	"Pictures"
0	"Public"
152224	"Sites"
8	"System"
56	"bin"
3821872	"mail"
10605392	"src"
1264	"tools"

A function, written with a single line of R code, plots the data

In the Org-mode file:

#+name: directory-pie-chart(dirs = directories)
#+begin_src R :session R-pie-example :file ../../images/babel/dirs.png
  pie(dirs[,1], labels = dirs[,2])
#+end_src

HTML export of code:

pie(dirs[,1], labels = dirs[,2])

Using Code Blocks in Org Tables

:PROPERTIES: :CUSTOM_ID: spreadsheet :END:

In addition to passing data from tables as arguments to code blocks, and storing results as tables, Babel can be used in a third way with Org-mode tables. First note that Org-mode's existing spreadsheet functionality allows values in cells to be computed automatically from the values of other cells, using a =#+TBLFM= formula line. In this way, table computations can be carried out using calc and emacs lisp.

What Babel adds is the ability to use code blocks (in whatever language) in the #+TBLFM line to perform the necessary computation.

Example 1: Data Summaries Using R

As a simple example, we'll fill in a cell in an Org-mode table with the average value of a few numbers. First, let's make some data. The following source block creates an Org-mode table filled with five random numbers between 0 and 1.

#+name: tbl-example-data
#+begin_src R
runif(n=5, min=0, max=1)
#+end_src

0.836685163900256

0.696652316721156

0.382423302158713

0.987541858805344

0.994794291909784

Now we define a source block to calculate the mean of a table column.

In the Org-mode file:

#+name: R-mean
#+begin_src R :var x=""
colMeans(x)
#+end_src

HTML export of code:

colMeans(x)

Finally, we create the table which is going to make use of the R code. This is done using the org-sbe ('source block evaluate') macro in the table formula line.

In the Org-mode file:

#+tblname: summaries
|              mean |
|-------------------|
| 0.779619386699051 |
#+TBLFM: @2$1='(org-sbe "R-mean" (x "tbl-example-data()"))

HTML export of code:

mean
0.00

To recalculate the table formula, use C-u C-c C-c in the table. Notice that as things stand the calculated value doesn't change, because the data (held in the table above named =tbl-example-data=) are static. However, if you delete that data table, then the reference will be interpreted as a reference to the source block responsible for generating the data; each time the table formula is recalculated the source block will be evaluated again, and therefore the calculated average value will change.

Example 2: Babel Test Suite

While developing Babel, we used a suite of tests implemented as a large Org-mode table. To run the entire test suite we simply evaluate the table with C-u C-c C-c: all of the tests are run, the results are compared with expectations, and the table is updated with results and pass/fail statistics.

Here's a sample of our test suite.

In the Org-mode file:

#+TBLNAME: org-babel-tests
| functionality    | block        | arg |    expected |     results | pass |
|------------------+--------------+-----+-------------+-------------+------|
| basic evaluation |              |     |             |             | pass |
|------------------+--------------+-----+-------------+-------------+------|
| emacs lisp       | basic-elisp  |   2 |           4 |           4 | pass |
| shell            | basic-shell  |     |           6 |           6 | pass |
| ruby             | basic-ruby   |     |   org-babel |   org-babel | pass |
| python           | basic-python |     | hello world | hello world | pass |
| R                | basic-R      |     |          13 |          13 | pass |
#+TBLFM: $5='(if (= (length $3) 1) (sbe $2 (n $3)) (sbe $2)) :: $6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))

HTML export of code:

functionality	block	arg	expected	results	pass
basic evaluation					pass
emacs lisp	basic-elisp	2	4	4	pass
shell	basic-shell		6	6	pass
ruby	basic-ruby		org-babel	org-babel	pass
python	basic-python		hello world	hello world	pass
R	basic-R		13	13	pass

code blocks for tests

In the Org-mode file:

#+name: basic-elisp(n)
#+begin_src emacs-lisp
(* 2 n)
#+end_src

HTML export of code:

(* 2 n)

In the Org-mode file:

#+name: basic-shell
#+begin_src sh :results silent
expr 1 + 5
#+end_src

HTML export of code:

expr 1 + 5

In the Org-mode file:

#+name: date-simple
#+begin_src sh :results silent
date
#+end_src

HTML export of code:

date

In the Org-mode file:

#+name: basic-ruby
#+begin_src ruby :results silent
"org-babel"
#+end_src

HTML export of code:

"org-babel"

In the Org-mode file

#+name: basic-python
#+begin_src python :results silent
'hello world'
#+end_src

HTML export of code:

'hello world'

In the Org-mode file:

#+name: basic-R
#+begin_src R :results silent
b <- 9
b + 4
#+end_src

HTML export of code:

b <- 9 b + 4

The Library of Babel

:PROPERTIES: :CUSTOM_ID: library-of-babel :END:

(see also Org manual:Library-of-Babel)

As we saw above with the square example, once a source block function has been defined it can be called using the lob notation:

#+lob: square(x=6)

But what about code blocks that you want to make available to every Org-mode buffer?

