\n And the Lord said, Behold, the people i=
s one, and they have all\n one language; and this they begin to do; =
and now nothing will be\n restrained from them, which they have imag=
ined to do. Genesis\n 11:1-9\n
\n \n
\n#+end_=
html\n \n* Improving this document :noexport:\n** DONE Document sli=
ce indexing of tables\n** DONE Document synonymous alternatives\n {call,l=
ob}, {source, function, srcname}, {results, resname}\n** DONE Describe usef=
ul functions\n - `org-babel-execute-buffer'\n - `org-babel-execute-subt=
ree'\n\n** DONE Language support\n Hopefully we will be breaking out a sepa=
rate section for\neach language, and expanding the portion which documents =
the actual\nusage of header-arguments and noweb references as those section=
s are\nwoefully out of date.\n** DONE Document noweb references\n*** DONE W=
hy is :noweb needed for execution but not for tangling?\n** TODO Developmen=
ts\n- org-babel can now cache the results of source block execution to avoi=
d\n rerunning the same calculation. The cache uses a sha1 hash key of the\=
n source code body and the header arguments to determine if\n recalculation=
is required. These hash keys are kept mostly hidden in\n the #+resname li=
ne of the results of the block. This behavior is\n turned off by default. =
It is controlled through the :cache\n and :nocache header arguments. To e=
nable caching on a single block\n add the :cache header argument, to enable=
global caching change the\n value of your `org-babel-default-header-args' =
variable as follows\n\n (setq org-babel-default-header-args\n (cons '=
(:cache)\n (assq-delete-all :nocache org-babel-default-header-a=
rgs)))\n\n- It is now possible to fold results by tabbing on the beginning =
of the\n #+resname line. This can be done automatically to all results on\=
n opening of a file by adding the following to your org-mode hook\n\n (add-=
hook 'org-mode-hook 'org-babel-result-hide-all)\n\n- allow header argument =
values to be lisp forms, for example the\n following is now valid\n\n :file=
(format \"%s/images/pca-scatter.png\" dir)\n\n** DONE Useful variables\n =
- # -*- org-src-preserve-indentation: t -*-\n** TODO Language specific hea=
der arguments\n - org-babel: capture graphical output from R\n\n If =
a [:file filename.ext] header arg is provided, then all graphical\n outpu=
t from the source block is captured on disk, and output of the\n source b=
lock is a link to the resulting file, as with the\n graphics-only languag=
es such as gnuplot, ditaa, dot, asymptote. An\n attempt is made to find a=
graphics device corresponding to the file\n extension (currently .png, .=
jpg, .jpeg, .tiff, .bmp, .pdf, .ps,\n .postscript are recognised); if tha=
t fails, png format output is\n created.\n\n Additionally, values for s=
everal arguments to the R graphics\n device can be passed using header ar=
gs:\n\n :width :height :bg :units :pointsize\n :antialias :quality :com=
pression :res :type\n :family :title :fonts :version :paper :encoding\n =
:pagecentre :colormodel :useDingbats :horizontal\n\n Arguments to the R =
graphics device that are not supported as header\n args can be passed as =
a string in R argument syntax, using the header\n arg :R-dev-args\n\n A=
n example block is (although both bg and fg can be passed directly as\n h=
eader args)\n\n \\#+begin_src R :file z.pdf :width 8 :height 8 :R-dev-arg=
s bg=3D\"olivedrab\", fg=3D\"hotpink\"\n plot(matrix(rnorm(100), ncol=
=3D2), type=3D\"l\")\n \\#+end_src\n\n - Yes, I think we do want a vers=
ion of this for python and ruby et al. In\nyour example, the filename is cr=
eated in python. I suggest doing it\nslightly differently, something like t=
his.\n\n#+srcname: fileoutput\n#+begin_src python :file outfile.txt\n def s=
avetofile(result, filename):\n with open(filename, 'w') as f:\n =
f.write(str(result))\n savetofile(78, 'outfile.txt')\n 55\n#+end_src\n\n#+=
resname: fileoutput\n[[file:outfile.txt]]\n\nThis functionality is now avai=
lable for ruby & python in branch\nded-babel of git://orgmode.org/org-mode/=
babel.git.\n\nSo here, if you specify :file ruby/python blindly =
outputs a\nlink to , regardless of the contents of the\ncode. Res=
ponsibility for creating useful contents of lies\nwith the code.=
Notice that with this you have to specify the output file\ntwice: once as =
an org-babel directive, and once in the python code. This\nis in contrast t=
o the graphics languages (dot, ditaa, asymptote), where\nthe results *autom=
atically* get sent to the file specified by :file. The\nsame is also true n=
ow for graphical output from R.\n\nThe difference with python, ruby et al i=
s that they might create file\noutput in a variety of ways which we can't a=
nticipate, so we can't\nautomatically send output to the file. In contrast,=
the graphics\nlanguage *always* create file output and always do it in the=
same\nway. [And in R it is possible to divert all graphical output to file=
] A\npossible extension of the above might be to use a \"magic variable\" s=
o\nthat a python variable is created e.g. __org_babel_output_file__ that\na=
lways holds a string corresponding to the file specified by :file. Eric\nma=
y have further ideas / views here. \n\n\n** DONE What function is bound to =
C-c '?\n - this document notes two different functions\n* Introduction\n =
:PROPERTIES:\n :CUSTOM_ID: introduction\n :END:\n\n Babel is about lett=
ing [[file:languages.org][many different languages]] work together.\n Prog=
ramming languages live in blocks inside natural language\n [[http://orgmod=
e.org/][Org-mode]] documents. A piece of data may pass from a table to a\n=
Python code block, then maybe move on to an =3DR=3D code block, and\n fi=
nally end up embedded as a value in the middle of a paragraph or\n possibl=
y pass through a =3Dgnuplot=3D code block and end up as a plot\n embedded =
in the document.\n\n Through extending [[http://orgmode.org/][Org-mode]] w=
ith several features for editing\n exporting and executing source code Bab=
el turns Org-mode into a tool\n for both /Literate Programming/ and /Repro=
ducible Research/.\n\n Babel augments [[http://orgmode.org/manual/Literal-=
examples.html][Org-mode support for code blocks]] by providing:\n\n - inte=
ractive and on-export execution of code blocks;\n - code blocks as functio=
ns that can be parameterised, refer to\n other code blocks, and be calle=
d remotely; and\n - export to files for literate programming.\n\n* Overvie=
w\n Babel provides new features on a few different fronts, and\n differen=
t people may want to start in different places.\n\n - Using 'src' blocks i=
n Org mode ::\n If you are not familiar with creating 'src' blocks in an=
Org-mode\n buffer, and moving between that buffer and the language majo=
