Fix references to org-mode.git repo.

[Worg.git] / org-contrib / babel / intro.org

#+OPTIONS:    H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t *:t TeX:t LaTeX:nil skip:nil d:(HIDE) tags:not-in-toc
#+STARTUP:    align fold nodlcheck hidestars oddeven lognotestate hideblocks
#+SEQ_TODO:   TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@)
#+TAGS:       Write(w) Update(u) Fix(f) Check(c) noexport(n)
#+TITLE:      Babel: Introduction
#+AUTHOR:     Eric Schulte, Dan Davison, Tom Dye
#+EMAIL:      schulte.eric at gmail dot com, davison at stats dot ox dot ac dot uk, tsd at tsdye dot com
#+LANGUAGE:   en
#+STYLE:      <style type="text/css">#outline-container-introduction{ clear:both; }</style>
#+STYLE:      <style type="text/css">#table-of-contents{ max-width:100%; }</style>
#+LINK_UP:  index.php
#+LINK_HOME: http://orgmode.org/worg

#+begin_html
  <div id="subtitle" style="float: center; text-align: center;">
    <p>executable code blocks in org-mode</p>
  </div>
  <div id="logo" style="float: left; text-align: center; max-width: 340px; font-size: 8pt; margin-left: 1em;">
    <p>
      <img src="../../images/babel/tower-of-babel.png"  alt="Tower of Babel"/>
      <div id="attr" style="margin: -0.5em;">
        The Tower of Babel by
        <a href="http://commons.wikimedia.org/wiki/Pieter_Brueghel_the_Elder" title="">
          <b>Pieter Brueghel the Elder</b>
        </a>
      </div>
      <p>
        And the Lord said, Behold, the people is one, and they have all
        one language; and this they begin to do; and now nothing will be
        restrained from them, which they have imagined to do. Genesis
        11:1-9
      </p>
    </p>
  </div>
#+end_html
  
* Improving this document                                          :noexport:
** DONE Document slice indexing of tables
** DONE Document synonymous alternatives
   {call,lob}, {source, function, srcname}, {results, resname}
** DONE Describe useful functions
   - `org-babel-execute-buffer'
   - `org-babel-execute-subtree'

** DONE Language support
 Hopefully we will be breaking out a separate section for
each language, and expanding the portion which documents the actual
usage of header-arguments and noweb references as those sections are
woefully out of date.
** DONE Document noweb references
*** DONE Why is :noweb needed for execution but not for tangling?
** TODO Developments
- org-babel can now cache the results of source block execution to avoid
 rerunning the same calculation.  The cache uses a sha1 hash key of the
 source code body and the header arguments to determine if
 recalculation is required.  These hash keys are kept mostly hidden in
 the #+resname line of the results of the block.  This behavior is
 turned off by default.  It is controlled through the :cache
 and :nocache header arguments.  To enable caching on a single block
 add the :cache header argument, to enable global caching change the
 value of your `org-babel-default-header-args' variable as follows

 (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
 #+resname line.  This can be done automatically to all results on
 opening of a file by adding the following to your org-mode hook

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

- allow header argument values to be lisp forms, for example the
 following is now valid

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

** DONE Useful variables
   - # -*- org-src-preserve-indentation: t -*-
** TODO Language specific header arguments
   -    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
your example, the filename is created in python. I suggest doing it
slightly differently, something like this.

#+srcname: fileoutput
#+begin_src python :file outfile.txt
 def savetofile(result, filename):
     with open(filename, 'w') as f:
         f.write(str(result))
 savetofile(78, 'outfile.txt')
 55
#+end_src

#+resname: fileoutput
[[file:outfile.txt]]

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 <filepath> ruby/python blindly outputs a
link to <filepath>, regardless of the contents of the
code. Responsibility for creating useful contents of <filepath> 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 '?
   - this document notes two different functions
* Introduction
  :PROPERTIES:
  :CUSTOM_ID: introduction
  :END:
  Babel extends the very excellent [[http://orgmode.org/][Org-mode]] with several features for
  working with source code, including code execution. Org-mode is an
  [[http://www.gnu.org/software/emacs/][Emacs]] major mode for doing almost anything with plain text. If you
  are not familiar with Org-mode please take a moment to read the
  [[http://orgmode.org/][Org-mode]] homepage before continuing.

  As its name implies, Babel will execute code in many different
  languages. The results of code execution --- text, tables and
  graphics --- can be used as input to other code blocks or integrated
  into the powerful publishing facilities of Org-mode.

