Merge branch 'R-output-eval-bug'

[org-mode.git] / org-babel-worg.org

#+OPTIONS:    H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:t -:t f:t *:t TeX:t LaTeX:t 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) 
#+TITLE:      Org-babel
#+AUTHOR:     Dan Davison, Eric Schulte
#+EMAIL:      davison at stats dot ox dot ac dot uk
#+LANGUAGE:   en
#+CATEGORY:   worg

#+begin_html
  <div id="subtitle">
    <p>executable source code blocks in org-mode</p>
  </div>
  <div id="logo">
    <p>
      <img src="images/tower-of-babel.png"  alt="images/tower-of-babel.png"
           title="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"/>
      <div id="attr">
        from
        <a href="http://www.flickr.com/photos/23379658@N05/" title=""><b>Martijn Streefkerk</b></a>
      </div>
    </p>
  </div>
#+end_html

#+begin_html
  <p>
  </p>
#+end_html

* Introduction
  :PROPERTIES:
  :CUSTOM_ID: introduction
  :END:
  Org-babel is an extension to the very excellent [[http://orgmode.org/][Org-mode]]; 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 [[http://orgmode.org/][the Org-mode
  homepage]] before continuing.

  Org-babel provides the following modifications to [[http://orgmode.org/manual/Literal-examples.html][the existing
  support]] for blocks of source code examples in the org-mode core.
  1. interactive source code execution
  2. arguments to source code blocks
  3. exportation of source code blocks to files (literate programming)

Much of this document includes interactive examples.  The reader is
encouraged to grab either the plain text version of this file
#+HTML: <a href="org-babel-worg.org">org-babel-worg.org</a>
which can be read and run in Emacs or the htmlized version of the
plain text of this file
#+HTML: <a href="org-babel-worg.org.html">org-babel-worg.html</a>
which is viewable through the web browser.

* Getting started
  :PROPERTIES:
  :CUSTOM_ID: getting-started
  :END:

  1) Grab the latest code from the git repo at [[http://github.com/eschulte/org-babel/tree/master][github/org-babel]]
     #+begin_src sh
     git clone git://github.com/eschulte/org-babel.git
     #+end_src

  2) Add the following lines to your .emacs, replacing the path as
     appropriate. A good place to check that things are up and running
     would the examples in [[* Basic org-babel functionality][Basic org-babel functionality]].
     #+begin_src emacs-lisp
       (add-to-list 'load-path "/path/to/org-babel/lisp")
       (require 'org-babel-init)
     #+end_src

  3) Then activate the subset of supported Org-babel languages which
     you will want to be able to execute on your system.  The
     following can be added to your .emacs and used to activate
     languages.  It includes a brief list of the requirements for each
     language.  *Note*: this also serves as the list of languages
     currently supported by Org-babel.
     #+begin_src emacs-lisp 
       ;; Uncomment each of the following require lines if you want org-babel
       ;; to support that language.  Each language has a comment explaining
       ;; it's dependencies.  See the related files in lisp/langs for more
       ;; detailed explanations of requirements.
       ;; (require 'org-babel-R)         ;; R and ess-mode
       ;; (require 'org-babel-asymptote) ;; asymptote
       ;; (require 'org-babel-css)       ;; none
       ;; (require 'org-babel-ditaa)     ;; ditaa
       ;; (require 'org-babel-dot)       ;; dot
       ;; (require 'org-babel-gnuplot)   ;; gnuplot, and gnuplot-mode
       ;; (require 'org-babel-haskell)   ;; haskell, haskell-mode, inf-haskell
       ;; (require 'org-babel-ocaml)     ;; ocaml, and tuareg-mode
       ;; (require 'org-babel-python)    ;; python, and python-mode
       ;; (require 'org-babel-ruby)      ;; ruby, irb, ruby-mode, and inf-ruby
       ;; (require 'org-babel-sass)      ;; sass, sass-mode
       ;; (require 'org-babel-sql)       ;; none
       ;; 
       ;; Once you've activated languages, load the library of babel for
       ;; pre-built helpers in the languages you will be using.
       (org-babel-load-library-of-babel)
     #+end_src
  