r-mode\n edit buffer, then you should have a look at the relevant sectio=
n\n in the [[http://orgmode.org/manual/Literal-examples.html][Org manual=
]] and [[#source-code-blocks][below]], try it out, and come back.\n - Exec=
uting code ::\n The core of Babel is its ability to execute code in Org-=
mode\n 'src' blocks, taking input from other blocks and tables, with\n =
output to further blocks and tables. This is described starting\n [[#s=
ource-code-execution][here]].\n - Literate Programming ::\n If you are =
a programmer writing code that you would normally\n execute in some othe=
r way (e.g. from the command line, or sourcing\n it into an interactive =
session), then a simple introduction to\n Babel is to place your code in=
blocks in an Org-mode file, and to\n use Babel's [[#literate-programmin=
g][Literate Programming]] support to extract pure code\n from your Org f=
iles.\n \n All of these use cases, as well as exhaustive documentation =
of the\n features of Babel are covered in the [[http://orgmode.org/manual/=
Working-With-Source-Code.html#Working-With-Source-Code][Working with Source=
Code]]\n section of the Org manual.\n\n* Initial Configuration\n :PROPER=
TIES:\n :CUSTOM_ID: getting-started\n :results: silent\n :END:\n\n If =
you have a working Emacs installation, then getting started with\n Babel i=
s a simple process.\n\n 1) It is strongly recommended that you update to t=
he latest version\n of Org-mode by [[file:../../org-faq.org::keeping-cu=
rrent-with-Org-mode-development][keeping current with Org-mode development]=
]. As of\n Org-mode 7.0, Babel is included as part of Org-mode.\n\n 2=
) Optionally activate the subset of languages that you will want\n to e=
xecute with Babel. See [[file:languages.org::#configure][Configure active =
languages]]\n instructions. Emacs Lisp is activated by default so this=
step\n can be skipped for now and all =3Demacs-lisp=3D examples will s=
till\n work as expected.\n\n 3) Evaluate your modified .emacs.\n\n* Co=
de Blocks\n :PROPERTIES:\n :CUSTOM_ID: source-code-blocks\n :END:\=
n\n** Code Blocks in Org\n :PROPERTIES:\n :CUSTOM_ID: source-code-blo=
cks-org\n :END:\n\n Babel is all about [[http://orgmode.org/manual/Li=
teral-examples.html][code blocks]] in Org-mode. If you are\n unfamiliar =
with the notion of a code block in Org-mode, where they\n are called 'sr=
c' blocks, please have a look at the [[http://orgmode.org/manual/Literal-ex=
amples.html][Org-mode manual]]\n before proceeding.\n\n Code blocks i=
n [[#reference-and-documentation][supported languages]] can occur anywhere =
in an\n Org-mode file. Code blocks can be entered directly into\n th=
e Org-mode file, but it is often easier to enter code with the\n functio=
n =3Dorg-edit-src-code=3D, which is called with the keyboard\n shortcut,=
C-c '. This places the code block in a new\n buffer with the appropria=
te mode activated.\n\n#+begin_src org\n ,#+begin_src language org-switches=
\n ,body\n ,#+end_src\n#+end_src\n\n For example, a code block of [[ht=
tp://www.ruby-lang.org/][ruby]] code looks like this in\n an Org-mode fi=
le:\n\n#+begin_src org\n ,#+begin_src ruby\n ,require 'date'\n ,\"This f=
ile was last evaluated on #{Date.today}\"\n ,#+end_src\n#+end_src\n\n** Co=
de Blocks in Babel\n :PROPERTIES:\n :CUSTOM_ID: source-code-blocks-ba=
bel\n :END:\n\nBabel adds some new elements to code blocks. The basic\ns=
tructure becomes:\n\n#+begin_src org\n ,#+begin_src language org-switches=
header-arguments\n ,body\n ,#+end_src\n#+end_src\n\n\n- language :: The =
language of the code in the source-code block. Valid\n values must be m=
embers of =3Dorg-babel-interpreters=3D.\n- header-arguments :: Header argum=
ents control many facets of the\n evaluation and output of source-code =
blocks. See the [[file:reference.org::#header-arguments][Header\n Argu=
ments]] section for a complete review of available header\n arguments.\=
n- body :: The source code to be evaluated. An important key-binding\n =
is =3D=E2=80=8BC-c '=E2=80=8B=3D. This calls =3Dorg-edit-src-code=3D, a f=
unction that brings\n up an edit buffer containing the code using the E=
macs major mode\n appropriate to the language. You can edit your code =
block\n as you regularly would in Emacs.\n\n* Source Code Execution\n =
:PROPERTIES:\n :CUSTOM_ID: source-code-execution\n :END:\n\nBabel e=
xecutes code blocks for *interpreted* languages such\nas shell, python, R, =
etc. by passing code to the interpreter, which\nmust be installed on your s=
ystem. You control what is done with the\nresults of execution. \n\nHere a=
re examples of code blocks in three different languages,\nfollowed by their=
output. If you are viewing the Org-mode version of\nthis document in Emacs=
, place point anywhere inside a block and press\nC-c C-c to run the code[fn=
:1] (and feel free to alter it!).\n*** Ruby\nIn the Org-mode file:\n: #+beg=
in_src ruby\n: \"This file was last evaluated on #{Date.today}\"\n: #+end_s=
rc\n\nHTML export of code:\n#+begin_src ruby\n\"This file was last evaluate=
d on #{Date.today}\"\n#+end_src\n\nHTML export of the resulting string:\n#+=
resname:\n: This file was last evaluated on 2009-08-09\n\n*** Shell\nIn the=
Org-mode file:\n: #+begin_src sh\n: echo \"This file takes up `du -h org=
-babel.org |sed 's/\\([0-9k]*\\)[ ]*org-babel.org/\\1/'`\"\n: #+end_src\n\n=
HTML export of code:\n#+begin_src sh\n echo \"This file takes up `du -h or=
g-babel.org |sed 's/\\([0-9k]*\\)[ ]*org-babel.org/\\1/'`\"\n#+end_src\n\nH=
TML export of the resulting string:\n#+resname:\n: This file takes up 36K\=
n\n*** [[http://www.r-project.org/][R]] \n What are the most common wor=
ds in this file?\nIn the Org-mode file:\n: #+begin_src R :colnames yes\n: =
words <- tolower(scan(\"intro.org\", what=3D\"\", na.strings=3Dc(\"|\",\":=
\")))\n: t(sort(table(words[nchar(words) > 3]), decreasing=3DTRUE)[1:10])=
\n: #+end_src\n\nHTML export of code:\n#+begin_src R :colnames yes\n words=
<- tolower(scan(\"intro.org\", what=3D\"\", na.strings=3Dc(\"|\",\":\")))\=
n t(rev(sort(table(words[nchar(words) > 3])))[1:10])\n#+end_src\n#+results=
:\n| code | source | org-mode | #+end_src | #+begin_src | this | block | th=
at | org-babel | with |\n|------+--------+----------+-----------+----------=
---+------+-------+------+-----------+------|\n| 64 | 62 | 44 |=
42 | 41 | 36 | 34 | 28 | 28 | 27 |\n\n*** =
[[http://ditaa.sourceforge.net/][ditaa]]\n\nIn the Org-mode file:\n: #+begi=
n_src ditaa :file blue.png :cmdline -r\n: +---------+\n: | cBLU |\n: | =
|\n: | +----+\n: | |cPNK|\n: | | |\n: +----+----+\n: #+e=
nd_src\n\nHTML export of code:\n#+begin_src ditaa :file blue.png :cmdline -=
r\n+---------+\n| cBLU |\n| |\n| +----+\n| |cPNK|\n| | =