  Babel augments [[http://orgmode.org/manual/Literal-examples.html][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
    other code blocks, and be called remotely; and
  - 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 ::
    If you are not familiar with creating 'src' blocks in an Org-mode
    buffer, and moving between that buffer and the language major-mode
    edit buffer, then you should have a look at the relevant section
    in the [[http://orgmode.org/manual/Literal-examples.html][Org manual]] and [[#source-code-blocks][below]], try it out, and come back.
  - Executing code ::
    The core of Babel is its ability to execute code in Org-mode
    'src' blocks, taking input from other blocks and tables, with
    output to further blocks and tables. This is described starting
    [[#source-code-execution][here]].
  - Literate Programming ::
    If you are a programmer writing code that you would normally
    execute in some other way (e.g. from the command line, or sourcing
    it into an interactive session), then a simple introduction to
    Babel is to place your code in blocks in an Org-mode file, and to
    use Babel's [[#literate-programming][Literate Programming]] support to extract pure code
    from your Org files.
    
  All of these use cases, as well as exhaustive documentation of the
  features of Babel are covered in the [[http://orgmode.org/manual/Working-With-Source-Code.html#Working-With-Source-Code][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) It is strongly recommended that you update to the latest version
     of Org-mode by [[file:../../org-faq.org::keeping-current-with-Org-mode-development][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 [[file:languages.org::#configure][Configure active languages]]
     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) 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 [[http://orgmode.org/manual/Literal-examples.html][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 [[http://orgmode.org/manual/Literal-examples.html][Org-mode manual]]
    before proceeding.

    Code blocks in [[#reference-and-documentation][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 org
  ,#+begin_src language org-switches
  ,body
  ,#+end_src
#+end_src

    For example, a code block of [[http://www.ruby-lang.org/][ruby]] code looks like this in
    an Org-mode file:

#+begin_src org
  ,#+begin_src ruby
  ,require 'date'
  ,"This file was last evaluated on #{Date.today}"
  ,#+end_src
#+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 org
  ,#+begin_src language  org-switches header-arguments
  ,body
  ,#+end_src
#+end_src


- language :: The language of the code in the source-code block. Valid
     values must be members of =org-babel-interpreters=.
- header-arguments :: Header arguments control many facets of the
     evaluation and output of source-code blocks.  See the [[file:reference.org::#header-arguments][Header
     Arguments]] section for a complete review of available header
     arguments.
- body :: The source code to be evaluated.  An important key-binding
     is =​C-c '​=.  This calls =org-edit-src-code=, a function that brings
     up an edit buffer containing the code using the Emacs major mode
     appropriate to the language.  You can edit your code block
     as you regularly would in Emacs.

* 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. 

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 code[fn:1] (and feel free to alter it!).
*** Ruby
In the Org-mode file:
: #+begin_src ruby
: "This file was last evaluated on #{Date.today}"
: #+end_src

HTML export of code:
#+begin_src ruby
"This file was last evaluated on #{Date.today}"
#+end_src

HTML export of the resulting string:
#+resname:
: 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:
#+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 the resulting string:
#+resname:
: This file takes up  36K

*** [[http://www.r-project.org/][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:
#+begin_src R :colnames yes
  words <- tolower(scan("intro.org", what="", na.strings=c("|",":")))
  t(rev(sort(table(words[nchar(words) > 3])))[1:10])
#+end_src
#+results:
| code | source | org-mode | #+end_src | #+begin_src | this | block | that | org-babel | with |
|------+--------+----------+-----------+-------------+------+-------+------+-----------+------|
|   64 |     62 |       44 |        42 |          41 |   36 |    34 |   28 |        28 |   27 |

*** [[http://ditaa.sourceforge.net/][ditaa]]

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

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

HTML export of the resulting image:
#+resname:
[[file:../../images/babel/blue.png]]

** Capturing the Results of Code Evaluation
   :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.
*** =:results value= (functional mode)
   :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.

#+begin_src python :results value
import time
print("Hello, today's date is %s" % time.ctime())
print('Two plus two is')
return 2 + 2
#+end_src

#+resname:
: 4

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.[fn:2]

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

#+srcname: name
#+begin_src python :results output
import time
print("Hello, today's date is %s" % time.ctime())
print('Two plus two is')
2 + 2
#+end_src

#+resname: name
: 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 [[http://ess.r-project.org/][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.