* Basic org-babel functionality
  :PROPERTIES:
  :CUSTOM_ID: basic-functionality
  :END:
*** Source code execution
    :PROPERTIES:
    :CUSTOM_ID: source-code-execution
    :END:
    For interpreted languages such as shell, python, R, etc, org-babel
    allows source blocks to be executed: the code is passed to the
    interpreter and you have control over what is done with the
    results of excecution. E.g. place point anywhere in the following
    block and use =C-c C-c= to run the code:
    
    *Note:* calling =C-c C-o= on a source-code block will open the
    blocks results

[[http://www.ruby-lang.org/][Ruby]] source code
#+begin_src ruby
"This file was last evaluated on #{Date.today}"
#+end_src

Results of Ruby evaluation
#+resname:
: This file was last evaluated on 2009-08-09

[[http://www.r-project.org/][R]] source code
#+begin_src R :results value
x = 4
date()
c(5, 10)
#+end_src

Results of R evaluation
#+resname:
|  5 |
| 10 |

[[http://ditaa.sourceforge.net/][ditaa]] source code
#+begin_src ditaa :file images/blue.png :cmdline -r
+---------+
| cBLU    |
|         |
|    +----+
|    |cPNK|
|    |    |
+----+----+
#+end_src

#+resname:
[[file:images/blue.png]]

*** What happens to the results?
    :PROPERTIES:
    :CUSTOM_ID: results
    :END:
    Org-babel provides two fundamentally different modes for capturing
    the results of code evaluation, specified by the :results header
    argument:
**** :results value
     This means that the 'result' of code evaluation is defined to be
     the *value* of the last statement in the block. Thus with this
     setting, one can view the code block as a function with a return
     value. And not only can one view it that way, but you can
     actually use the return value of one source block as input for
     another (see later). This setting is the default.
**** :results output
     With this setting, org-babel captures all the text output of the
     code block and places it in the org buffer. One can think of this
     as a 'scripting' mode: the code block contains a series of
     commands, and you get the output of all the commands. Unlike in
     the 'functional' mode specified by =:results value=, the code
     block has no return value. (This mode will be familiar to Sweave
     users).
**** Additional :results settings
     
*** Arguments to source code blocks
    :PROPERTIES:
    :CUSTOM_ID: arguments-to-source-code-blocks
    :END:
    In addition to evaluation of code blocks, org-babel allows them to
    be parameterised (i.e. have arguments). Thus source code blocks
    now have the status of *functions*.

Inputs for 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 |

in the Org-mode buffer this looks like
: #+tblname: fibonacci-inputs
: | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
: | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |

[[http://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code
#+srcname: 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

in the Org-mode buffer this looks like
: #+srcname: 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

Results of Emacs Lisp code evaluation
#+resname:
| 1 | 1 | 2 |  3 |  5 |   8 |  13 |  21 |   34 |   55 |
| 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |

* A meta-programming language for org-mode
  :PROPERTIES:
  :CUSTOM_ID: meta-programming-language
  :END:

Since information can pass freely between source-code blocks and
org-mode tables you can mix and match languages using each language
for those tasks to which it is suited.  This makes Org-mode files with
Org-babel into a kind of meta-functional programming language in which
functions from many languages can work together.

As an example, lets take some system diagnostics in the shell, and
then graph them with R.

1. Shell source code
#+srcname: directories
   #+begin_src bash :results replace
   cd ~ && du -sc * |grep -v total
   #+end_src
2. Results of the shell source code (on my system, grab this org-mode
   files and try running it on your own)
#+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"     |
3. R source code (which calls the previous shell source code)
#+srcname: directory-pie
   #+begin_src R :var dirs = directories :session R-pie-example
   pie(dirs[,1], labels = dirs[,2])
   #+end_src
4. Results of R code [[file:images/dirs.png]]

* Spreadsheet plugins for org-mode in any language
  :PROPERTIES:
  :CUSTOM_ID: spreadsheet
  :END:

*NOTE*: Maybe in-addition-to/in-stead-of this example we should do a
more traditional "spreadsheet" example with R [Eric]

Not only can Org-babel pass entire tables of data to source code
blocks (see [[arguments-to-source-code-blocks]]), Org-babel can also be
used to call source code blocks from *within* tables using the
Org-mode's [[http://orgmode.org/manual/The-spreadsheet.html#The-spreadsheet][existing spreadsheet functionality]].