|\n+----+----+\n#+end_src\n\nHTML export of the resulting image:\n#+resn=
ame:\n[[file:../../images/babel/blue.png]]\n\n** Capturing the Results of C=
ode Evaluation\n :PROPERTIES:\n :CUSTOM_ID: results\n :END:\n Babel=
provides two fundamentally different modes for capturing\n the results o=
f code evaluation: functional mode and scripting\n mode. The choice of m=
ode is specified by the =3D:results=3D header\n argument.\n*** =3D:result=
s value=3D (functional mode)\n :PROPERTIES:\n :CUSTOM_ID: results-value=
\n :END:\n The 'result' of code evaluation is the *value* of the last=
\n statement in the code block. In functional mode, the\n code bloc=
k is a function with a return value. The return\n value of one code blo=
ck can be used as input for another\n code block, even one in a differe=
nt language. In this\n way, Babel becomes a [[meta-programming-languag=
e]]. If the block\n returns tabular data (a vector, array or table of s=
ome sort) then\n this will be held as an Org-mode table in the buffer. =
This\n setting is the default.\n \n For example, consider the f=
ollowing block of python code and its\n output.\n\n#+begin_src python :=
results value\nimport time\nprint(\"Hello, today's date is %s\" % time.ctim=
e())\nprint('Two plus two is')\nreturn 2 + 2\n#+end_src\n\n#+resname:\n: 4\=
n\nNotice that, in functional mode, the output consists of the value of\nth=
e last statement and nothing else.\n\n*** =3D:results output=3D (scripting =
mode)\n :PROPERTIES:\n :CUSTOM_ID: results-output\n :END:\n\n In =
scripting mode, Babel captures the text output of the\n code block and =
places it in the Org-mode buffer. It is\n called scripting mode because=
the code block contains a series of\n commands, and the output of each=
command is returned. Unlike\n functional mode, the code block itself h=
as no return value\n apart from the output of the commands it contains.=
[fn:2]\n\n Consider the result of evaluating this code block with\n =
scripting mode.\n\n#+srcname: name\n#+begin_src python :results output\nim=
port time\nprint(\"Hello, today's date is %s\" % time.ctime())\nprint('Two =
plus two is')\n2 + 2\n#+end_src\n\n#+resname: name\n: Hello, today's date i=
s Wed Nov 11 18:50:36 2009\n: Two plus two is\n\nHere, scripting mode retur=
ned the text that python sent to =3Dstdout=3D. Because\nthe code block doe=
sn't include a =3Dprint()=3D statement for the last\nvalue, =3D(2 + 2)=3D, =
4 does not appear in the results.\n\n** Session-based Evaluation\n For so=
me languages, such as python, R, ruby and shell, it is\n possible to run =
an interactive session as an \"inferior process\"\n within Emacs. This me=
ans that an environment is created containing\n data objects that persist=
between different source code\n blocks. Babel supports evaluation of cod=
e within such sessions\n with the =3D:session=3D header argument. If the =
header argument is\n given a value then that will be used as the name of =
the session.\n Thus, it is possible to run separate simultaneous sessions=
in the\n same language.\n\n Session-based evaluation is particularly u=
seful for prototyping and\n debugging. The function =3Dorg-babel-pop-to-=
session=3D can be used to\n switch to the session buffer.\n\n Once a co=
de block is finished, it is often best to execute it\n outside of a sessi=
on, so the state of the environment in which it\n executes will be certai=
n.\n\n With R, the session will be under the control of [[http://ess.r-pr=
oject.org/][Emacs Speaks\n Statistics]] as usual, and the full power of E=
SS is thus still\n available, both in the R session, and when switching t=
o the R code\n edit buffer with =3D=E2=80=8BC-c '=E2=80=8B=3D.\n\n** Argu=
ments to Code Blocks\n :PROPERTIES:\n :CUSTOM_ID: arguments-to-source-c=
ode-blocks\n :END:\n Babel supports parameterisation of code blocks, i.=
e.,\n arguments can be passed to code blocks, which gives them\n the st=
atus of *functions*. Arguments can be passed to code blocks in\n both fun=
ctional and scripting modes.\n\n*** Simple example of using a code block as=
a function\n\n First let's look at a very simple example. The followin=
g source\n code block defines a function, using python, that squares it=
s argument.\n\n#+srcname: square(x)\n#+begin_src python\nreturn x*x\n#+end_=
src\n\nIn the Org-mode file, the function looks like this:\n: #+source: squ=
are(x)\n: #+begin_src python\n: return x*x\n: #+end_src\n\n\nNow we use the=
source block:\n\n: #+call: square(x=3D6)\n(/for information on the/ =3Dcal=
l=3D /syntax see/ [[library-of-babel]])\n\n#+call: square(x=3D6)\n\n#+resul=
ts: square(x=3D6)\n: 36\n\n*** A more complex example using an Org-mode tab=
le as input\n\n In this example we define a function called =3Dfibonacc=
i-seq=3D, using\n Emacs Lisp. The function =3Dfibonacci-seq=3D compute=
s a Fibonacci\n sequence. The function takes a single argument, in thi=
s case, a\n reference to an Org-mode table.\n\n Here is the Org-mod=
e table that is passed to =3Dfibonacci-seq=3D:\n\n#+tblname: fibonacci-inpu=
ts\n| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |\n| 2 | 4 | 6 | 8 | 10 |=
12 | 14 | 16 | 18 | 20 |\n\nThe table looks like this in the Org-mode buff=
er:\n: #+tblname: fibonacci-inputs\n: | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |=
9 | 10 |\n: | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |\n\nThe [[http=
://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code:\=
n#+srcname: fibonacci-seq(fib-inputs=3Dfibonacci-inputs)\n#+begin_src emacs=
-lisp\n (defun fibonacci (n)\n (if (or (=3D n 0) (=3D n 1))\n n\=
n (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))\n \n (mapcar (lambda=
(row)\n (mapcar #'fibonacci row)) fib-inputs)\n#+end_src\n\nIn =
the Org-mode buffer the function looks like this:\n: #+srcname: fibonacci-s=
eq(fib-inputs=3Dfibonacci-inputs)\n: #+begin_src emacs-lisp\n: (defun fib=
onacci (n)\n: (if (or (=3D n 0) (=3D n 1))\n: n\n: (+ (fi=
bonacci (- n 1)) (fibonacci (- n 2)))))\n: \n: (mapcar (lambda (row)\n:=
(mapcar #'fibonacci row)) fib-inputs)\n: #+end_src\n\nThe retu=
rn value of =3Dfibonacci-seq=3D is a table:\n#+resname:\n| 1 | 1 | 2 | 3 |=
5 | 8 | 13 | 21 | 34 | 55 |\n| 1 | 3 | 8 | 21 | 55 | 144 | 377 | =
987 | 2584 | 6765 |\n\n** In-line Code Blocks\n Code can be evaluated in=
-line using the following syntax:\n\n: Without header args: src_lang{code} =
or with header args: src_lang[args]{code},\n: for example src_python[:sessi=
on]{10*x}, where x is a variable existing in the \n: python session.\n\n** =
Code Block Body Expansion\n Babel \"expands\" code blocks prior to eval=
uation, i.e., the\n evaluated code comprises the code block contents au=
gmented with\n code that assigns referenced data to variables. It is po=