In addition to the current buffer, Babel searches for pre-defined code block functions in the Library of Babel. This is a user-extensible collection of ready-made source code blocks for handling common tasks. One use for the Library of Babel (not yet done!) will be to provide a choice of data graphing procedures for data held in Org-mode tables, using languages such as R, gnuplot, asymptote, etc. If you implement something that might be of use to other Org-mode users, please consider adding it to the Library of Babel; similarly, feel free to request help solving a problem using external code via Babel -- there's always a chance that other Babel users will be able to contribute some helpful code.

Babel comes pre-populated with the code blocks located in the file -- raw file at @@html: library-of-babel.org@@ --. It is possible to add code blocks to the library from any Org-mode file using the org-babel-lob-ingest (bound to C-c C-v l).

#+name: add-file-to-lob #+begin_src emacs-lisp (org-babel-lob-ingest "path/to/file.org") #+end_src

Note that it is possible to pass table values or the output of a source-code block to Library of Babel functions. It is also possible to reference Library of Babel functions in arguments to code blocks.

Literate Programming

:PROPERTIES: :CUSTOM_ID: literate-programming :END:

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a /computer/ what to do, let us concentrate rather on explaining to /human beings/ what we want a computer to do.

The practitioner of literate programming can be regarded as an essayist, whose main concern is with exposition and excellence of style. Such an author, with thesaurus in hand, chooses the names of variables carefully and explains what each variable means. He or she strives for a program that is comprehensible because its concepts have been introduced in an order that is best for human understanding, using a mixture of formal and informal methods that reinforce each other.

-- Donald Knuth

Babel supports Literate Programming (LP) by allowing the act of programming to take place inside of Org-mode documents. The Org-mode file can then be exported (woven in LP speak) to HTML or LaTeX for consumption by a human, and the embedded source code can be extracted (tangled in LP speak) into structured source code files for consumption by a computer.

To support these operations Babel relies on Org-mode's existing exporting functionality for weaving of documentation, and on the =org-babel-tangle= function which makes use of Noweb reference syntax for tangling of code files.

The following example demonstrates the process of tangling in Babel.

Simple Literate Programming Example (Noweb syntax)

:PROPERTIES: :CUSTOM_ID: literate-programming-example :END:

Tangling functionality is controlled by the tangle family of tangle header arguments. These arguments can be used to turn tangling on or off (the default), either for the code block or the Org-mode heading level.

The following code blocks demonstrate how to tangle them into a single source code file using org-babel-tangle.

The following two code blocks have no tangle header arguments and so will not, by themselves, create source code files. They are included in the source code file by the third code block, which does have a tangle header argument.

In the Org-mode file:

#+name: hello-world-prefix
#+begin_src sh :exports none
  echo "/-----------------------------------------------------------\\"
#+end_src

HTML export of code:

echo "/-----------------------------------------------------------\\"

In the Org-mode file

#+name: hello-world-postfix
#+begin_src sh :exports none
  echo "\-----------------------------------------------------------/"
#+end_src

HTML export of code:

echo "\-----------------------------------------------------------/"

The third code block does have a tangle header argument indicating the name of the file to which the tangled source code will be written. It also has Noweb style references to the two previous code blocks. These references will be expanded during tangling to include them in the output file as well.

In the Org-mode file:

#+name: hello-world
#+begin_src sh :tangle hello :exports none :noweb yes
  <>
  echo "|                       hello world                         |"
  <>
#+end_src

HTML export of code:

<> echo "| hello world |" <>

Calling org-babel-tangle will result in the following shell source code being written to the hello.sh file:

#!/usr/bin/env sh

echo "/-----------------------------------------------------------\\" echo "| hello world |" echo "\-----------------------------------------------------------/"

In addition, the following syntax can be used to insert the *results* of evaluating a code block, in this case one named example-block.

# <>

Any optional arguments can be passed to example-block() by placing the arguments inside the parentheses following the convention defined when calling source block functions (see the Library of babel). For example,

# <>

sets the value of argument \"a\" equal to \"9\". Note that these arguments are not evaluated in the current source-code block but are passed literally to example-block().