In fact the functional test suite for Org-babel is implemented as a
large Org-mode table.  To run the entire test suite you simple
evaluate the table =C-u C-c C-c=, and all of the tests are run
updating the table with pass/fail statistics.

Here's a sample of our test suite.

#+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) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
#+TBLFM: $5=""::$6=""

*** code blocks for tests

#+srcname: basic-elisp
#+begin_src emacs-lisp :var n=7
(* 2 n)
#+end_src

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

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

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

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

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

* Library of Babel
  :PROPERTIES:
  :CUSTOM_ID: library-of-babel
  :END:
  What about those source code blocks which are so useful you want to
  have them available in every org-mode buffer?

  The [[file:library-of-babel.org][Library of Babel]] is an extensible collection of ready-made and
  easily-shortcut-callable source-code blocks for handling common
  tasks.  Org-babel comes pre-populated with the source-code blocks
  located in the [[file:library-of-babel.org][library-of-babel.org]] file. It is possible to add
  source-code blocks from any org-mode file to the library by calling

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

* 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
an article of research all data, code, and tools required to reproduce
the results discussed in the paper.  As such the paper becomes not
only a document describing the research but a complete laboratory
reproducing the research.

Org-mode already has exceptional support for [[http://orgmode.org/manual/Exporting.html#Exporting][exporting to html and
LaTeX]].  Org-babel makes Org-mode a tool for RR by *activating* the
data and source code embedded into Org-mode documents making the
entire document executable.  This makes it not only possible, but
natural to distribute research in a format that encourages readers to
recreate your results, and perform their own analysis.

Existing RR tools like [[http://en.wikipedia.org/wiki/Sweave][Sweave]] provide for the embedding of [[http://www.r-project.org/][R]] code into
LaTeX documents.  While this is very useful, such documents often
still require a large degree of "glue code" in the form of external
shell scripts, python scripts, and Makefiles.  To our knowledge
Org-babel is the only RR tool which allows multiple languages and data
to coexist and cooperate inside of a single document.

* 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

Org-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 Org-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]] [[reference-expansion][reference syntax]]
for *tangling* of code files.

The [[literate-programming-example][following example]] demonstrates the process of *tangling* in
Org-babel.

*** Simple Literate Programming Example (Noweb syntax)
    :PROPERTIES:
    :CUSTOM_ID: literate-programming-example
    :END:

Tangling functionality is controlled by the =tangle= family of
[[header-arguments]].  These arguments can be used to turn tangling on or
off (the default) on the source code block, or the outline heading
level.

The following demonstrates the combination of three source code blocks
into a single source code file using =org-babel-tangle=.

The following two blocks will not be tangled by default since they
have no =tangle= header arguments.

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

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

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

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


The third block does have a =tangle= header argument indicating the
name of the file to which it should be written.  It also has [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]]
style references to the two previous source code blocks which will be
expanded during tangling to include them in the output file as well.

#+srcname: hello-world
#+begin_src sh :tangle hello :exports none
  # <<hello-world-prefix>>
  echo "|                       hello world                         |"
  # <<hello-world-postfix>>
#+end_src

: #+srcname: hello-world
: #+begin_src sh :tangle hello :exports none
:   # <<hello-world-prefix>>
:   echo "|                       hello world                         |"
:   # <<hello-world-postfix>>
: #+end_src

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

#+srcname: hello-world-output
#+begin_src sh 
  #!/usr/bin/env sh
  # generated by org-babel-tangle
  
  # [[file:~/src/org-babel/org-babel-worg.org::#literate-programming-example][block-16]]
  # <<hello-world-prefix>>
  echo "/-----------------------------------------------------------\\"
  
  echo "|                       hello world                         |"
  # <<hello-world-postfix>>
  echo "\-----------------------------------------------------------/"
  # block-16 ends here
#+end_src

*** Emacs Initialization with Org-babel
Org-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 embedded in a literate Org-mode file in the
same way that you might load a regular elisp file.