ssible to\n preview expanded contents, and also to expand code during\n=
tangling. Expansion takes into account header arguments and\n var=
iables.\n\n- preview :: =3DC-c M-b p=3D is bound to =3Dorg-babel-expand-src=
-block=3D. It\n can be used inside a code block to preview the expande=
d\n contents. This facility is useful for debugging.\n\n- tangling :: T=
he expanded body can be tangled. Tangling this way includes\n variable=
values that may be \n - the results of other code blocks, \n=
- variables stored in headline properties, or \n =
- tables. \n\n One possible use for tangling expanded code block is f=
or emacs\n initialization. Values such as user names and passwords can=
be\n stored in headline properties or in tables. The =3D:no-expand=3D=
\n header argument can be used to inhibit expansion of a code block\n =
during tangling.\n\nHere is an example of a code block and its resulting=
expanded body.\n\nThe data are kept in a table:\n#+tblname: user-data\n| u=
sername | john-doe |\n| password | abc123 |\n\nThe code block refers to t=
he data table:\n#+srcname: setup-my-account\n#+begin_src emacs-lisp :rownam=
es yes :var data=3Duser-data\n (setq my-special-username (first (first dat=
a)))\n (setq my-special-password (first (second data)))\n#+end_src\n \nWi=
th point inside the code block, =3DC-c M-b p=3D expands the contents:\n#+b=
egin_src emacs-lisp\n (let ((data (quote ((\"john-doe\") (\"abc123\")))))\=
n (setq my-special-username (first (first data)))\n (setq my-special-pass=
word (first (second data)))\n )\n#+end_src\n\n\n** A Meta-programming Lang=
uage for Org-mode\n :PROPERTIES:\n :CUSTOM_ID: meta-programming-language\=
n :END:\n\nBecause the return value of a function written in one language =
can be\npassed to a function written in another language, or to an Org-mode=
\ntable, which is itself programmable, Babel can be used as a\nmeta-functio=
nal programming language. With Babel, functions from\nmany languages can w=
ork together. You can mix and match languages,\nusing each language for th=
e tasks to which it is best suited.\n\nFor example, let's take some system =
diagnostics in the shell and graph them with R.\n\n1. Create a code block, =
using shell code, to list\n directories in our home directory, together w=
ith their\n sizes. Babel automatically converts the output into an Org-mo=
de\n table.\n \n: #+srcname: directories\n: #+begin_src sh :results rep=
lace\n: cd ~ && du -sc * |grep -v total\n: #+end_src\n \n#+resname: dir=
ectories\n| 72 | \"Desktop\" |\n| 12156104 | \"Documents\" |\n| 34=
82440 | \"Downloads\" |\n| 2901720 | \"Library\" |\n| 57344 | \"Movie=
s\" |\n| 16548024 | \"Music\" |\n| 120 | \"News\" |\n| 76=
49472 | \"Pictures\" |\n| 0 | \"Public\" |\n| 152224 | \"Sites=
\" |\n| 8 | \"System\" |\n| 56 | \"bin\" |\n| 38=
21872 | \"mail\" |\n| 10605392 | \"src\" |\n| 1264 | \"tools=
\" |\n\n2. A function, written with a single line of R code, plots the =
data\n in the Org-mode table as a\n pie-chart. Note how this code block=
uses the =3Dsrcname=3D\n of the previous code block to obtain the data.\=
n\nIn the Org-mode file: \n: #+srcname: directory-pie-chart(dirs =3D direct=
ories)\n: #+begin_src R :session R-pie-example :file ../../images/babel/dir=
s.png\n: pie(dirs[,1], labels =3D dirs[,2])\n: #+end_src\n\nHTML export o=
f code:\n#+srcname: directory-pie-chart(dirs =3D directories)\n#+begin_src =
R :session R-pie-example :file ../../images/babel/dirs.png\n pie(dirs[,1],=
labels =3D dirs[,2])\n#+end_src\n [[file:../../images/babel/dirs.png]]\n\n=
* Using Code Blocks in Org Tables\n :PROPERTIES:\n :CUSTOM_ID: spreadshee=
t\n :END:\n\nIn addition to passing data from tables as [[arguments-to-sou=
rce-code-blocks][arguments]] to code\nblocks, and [[#results-value][storing=
]] results as tables, Babel can be used in a\nthird way with Org-mode table=
s. First note that Org-mode's [[http://orgmode.org/manual/The-spreadsheet.h=
tml#The-spreadsheet][existing\nspreadsheet functionality]] allows values in=
cells to be computed\nautomatically from the values of other cells, using =
a =3D#+TBLFM=3D\nformula line. In this way, table computations can be carri=
ed out using\n[[http://orgmode.org/manual/Formula-syntax-for-Calc.html#Form=
ula-syntax-for-Calc][calc]] and [[http://orgmode.org/manual/Formula-syntax-=
for-Lisp.html#Formula-syntax-for-Lisp][emacs lisp]].\n\nWhat Babel adds is =
the ability to use code blocks (in whatever\nlanguage) in the =3D#+TBLFM=3D=
line to perform the necessary computation.\n\n*** Example 1: Data Summarie=
s Using R\nAs a simple example, we'll fill in a cell in an Org-mode table w=
ith the\naverage value of a few numbers. First, let's make some data. The\n=
following source block creates an Org-mode table filled with five random\nn=
umbers between 0 and 1.\n\n: #+srcname: tbl-example-data()\n: #+begin_src R=
\n: runif(n=3D5, min=3D0, max=3D1)\n: #+end_src\n\n#+resname: tbl-example-=
data\n| 0.836685163900256 |\n| 0.696652316721156 |\n| 0.382423302158713 |\n=
| 0.987541858805344 |\n| 0.994794291909784 |\n\nNow we define a source bloc=
k to calculate the mean.\n\nIn the Org-mode file:\n: #+srcname: R-mean(x)\n=
: #+begin_src R \n: mean(x)\n: #+end_src\n\nHTML export of code:\n#+srcname=
: R-mean(x)\n#+begin_src R \nmean(x)\n#+end_src\n\nFinally, we create the t=
able which is going to make use of the R\ncode. This is done using the =3Ds=
be=3D ('source block evaluate') macro in\nthe table formula line.\n\nIn the=
Org-mode file:\n: #+tblname: summaries\n: | mean |\n: |------=
-------------|\n: | 0.779619386699051 |\n: #+TBLFM: @2$1=3D'(sbe \"R-mean\"=
(x \"tbl-example-data()\"))\n\nHTML export of code:\n#+tblname: summaries\=
n| mean |\n|------|\n| 0.78 |\n#+TBLFM: @2$1=3D'(sbe R-mean (x tbl-example-=
data));%.2f\n\nTo recalculate the table formula, use C-u C-c C-c in the\nta=
ble. Notice that as things stand the calculated value doesn't\nchange, beca=
use the data (held in the table above named\n=3Dtbl-example-data=3D) are st=
atic. However, if you delete that data table,\nthen the reference will be i=
nterpreted as a reference to the source\nblock responsible for generating t=
he data; each time the table formula\nis recalculated the source block will=
be evaluated again, and\ntherefore the calculated average value will chang=
e.\n\n*** Example 2: Babel Test Suite\nWhile developing Babel, we used a su=
ite of tests implemented\nas a large Org-mode table. To run the entire tes=
t suite we simply\nevaluate the table with C-u C-c C-c: all of the tests ar=
e run,\nthe results are compared with expectations, and the table is update=
d\nwith results and pass/fail statistics.\n\nHere's a sample of our test su=
ite.\n\nIn the Org-mode file:\n\n: #+TBLNAME: org-babel-tests\n: | function=