Emacs Initialization with Babel

:PROPERTIES: :CUSTOM_ID: emacs-initialization :END:

Babel has special support for embedding your Emacs initialization into Org-mode files. The org-babel-load-file function can be used to load the Emacs Lisp code blocks embedded in a literate Org-mode file in the same way that you might load a regular Emacs Lisp file, such as .emacs.

This allows you to make use of the nice features of Org-mode, such as folding, tags, notes, HTML export, etc., to organize and maintain your Emacs initialization.

To try this out, either see the simple Literate Emacs Initialization example, or check out the Babel Literate Programming version of Phil Hagelberg's excellent emacs-starter-kit available at Org-babel-emacs-starter-kit.

Literate Emacs Initialization

:PROPERTIES: :CUSTOM_ID: literate-emacs-init :END:

For a simple example of usage, follow these 5 steps:

1) create a directory named =.emacs.d= in the base of your home directory; #+begin_src sh mkdir ~/.emacs.d #+end_src 2) checkout the latest version of Org-mode into the src subdirectory of this new directory; #+begin_src sh cd ~/.emacs.d mkdir src cd src git clone git://orgmode.org/org-mode.git #+end_src 3) place the following code block in a file called init.el in your Emacs initialization directory (~/.emacs.d). #+name: emacs-init #+begin_src emacs-lisp ;;; init.el --- Where all the magic begins ;; ;; This file loads Org-mode and then loads the rest of our Emacs initialization from Emacs lisp ;; embedded in literate Org-mode files.

;; Load up Org Mode and (now included) Org Babel for elisp embedded in Org Mode files (setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))

(let* ((org-dir (expand-file-name "lisp" (expand-file-name "org" (expand-file-name "src" dotfiles-dir)))) (org-contrib-dir (expand-file-name "lisp" (expand-file-name "contrib" (expand-file-name ".." org-dir)))) (load-path (append (list org-dir org-contrib-dir) (or load-path nil)))) ;; load up Org-mode and Org-babel (require 'org-install) (require 'ob-tangle))

;; load up all literate org-mode files in this directory (mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))

;;; init.el ends here #+end_src 4) implement all of your Emacs customizations inside of Emacs Lisp code blocks embedded in Org-mode files in this directory; and 5) re-start Emacs to load the customizations.

Reproducible Research

:PROPERTIES: :CUSTOM_ID: reproducable-research :END:

An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures.

-- D. Donoho

Reproducible Research (RR) is the practice of distributing, along with a research publication, all data, software source code, and tools required to reproduce the results discussed in the publication. As such the RR package not only describes the research and its results, but becomes a complete laboratory in which the research can be reproduced and extended.

Org-mode already has exceptional support for exporting to HTML and LaTeX. Babel makes Org-mode a tool for RR by activating the data and code blocks embedded in Org-mode documents; the entire document becomes executable. This makes it possible, and natural, to distribute research in a format that encourages readers to recreate results and perform their own analyses.

it supports multiple languages (we're not aware of other RR tools that do this);
the export process is flexible and powerful, including HTML as a
the document can make use of Org-mode features that support [[https://orgmode.org/manual/Agenda-Views.html#Agenda-Views][project

Footnotes

block's results in a separate buffer.

Calling =C-c C-o= on a code block will open the
This mode will be familiar to Sweave users.

intro.org 41 KB History Raw

Improving this document noexport

DONE Document slice indexing of tables

DONE Document synonymous alternatives

DONE Describe useful functions

DONE Language support

DONE Document noweb references

DONE Why is

TODO Developments

DONE Useful variables

TODO Language specific header arguments

DONE What function is bound to C-c '?

Introduction

Overview

Initial Configuration

Code Blocks

Code Blocks in Org

Code Blocks in Babel

Source Code Execution

Ruby

Shell

R

ditaa

Capturing the Results of Code Evaluation

:results value (functional mode)

:results output (scripting mode)

Session-based Evaluation

Arguments to Code Blocks

Simple example of using a code block as a function

A more complex example using an Org-mode table as input

In-line Code Blocks

Code Block Body Expansion

A Meta-programming Language for Org-mode

Using Code Blocks in Org Tables

Example 1: Data Summaries Using R

Example 2: Babel Test Suite

code blocks for tests

The Library of Babel

Literate Programming

Simple Literate Programming Example (Noweb syntax)

Emacs Initialization with Babel

Literate Emacs Initialization

Reproducible Research

Footnotes

intro.org 41 KB

History Raw

`:results value` (functional mode)

`:results output` (scripting mode)