#+srcname: square(x)
#+begin_src python
return x*x
#+end_src

In the Org-mode file, the function looks like this:
: #+source: square(x)
: #+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]])

#+call: square(x=6)

#+results: square(x=6)
: 36

*** 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=:

#+tblname: fibonacci-inputs
| 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 [[http://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code:
#+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
#+begin_src emacs-lisp
  (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

In the Org-mode buffer the function looks like this:
: #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
: #+begin_src emacs-lisp
:   (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:
#+resname:
| 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
     can be used inside a code block to preview the expanded
     contents. This facility is useful for debugging.

- tangling :: The expanded body can be tangled.  Tangling this way includes
     variable values that  may be 
              - the results of other code blocks, 
              - variables stored in headline properties, or 
              - tables.  

     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:
#+tblname: user-data
| username | john-doe |
| password | abc123   |

The code block refers to the data table:
#+srcname: setup-my-account
#+begin_src emacs-lisp :rownames yes :var data=user-data
  (setq my-special-username (first (first data)))
  (setq my-special-password (first (second data)))
#+end_src
  
With point inside the code block,  =C-c M-b p= expands the contents:
#+begin_src emacs-lisp
  (let ((data (quote (("john-doe") ("abc123")))))
  (setq my-special-username (first (first data)))
  (setq my-special-password (first (second data)))
  )
#+end_src


** 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.

1. Create a code block, using shell code, to list
   directories in our home directory, together with their
   sizes. Babel automatically converts the output into an Org-mode
   table.
   
: #+srcname: directories
: #+begin_src sh :results replace
:   cd ~ && du -sc * |grep -v total
: #+end_src
   
#+resname: directories
|       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"     |

2. A function, written with a single line of R code, plots the data
   in the Org-mode table as a
   pie-chart. Note how this code block uses the =srcname=
   of the previous code block to obtain the data.

In the Org-mode file: 
: #+srcname: 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:
#+srcname: 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
 [[file:../../images/babel/dirs.png]]

* Using Code Blocks in Org Tables
  :PROPERTIES:
  :CUSTOM_ID: spreadsheet
  :END:

In addition to passing data from tables as [[arguments-to-source-code-blocks][arguments]] to code
blocks, and [[#results-value][storing]] results as tables, Babel can be used in a
third way with Org-mode tables. First note that Org-mode's [[http://orgmode.org/manual/The-spreadsheet.html#The-spreadsheet][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
[[http://orgmode.org/manual/Formula-syntax-for-Calc.html#Formula-syntax-for-Calc][calc]] and [[http://orgmode.org/manual/Formula-syntax-for-Lisp.html#Formula-syntax-for-Lisp][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.

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

#+resname: tbl-example-data
| 0.836685163900256 |
| 0.696652316721156 |
| 0.382423302158713 |
| 0.987541858805344 |
| 0.994794291909784 |

Now we define a source block to calculate the mean.

In the Org-mode file:
: #+srcname: R-mean(x)
: #+begin_src R 
: mean(x)
: #+end_src

HTML export of code:
#+srcname: R-mean(x)
#+begin_src R 
mean(x)
#+end_src

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

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

HTML export of code:
#+tblname: summaries
| mean |
|------|
| 0.78 |
#+TBLFM: @2$1='(sbe R-mean (x tbl-example-data));%.2f

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:

#+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))

**** code blocks for tests

In the Org-mode file:

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

HTML export of code:

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

In the Org-mode file:
: #+srcname: basic-shell
: #+begin_src sh :results silent
: expr 1 + 5
: #+end_src

HTML export of code:
#+srcname: basic-shell
#+begin_src sh :results silent
  expr 1 + 5
#+end_src

In the Org-mode file:
: #+srcname: date-simple
: #+begin_src sh :results silent
: date
: #+end_src

HTML export of code:
#+srcname: date-simple
#+begin_src sh :results silent
  date
#+end_src

In the Org-mode file:
: #+srcname: basic-ruby
: #+begin_src ruby :results silent
: "org-babel"
: #+end_src

HTML export of code:
#+srcname: basic-ruby
#+begin_src ruby :results silent
  "org-babel"
#+end_src

In the Org-mode file
: #+srcname: basic-python
: #+begin_src python :results silent
: 'hello world'
: #+end_src

HTML export of code:
#+srcname: basic-python
#+begin_src python :results silent
  'hello world'
#+end_src