ality | block | arg | expected | results | pass |\n: |----=
--------------+--------------+-----+-------------+-------------+------|\n: =
| basic evaluation | | | | | pass =
|\n: |------------------+--------------+-----+-------------+-------------+-=
-----|\n: | emacs lisp | basic-elisp | 2 | 4 | =
4 | pass |\n: | shell | basic-shell | | 6 | =
6 | pass |\n: | ruby | basic-ruby | | org-babel |=
org-babel | pass |\n: | python | basic-python | | hello wo=
rld | hello world | pass |\n: | R | basic-R | | =
13 | 13 | pass |\n: #+TBLFM: $5=3D'(if (=3D (length $3) 1) (=
sbe $2 (n $3)) (sbe $2)) :: $6=3D'(if (string=3D $4 $5) \"pass\" (format \"=
expected %S but was %S\" $4 $5))\n\nHTML export of code:\n\n#+TBLNAME: org-=
babel-tests\n| functionality | block | arg | expected | re=
sults | pass |\n|------------------+--------------+-----+-------------+----=
---------+------|\n| basic evaluation | | | | =
| pass |\n|------------------+--------------+-----+------------=
-+-------------+------|\n| emacs lisp | basic-elisp | 2 | =
4 | 4 | pass |\n| shell | basic-shell | | =
6 | 6 | pass |\n| ruby | basic-ruby | | =
org-babel | org-babel | pass |\n| python | basic-python | |=
hello world | hello world | pass |\n| R | basic-R | =
| 13 | 13 | pass |\n#+TBLFM: $5=3D'(if (=3D (length $3)=
1) (sbe $2 (n $3)) (sbe $2)) :: $6=3D'(if (string=3D $4 $5) \"pass\" (form=
at \"expected %S but was %S\" $4 $5))\n\n**** code blocks for tests\n\nIn t=
he Org-mode file:\n\n: #+srcname: basic-elisp(n)\n: #+begin_src emacs-lisp\=
n: (* 2 n)\n: #+end_src\n\nHTML export of code:\n\n#+srcname: basic-elisp(n=
)\n#+begin_src emacs-lisp\n (* 2 n)\n#+end_src\n\nIn the Org-mode file:\n:=
#+srcname: basic-shell\n: #+begin_src sh :results silent\n: expr 1 + 5\n: =
#+end_src\n\nHTML export of code:\n#+srcname: basic-shell\n#+begin_src sh :=
results silent\n expr 1 + 5\n#+end_src\n\nIn the Org-mode file:\n: #+srcna=
me: date-simple\n: #+begin_src sh :results silent\n: date\n: #+end_src\n\nH=
TML export of code:\n#+srcname: date-simple\n#+begin_src sh :results silent=
\n date\n#+end_src\n\nIn the Org-mode file:\n: #+srcname: basic-ruby\n: #+=
begin_src ruby :results silent\n: \"org-babel\"\n: #+end_src\n\nHTML export=
of code:\n#+srcname: basic-ruby\n#+begin_src ruby :results silent\n \"org=
-babel\"\n#+end_src\n\nIn the Org-mode file\n: #+srcname: basic-python\n: #=
+begin_src python :results silent\n: 'hello world'\n: #+end_src\n\nHTML exp=
ort of code:\n#+srcname: basic-python\n#+begin_src python :results silent\n=
'hello world'\n#+end_src\n\nIn the Org-mode file:\n: #+srcname: basic-R\n=
: #+begin_src R :results silent\n: b <- 9\n: b + 4\n: #+end_src\n\nHTML exp=
ort of code:\n#+srcname: basic-R\n#+begin_src R :results silent\n b <- 9\n=
b + 4\n#+end_src\n\n* The Library of Babel\n :PROPERTIES:\n :CUSTOM_ID:=
library-of-babel\n :END:\n\n (see also [[http://orgmode.org/manual/Libra=
ry-of-Babel.html#Library-of-Babel][Org manual:Library-of-Babel]])\n\n As w=
e saw above with the [[*Simple%20example%20of%20using%20a%20source%20block%=
20as%20a%20function][=3Dsquare=3D]] example, once a source block\n functio=
n has been defined it can be called using the =3Dlob=3D notation:\n\n : #+=
lob: square(x=3D6)\n\n But what about code blocks that you want to make av=
ailable to\n every Org-mode buffer?\n\n In addition to the current buffer=
, Babel searches for\n pre-defined code block functions in the Library of\=
n Babel. This is a user-extensible collection of ready-made source\n code=
blocks for handling common tasks. One use for the Library of\n Babel (no=
t yet done!) will be to provide a choice of data graphing\n procedures for=
data held in Org-mode tables, using languages such as\n R, gnuplot, asymp=
tote, etc. If you implement something that might be\n of use to other Org-=
mode users, please consider adding it to the\n Library of Babel; similarly=
, feel free to request help solving a\n problem using external code via Ba=
bel -- there's always a chance\n that other Babel users will be able to co=
ntribute some helpful\n code.\n\n Babel comes pre-populated with the code=
blocks located in\n the [[file:library-of-babel.org][Library of Babel]] f=
ile -- raw file at\n#+html: library-of-babel.org\n =
--. It is possible to add code blocks to the library from any\n Org-mode f=
ile using the =3Dorg-babel-lob-ingest=3D (bound to =3DC-c C-v\n l=3D).\n\n=
#+srcname: add-file-to-lob\n #+begin_src emacs-lisp \n (org-babel-lob-i=
ngest \"path/to/file.org\")\n #+end_src\n\n Note that it is possible to p=
ass table values or the output of a\n source-code block to Library of Babe=
l functions. It is also possible\n to reference Library of Babel functions=
in arguments to code blocks.\n\n* Literate Programming\n :PROPERTIES:\n =
:CUSTOM_ID: literate-programming\n :END:\n\n#+begin_quote\nLet us change o=
ur traditional attitude to the construction of\nprograms: Instead of imagin=
ing that our main task is to instruct a\n/computer/ what to do, let us conc=
entrate rather on explaining to\n/human beings/ what we want a computer to =
do.\n\nThe practitioner of literate programming can be regarded as an\nessa=
yist, whose main concern is with exposition and excellence of\nstyle. Such =
an author, with thesaurus in hand, chooses the names of\nvariables carefull=
y and explains what each variable means. He or she\nstrives for a program t=
hat is comprehensible because its concepts have\nbeen introduced in an orde=
r that is best for human understanding,\nusing a mixture of formal and info=
rmal methods that reinforce each\nother.\n\n -- Donald Knuth\n#+end_quote\n=
\nBabel supports [[http://en.wikipedia.org/wiki/Literate_programming][Liter=
ate Programming]] (LP) by allowing the act of\nprogramming to take place in=
side of Org-mode documents. The Org-mode\nfile can then be exported (*wove=
n* in LP speak) to HTML or LaTeX for\nconsumption by a human, and the embed=
ded source code can be extracted\n(*tangled* in LP speak) into structured s=
ource code files for\nconsumption by a computer.\n\nTo support these operat=
ions Babel relies on Org-mode's [[http://orgmode.org/manual/Exporting.html#=
Exporting][existing\nexporting functionality]] for *weaving* of documentati=
on, and on the\n=3Dorg-babel-tangle=3D function which makes use of [[http:/=
/www.cs.tufts.edu/~nr/noweb/][Noweb]] [[noweb-reference-syntax][reference s=
yntax]]\nfor *tangling* of code files.\n\nThe [[literate-programming-exampl=
e][following example]] demonstrates the process of *tangling* in\nBabel.\n\=
n*** Simple Literate Programming Example (Noweb syntax)\n :PROPERTIES:\n=
:CUSTOM_ID: literate-programming-example\n :END:\n\nTangling functio=