This allows you to have all the niceness of Org-mode (folding, tags,
notes, html export, etc...) available in your emacs initialization.

To try this out either see the simple [[literate-emacs-init][Literate Emacs Initialization]]
example directly below, or check out the Org-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 4 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 versions of Org-mode and Org-babel into the src
   subdirectory of this new directory
   #+begin_src sh
   cd ~/.emacs.d
   mkdir src
   cd src
   git clone git://repo.or.cz/org-mode.git
   git clone git://github.com/eschulte/org-babel.git
   #+end_src
3) place the following 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 both
     ;; - Org-mode : http://orgmode.org/ and
     ;; - Org-babel: http://eschulte.github.com/org-babel/
     ;;
     ;; It then loads the rest of our Emacs initialization from Emacs lisp
     ;; embedded in literate Org-mode files.
     
     ;; Load up Org Mode and Org Babel for elisp embedded in Org Mode files
     (setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
     (add-to-list 'load-path (expand-file-name
                              "lisp" (expand-file-name
                                      "org" (expand-file-name
                                             "src" dotfiles-dir))))
     (add-to-list 'load-path (expand-file-name
                              "lisp" (expand-file-name
                                      "org-babel" (expand-file-name
                                                   "src" dotfiles-dir))))
     (require 'org-babel-init)
     
     ;; 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 elisp
   source-code blocks located in Org-mode files in this directory.
   They will be loaded by emacs on startup.

* Reference / Documentation
  :PROPERTIES:
  :CUSTOM_ID: reference-and-documentation
  :END:

*** Source Code block syntax

The basic syntax of source-code blocks is as follows:

: #+srcname: name
: #+begin_src language header-arguments
: body
: #+end_src

- name :: This name is associated with the source-code block.  This is
     similar to the =#+TBLNAME= lines which can be used to name tables
     in org-mode files.  By referencing the srcname of a source-code
     block it is possible to evaluate the block for other places,
     files, or from inside tables.
- 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
     input to, evaluation of, and output of source-code blocks.  See
     the [[* Header Arguments][Header Arguments]] section for a complete review of available
     header arguments.
- body :: The actual source code which will be evaluated.  This can be
          edited with `org-edit-special'.

*** Header Arguments
     :PROPERTIES:
     :CUSTOM_ID: header-arguments
     :END:

- results :: results arguments specify what should be done with the
             output of source-code blocks
  - The following options are mutually exclusive, and specify how the
    results should be collected from the source-code block
    - value ::
    - output :: 
  - The following options are mutually exclusive and specify what type
    of results the code block will return
    - vector :: specifies that the results should be interpreted as a
                multidimensional vector (even if the vector is
                trivial), and will be inserted into the org-mode file
                as a table
    - scalar :: specifies that the results should be interpreted as a
                scalar value, and will be inserted into the org-mode
                file as quoted text
    - file :: specifies that the results should be interpreted as the
              path to a file, and will be inserted into the org-mode
              file as a link
  - The following options specify how the results should be inserted
    into the org-mode file
    - replace :: the current results replace any previously inserted
                 results from the code block
    - silent :: rather than being inserted into the org-mode file the
                results are echoed into the message bar
- exports :: exports arguments specify what should be included in html
             or latex exports of the org-mode file
  - code :: the body of code is included into the exported file
  - results :: the results of evaluating the code is included in the
               exported file
  - both :: both the code and results are included in the exported
            file
  - none :: nothing is included in the exported file
- tangle :: tangle arguments specify whether or not the source-code
            block should be included in tangled extraction of
            source-code files
  - yes :: the source-code block is exported to a source-code file
           named after the basename (name w/o extension) of the
           org-mode file
  - no :: (default) the source-code block is not exported to a
          source-code file
  - other :: any other string passed to the =tangle= header argument
             is interpreted as a file basename to which the block will
             be exported

*** Noweb reference syntax
The [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]] Literate Programming system allows named blocks of code to
be referenced by using a =<<code-block-name>>= syntax.  When a
document is tangled these references are replaced with the named code.
An example is provided in the [[literate-programming-example]] in this
document.