In the Org-mode file:
: #+srcname: basic-R
: #+begin_src R :results silent
: b <- 9
: b + 4
: #+end_src

HTML export of code:
#+srcname: basic-R
#+begin_src R :results silent
  b <- 9
  b + 4
#+end_src

* The Library of Babel
  :PROPERTIES:
  :CUSTOM_ID: library-of-babel
  :END:

  (see also [[http://orgmode.org/manual/Library-of-Babel.html#Library-of-Babel][Org manual:Library-of-Babel]])

  As we saw above with the [[*Simple%20example%20of%20using%20a%20source%20block%20as%20a%20function][=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:library-of-babel.org][Library of Babel]] file -- raw file at
#+html: <a href="http://repo.or.cz/w/org-mode.git/blob/HEAD:/contrib/babel/library-of-babel.org">library-of-babel.org</a>
  --. 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=).

  #+srcname: 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:

#+begin_quote
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
#+end_quote

Babel supports [[http://en.wikipedia.org/wiki/Literate_programming][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 [[http://orgmode.org/manual/Exporting.html#Exporting][existing
exporting functionality]] for *weaving* of documentation, and on the
=org-babel-tangle= function which makes use of [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]] [[noweb-reference-syntax][reference syntax]]
for *tangling* of code files.

The [[literate-programming-example][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][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:
: #+srcname: hello-world-prefix
: #+begin_src sh :exports none
:   echo "/-----------------------------------------------------------\\"
: #+end_src

HTML export of code:
#+srcname: hello-world-prefix
#+begin_src sh :exports none
  echo "/-----------------------------------------------------------\\"
#+end_src

In the Org-mode file
: #+srcname: hello-world-postfix
: #+begin_src sh :exports none
:   echo "\-----------------------------------------------------------/"
: #+end_src

HTML export of code:
#+srcname: hello-world-postfix
#+begin_src sh :exports none
  echo "\-----------------------------------------------------------/"
#+end_src


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 [[http://www.cs.tufts.edu/~nr/noweb/][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:
: #+srcname: hello-world
: #+begin_src sh :tangle hello :exports none :noweb yes
:   <<hello-world-prefix>>
:   echo "|                       hello world                         |"
:   <<hello-world-postfix>>
: #+end_src

HTML export of code:
#+srcname: hello-world
#+begin_src sh :tangle hello.sh :exports none :noweb yes
  <<hello-world-prefix>>
  echo "|                       hello world                         |"
  <<hello-world-postfix>>
#+end_src


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

#+srcname: hello-world-output
#+begin_src sh 
#!/usr/bin/env sh

# [[file:~/org/temp/index.org::*Noweb%20test][hello-world]]

echo "/-----------------------------------------------------------\\"
echo "|                       hello world                         |"
echo "\-----------------------------------------------------------/"
# hello-world ends here
#+end_src

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

: # <<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][Library of babel]]). For example,

: # <<example-block(a=9)>>

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:

#+attr_html: style="float:left;"
[[file:../../images/babel/dot-emacs.png]]

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-init][Literate Emacs Initialization]]
example, or check out the Babel Literate Programming version of
Phil Hagelberg's excellent [[http://github.com/technomancy/emacs-starter-kit/tree/master][emacs-starter-kit]] available at
[[http://github.com/eschulte/emacs-starter-kit/tree/master][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=).
   #+srcname: 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:
#+begin_quote 
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
#+end_quote

[[http://reproducibleresearch.net/index.php/Main_Page][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 [[http://orgmode.org/manual/Exporting.html#Exporting][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.

One notable existing RR tool is [[http://en.wikipedia.org/wiki/Sweave][Sweave]], which provides a mechanism for
embedding [[http://www.r-project.org/][R]] code into LaTeX documents.  Sweave is a mature
and very useful tool, but we believe that Babel has several
advantages:
 - it supports multiple languages (we're not aware of other RR tools that do this);
 - the [[http://orgmode.org/manual/Exporting.html#Exporting][export process]] is flexible and powerful, including HTML as a
   target in addition to LaTeX; and
 - the document can make use of Org-mode features that support [[http://orgmode.org/manual/Agenda-Views.html#Agenda-Views][project
   planning]] and [[http://orgmode.org/manual/TODO-Items.html#TODO-Items][task management]].

* Footnotes
[fn:1] Calling =C-c C-o= on a code block will open the
block's results in a separate buffer.

[fn:2]  This mode will be familiar to Sweave users.