nality is controlled by the =3Dtangle=3D family of [[tangle-header-argument=
s][Tangle\nheader arguments]]. These arguments can be used to turn tanglin=
g on or\noff (the default), either for the code block or the Org-mode\nhead=
ing level.\n\nThe following code blocks demonstrate how to tangle them into=
a\nsingle source code file using =3Dorg-babel-tangle=3D.\n\nThe following =
two code blocks have no =3Dtangle=3D header arguments\nand so will not, by =
themselves, create source code files. They are\nincluded in the source cod=
e file by the third code block, which\ndoes have a =3Dtangle=3D header argu=
ment.\n\nIn the Org-mode file:\n: #+srcname: hello-world-prefix\n: #+begin_=
src sh :exports none\n: echo \"/-----------------------------------------=
------------------\\\\\"\n: #+end_src\n\nHTML export of code:\n#+srcname: h=
ello-world-prefix\n#+begin_src sh :exports none\n echo \"/----------------=
-------------------------------------------\\\\\"\n#+end_src\n\nIn the Org-=
mode file\n: #+srcname: hello-world-postfix\n: #+begin_src sh :exports none=
\n: echo \"\\-----------------------------------------------------------/=
\"\n: #+end_src\n\nHTML export of code:\n#+srcname: hello-world-postfix\n#+=
begin_src sh :exports none\n echo \"\\------------------------------------=
-----------------------/\"\n#+end_src\n\n\nThe third code block does have a=
=3Dtangle=3D header argument\nindicating the name of the file to which the=
tangled source code will\nbe written. It also has [[http://www.cs.tufts.e=
du/~nr/noweb/][Noweb]] style references to the two previous\ncode blocks. =
These references will be expanded during tangling\nto include them in the o=
utput file as well.\n\nIn the Org-mode file:\n: #+srcname: hello-world\n: #=
+begin_src sh :tangle hello :exports none :noweb yes\n: <>\n: echo \"| hello world =
|\"\n: <>\n: #+end_src\n\nHTML export of code:\n#=
+srcname: hello-world\n#+begin_src sh :tangle hello.sh :exports none :noweb=
yes\n <>\n echo \"| hello worl=
d |\"\n <>\n#+end_src\n\n\nCa=
lling =3Dorg-babel-tangle=3D will result in the following shell source\ncod=
e being written to the =3Dhello.sh=3D file:\n\n#+srcname: hello-world-outpu=
t\n#+begin_src sh \n#!/usr/bin/env sh\n\n# [[file:~/org/temp/index.org::*No=
web%20test][hello-world]]\n\necho \"/--------------------------------------=
---------------------\\\\\"\necho \"| hello world =
|\"\necho \"\\----------------------------------------=
-------------------/\"\n# hello-world ends here\n#+end_src\n\nIn addition, =
the following syntax can be used to insert the *results*\nof evaluating a c=
ode block, in this case one named =3Dexample-block=3D.\n\n: # <>\n\nAny optional arguments can be passed to =3Dexample-block()=3D by =
placing the\narguments inside the parentheses following the convention defi=
ned when\ncalling source block functions (see the [[library-of-babel][Libra=
ry of babel]]). For example,\n\n: # <>\n\nsets the va=
lue of argument \\\"a\\\" equal to \\\"9\\\". Note that\nthese arguments a=
re not evaluated in the current source-code\nblock but are passed literally=
to =3Dexample-block()=3D.\n\n*** Emacs Initialization with Babel\n :PRO=
PERTIES:\n :CUSTOM_ID: emacs-initialization\n :END:\n\n#+attr_html: s=
tyle=3D\"float:left;\"\n[[file:../../images/babel/dot-emacs.png]]\n\nBabel =
has special support for embedding your Emacs initialization\ninto Org-mode =
files. The =3Dorg-babel-load-file=3D function can be used\nto load the Ema=
cs Lisp code blocks embedded in a literate\nOrg-mode file in the same way t=
hat you might load a regular Emacs Lisp\nfile, such as .emacs.\n\nThis allo=
ws you to make use of the nice features of Org-mode, such as folding, tags,=
\nnotes, HTML export, etc., to organize and maintain your Emacs initializat=
ion.\n\nTo try this out, either see the simple [[literate-emacs-init][Liter=
ate Emacs Initialization]]\nexample, or check out the Babel Literate Progra=
mming version of\nPhil Hagelberg's excellent [[http://github.com/technomanc=
y/emacs-starter-kit/tree/master][emacs-starter-kit]] available at\n[[http:/=
/github.com/eschulte/emacs-starter-kit/tree/master][Org-babel-emacs-starter=
-kit]].\n\n***** Literate Emacs Initialization\n :PROPERTIES:\n :=
CUSTOM_ID: literate-emacs-init\n :END:\n\nFor a simple example of usag=
e, follow these 5 steps:\n\n1) create a directory named =3D.emacs.d=3D in t=
he base of your home\n directory;\n #+begin_src sh \n mkdir ~/.emacs.=
d\n #+end_src\n2) checkout the latest version of Org-mode into the src su=
bdirectory\n of this new directory;\n #+begin_src sh\n cd ~/.emacs.d\=
n mkdir src\n cd src\n git clone git://orgmode.org/org-mode.git\n #=
+end_src\n3) place the following code block in a file called =3Dinit.el=3D =
in your Emacs\n initialization directory (=3D~/.emacs.d=3D).\n #+srcnam=
e: emacs-init\n #+begin_src emacs-lisp \n ;;; init.el --- Where all t=
he magic begins\n ;;\n ;; This file loads Org-mode and then loads t=
he rest of our Emacs initialization from Emacs lisp\n ;; embedded in li=
terate Org-mode files.\n \n ;; Load up Org Mode and (now included) =
Org Babel for elisp embedded in Org Mode files\n (setq dotfiles-dir (fi=
le-name-directory (or (buffer-file-name) load-file-name)))\n \n (le=
t* ((org-dir (expand-file-name\n \"lisp\" (expand-file=
-name\n \"org\" (expand-file-name\n =
\"src\" dotfiles-dir))))\n (org-contri=
b-dir (expand-file-name\n \"lisp\" (expand-fil=
e-name\n \"contrib\" (expand-file-name=
\n \"..\" org-dir))))\n =
(load-path (append (list org-dir org-contrib-dir)\n =
(or load-path nil))))\n ;; load up Org-mode and Org-ba=
bel\n (require 'org-install)\n (require 'ob-tangle))\n \n =
;; load up all literate org-mode files in this directory\n (mapc #'o=
rg-babel-load-file (directory-files dotfiles-dir t \"\\\\.org$\"))\n \n=
;;; init.el ends here\n #+end_src\n4) implement all of your Emacs cu=
stomizations inside of Emacs Lisp\n code blocks embedded in Org-mode file=
s in this directory;\n and\n5) re-start Emacs to load the customizations=
.\n\n* Reproducible Research\n :PROPERTIES:\n :CUSTOM_ID: reproducable-re=
search\n :END:\n#+begin_quote \nAn article about computational science in =
a scientific publication is\nnot the scholarship itself, it is merely adver=
tising of the\nscholarship. The actual scholarship is the complete software=
\ndevelopment environment and the complete set of instructions which\ngener=
ated the figures.\n\n-- D. Donoho\n#+end_quote\n\n[[http://reproduciblerese=
arch.net/index.php/Main_Page][Reproducible Research]] (RR) is the practice =
of distributing, along with\na research publication, all data, software sou=
rce code, and tools\nrequired to reproduce the results discussed in the pub=
lication. As\nsuch the RR package not only describes the research and its =
results,\nbut becomes a complete laboratory in which the research can be\nr=
eproduced and extended.\n\nOrg-mode already has exceptional support for [[h=
ttp://orgmode.org/manual/Exporting.html#Exporting][exporting to HTML and\nL=
aTeX]]. Babel makes Org-mode a tool for RR by *activating* the\ndata and c=
ode blocks embedded in Org-mode documents; the\nentire document becomes exe=
cutable. This makes it possible, and natural, to\ndistribute research in a=
format that encourages readers to recreate\nresults and perform their own =
analyses.\n\nOne notable existing RR tool is [[http://en.wikipedia.org/wiki=
/Sweave][Sweave]], which provides a mechanism for\nembedding [[http://www.r=
-project.org/][R]] code into LaTeX documents. Sweave is a mature\nand very=
useful tool, but we believe that Babel has several\nadvantages:\n - it sup=
ports multiple languages (we're not aware of other RR tools that do this);\=
n - the [[http://orgmode.org/manual/Exporting.html#Exporting][export proces=
s]] is flexible and powerful, including HTML as a\n target in addition to=
LaTeX; and\n - the document can make use of Org-mode features that support=
[[http://orgmode.org/manual/Agenda-Views.html#Agenda-Views][project\n pl=
anning]] and [[http://orgmode.org/manual/TODO-Items.html#TODO-Items][task m=
anagement]].\n\n* Footnotes\n[fn:1] Calling =3DC-c C-o=3D on a code block w=
ill open the\nblock's results in a separate buffer.\n\n[fn:2] This mode wi=
ll be familiar to Sweave users.\n\n" 0 117 (fontified t face org-meta-line =
font-lock-fontified t) 117 118 (fontified t font-lock-fontified t face org-=
meta-line) 118 194 (fontified t face org-meta-line font-lock-fontified t) 1=
94 195 (fontified t font-lock-fontified t face org-meta-line) 195 265 (font=
ified t face org-meta-line font-lock-fontified t) 265 266 (fontified t font=
-lock-fontified t face org-meta-line) 266 326 (fontified t face org-meta-li=
ne font-lock-fontified t) 326 327 (fontified t font-lock-fontified t face o=
rg-meta-line) 327 335 (fontified t face org-document-info-keyword font-lock=
-fontified t) 335 341 (fontified t face font-lock-comment-face) 341 360 (fo=
ntified t face org-document-title font-lock-fontified t) 360 361 (fontified=
t) 361 370 (fontified t face org-document-info-keyword font-lock-fontified=
t) 370 375 (fontified t face font-lock-comment-face) 375 409 (fontified t =
face org-document-info font-lock-fontified t) 409 410 (fontified t) 410 418=
(fontified t face org-document-info-keyword font-lock-fontified t) 418 424=
(fontified t face font-lock-comment-face) 424 514 (fontified t face org-do=
cument-info font-lock-fontified t) 514 515 (fontified t) 515 531 (fontified=
t face org-meta-line font-lock-fontified t) 531 532 (fontified t font-lock=
-fontified t face org-meta-line) 532 623 (fontified t face org-meta-line fo=
nt-lock-fontified t) 623 624 (fontified t font-lock-fontified t face org-me=
ta-line) 624 706 (fontified t face org-meta-line font-lock-fontified t) 706=
707 (fontified t font-lock-fontified t face org-meta-line) 707 728 (fontif=
ied t face org-meta-line font-lock-fontified t) 728 729 (fontified t font-l=
ock-fontified t face org-meta-line) 729 742 (fontified t face org-meta-line=
font-lock-fontified t) 742 764 (fontified t org-no-flyspell t mouse-face h=
ighlight face org-meta-line keymap (keymap (follow-link . mouse-face) (mous=
e-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) font-lock-font=
ified t) 764 765 (fontified t org-no-flyspell t mouse-face highlight face o=
rg-meta-line keymap (keymap (follow-link . mouse-face) (mouse-3 . org-find-=
file-at-mouse) (mouse-2 . org-open-at-mouse)) rear-nonsticky (mouse-face hi=
ghlight keymap invisible intangible help-echo org-linked-text) font-lock-fo=
ntified t) 765 766 (fontified t font-lock-fontified t face org-meta-line) 7=
66 767 (fontified t) 767 779 (fontified t font-lock-fontified t face org-bl=
ock-begin-line font-lock-multiline t) 779 780 (fontified t font-lock-fontif=
ied t font-lock-multiline t face org-block-begin-line) 780 1019 (fontified =
t font-lock-fontified t font-lock-multiline t face org-block) 1019 1191 (fo=
ntified nil font-lock-fontified t font-lock-multiline t face org-block) 119=
1 1249 (fontified nil font-lock-fontified t org-no-flyspell t mouse-face hi=
ghlight face org-block keymap (keymap (follow-link . mouse-face) (mouse-3 .=
org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) font-lock-multiline=
t) 1249 1250 (fontified nil font-lock-fontified t org-no-flyspell t mouse-=
face highlight face org-block keymap (keymap (follow-link . mouse-face) (mo=
use-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) rear-nonstic=
ky (mouse-face highlight keymap invisible intangible help-echo org-linked-t=
ext) font-lock-multiline t) 1250 1599 (fontified nil font-lock-fontified t =
font-lock-multiline t face org-block) 1599 1600 (fontified nil font-lock-fo=
ntified t font-lock-multiline t face org-block) 1600 1610 (fontified t font=
-lock-fontified t face org-block-end-line font-lock-multiline t) 1610 1611 =
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file-at-mouse) (mouse-2 . org-open-at-mouse)) invisible org-link font-lock-=
multiline t help-echo "LINK: http://reproducibleresearch.net/index.php/Main=
_Page" rear-nonsticky (mouse-face highlight keymap invisible intangible hel=
p-echo org-linked-text)) 41100 41111 (fontified t org-no-flyspell t mouse-f=
ace highlight face org-link keymap (keymap (follow-link . mouse-face) (mous=
e-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) font-lock-mult=
iline t help-echo "LINK: http://reproducibleresearch.net/index.php/Main_Pag=
e") 41111 41112 (fontified t org-no-flyspell t mouse-face highlight face or=
g-link keymap (keymap (follow-link . mouse-face) (mouse-3 . org-find-file-a=
t-mouse) (mouse-2 . org-open-at-mouse)) rear-nonsticky (mouse-face highligh=
t keymap invisible intangible help-echo org-linked-text) font-lock-multilin=
e t help-echo "LINK: http://reproducibleresearch.net/index.php/Main_Page") =
41112 41120 (fontified t org-no-flyspell t keymap (keymap (follow-link . mo=
use-face) (mouse-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse))=
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d t org-no-flyspell t keymap (keymap (follow-link . mouse-face) (mouse-3 . =
org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) mouse-face highlight=
font-lock-multiline t help-echo "LINK: http://reproducibleresearch.net/ind=
ex.php/Main_Page" rear-nonsticky (mouse-face highlight keymap invisible int=
angible help-echo org-linked-text) face org-link) 41121 41122 (fontified t =
org-no-flyspell t invisible org-link keymap (keymap (follow-link . mouse-fa=
ce) (mouse-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) mouse=
-face highlight font-lock-multiline t help-echo "LINK: http://reproducibler=
esearch.net/index.php/Main_Page" face org-link) 41122 41123 (fontified t or=
g-no-flyspell t invisible org-link keymap (keymap (follow-link . mouse-face=
) (mouse-3 . org-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) mouse-f=
ace highlight font-lock-multiline t help-echo "LINK: http://reproducibleres=
earch.net/index.php/Main_Page" rear-nonsticky (mouse-face highlight keymap =
invisible intangible help-echo org-linked-text) face org-link) 41123 41173 =
(fontified t) 41173 42636 (fontified nil) 42636 42637 (fontified t) 42637 4=
2639 (fontified t face org-level-1) 42639 42648 (fontified t face org-level=
-1) 42648 42649 (fontified t) 42649 42655 (fontified t org-no-flyspell t mo=
use-face highlight keymap (keymap (follow-link . mouse-face) (mouse-3 . org=
-find-file-at-mouse) (mouse-2 . org-open-at-mouse)) help-echo "Footnote def=
inition" font-lock-fontified t font-lock-multiline t face org-footnote) 426=
55 42663 (fontified t) 42663 42664 (fontified t org-no-flyspell t) 42664 42=
673 (fontified t face (org-code) org-no-flyspell t font-lock-multiline t or=
g-emphasis t) 42673 42674 (fontified t org-no-flyspell t) 42674 42743 (font=
ified t) 42743 42749 (fontified t org-no-flyspell t mouse-face highlight ke=
ymap (keymap (follow-link . mouse-face) (mouse-3 . org-find-file-at-mouse) =
(mouse-2 . org-open-at-mouse)) help-echo "Footnote definition" font-lock-fo=
ntified t font-lock-multiline t face org-footnote) 42749 42796 (fontified t=
)) :emph-multiline t :for-backend html :skip-before-1st-heading nil :drawer=
s (HIDE) :todo-keywords t :tasks t :tags not-in-toc :priority nil :footnote=
s t :timestamps nil :archived-trees nil :select-tags ("export") :exclude-ta=
gs ("noexport") :add-text nil :LaTeX-fragments nil)
(org-split-string (org-export-preprocess-string region :emph-multiline t =
:for-backend (quote html) :skip-before-1st-heading (plist-get opt-plist :sk=
ip-before-1st-heading) :drawers (plist-get opt-plist :drawers) :todo-keywor=
ds (plist-get opt-plist :todo-keywords) :tasks (plist-get opt-plist :tasks)=
:tags (plist-get opt-plist :tags) :priority (plist-get opt-plist :priority=
) :footnotes (plist-get opt-plist :footnotes) :timestamps (plist-get opt-pl=
ist :timestamps) :archived-trees (plist-get opt-plist :archived-trees) :sel=
ect-tags (plist-get opt-plist :select-tags) :exclude-tags (plist-get opt-pl=
ist :exclude-tags) :add-text (plist-get opt-plist :text) :LaTeX-fragments (=
plist-get opt-plist :LaTeX-fragments)) "[=0D\n]")
(let* ((opt-plist (org-export-process-option-filters (org-combine-plists =
(org-default-export-plist) ext-plist (org-infile-export-plist)))) (body-onl=
y (or body-only (plist-get opt-plist :body-only))) (style (concat (if (plis=
t-get opt-plist :style-include-default) org-export-html-style-default) (pli=
st-get opt-plist :style) (plist-get opt-plist :style-extra) "\n" (if (plist=
-get opt-plist :style-include-scripts) org-export-html-scripts))) (html-ext=
ension (plist-get opt-plist :html-extension)) valid thetoc have-headings fi=
rst-heading-pos (odd org-odd-levels-only) (region-p (org-region-active-p)) =
(rbeg (and region-p (region-beginning))) (rend (and region-p (region-end)))=
(subtree-p (if (plist-get opt-plist :ignore-subtree-p) nil (when region-p =
(save-excursion (goto-char rbeg) (and (org-at-heading-p) (>=3D ... rend))))=
)) (level-offset (if subtree-p (save-excursion (goto-char rbeg) (+ (funcall=
outline-level) (if org-odd-levels-only 1 0))) 0)) (opt-plist (setq org-exp=
ort-opt-plist (if subtree-p (org-export-add-subtree-options opt-plist rbeg)=
opt-plist))) (org-current-export-dir (or pub-dir (org-export-directory :ht=
ml opt-plist))) (org-current-export-file buffer-file-name) (level 0) (line =
"") (origline "") txt todo (umax nil) (umax-toc nil) (filename (if to-buffe=
r nil (expand-file-name (concat (file-name-sans-extension (or ... ...)) "."=
html-extension) (file-name-as-directory (or pub-dir (org-export-directory =
:html opt-plist)))))) (current-dir (if buffer-file-name (file-name-director=
y buffer-file-name) default-directory)) (buffer (if to-buffer (cond ((eq to=
-buffer (quote string)) (get-buffer-create "*Org HTML Export*")) (t (get-bu=
ffer-create to-buffer))) (find-file-noselect filename))) (org-levels-open (=
make-vector org-level-max nil)) (date (plist-get opt-plist :date)) (author =
(plist-get opt-plist :author)) (html-validation-link (or org-export-html-va=
lidation-link "")) (title (org-html-expand (or (and subtree-p (org-export-g=
et-title-from-subtree)) (plist-get opt-plist :title) (and (not body-only) (=
not (plist-get opt-plist :skip-before-1st-heading)) (org-export-grab-title-=
from-buffer)) (and buffer-file-name (file-name-sans-extension (file-name-no=
ndirectory buffer-file-name))) "UNTITLED"))) (link-up (and (plist-get opt-p=
list :link-up) (string-match "\\S-" (plist-get opt-plist :link-up)) (plist-=
get opt-plist :link-up))) (link-home (and (plist-get opt-plist :link-home) =
(string-match "\\S-" (plist-get opt-plist :link-home)) (plist-get opt-plist=
:link-home))) (dummy (setq opt-plist (plist-put opt-plist :title title))) =
(html-table-tag (plist-get opt-plist :html-table-tag)) (quote-re0 (concat "=
^[ ]*" org-quote-string "\\>")) (quote-re (concat "^\\(\\*+\\)\\([ ]+" or=
g-quote-string "\\>\\)")) (inquote nil) (infixed nil) (inverse nil) (email =
(plist-get opt-plist :email)) (language (plist-get opt-plist :language)) (k=
eywords (plist-get opt-plist :keywords)) (description (plist-get opt-plist =
:description)) (num (plist-get opt-plist :section-numbers)) (lang-words nil=
) (head-count 0) cnt (start 0) ...) (let ((inhibit-read-only t)) (org-unmod=
ified (remove-text-properties (point-min) (point-max) (quote (:org-license-=
to-kill t))))) (message "Exporting...") (setq org-min-level (org-get-min-le=
vel lines level-offset)) (setq org-last-level org-min-level) (org-init-sect=
ion-numbers) (cond ((and date (string-match "%" date)) (setq date (format-t=
ime-string date))) (date) (t (setq date (format-time-string "%Y-%m-%d %T %Z=
")))) (setq lang-words (or (assoc language org-export-language-setup) (asso=
c "en" org-export-language-setup))) (set-buffer buffer) (let ((inhibit-read=
-only t)) (erase-buffer)) (fundamental-mode) (org-install-letbind) (and (fb=
oundp (quote set-buffer-file-coding-system)) (set-buffer-file-coding-system=
coding-system-for-write)) (let ((case-fold-search nil) (org-odd-levels-onl=
y odd)) (mapc (lambda (x) (set (make-local-variable (nth 2 x)) (plist-get o=
pt-plist (car x)))) org-export-plist-vars) (setq umax (if arg (prefix-numer=
ic-value arg) org-export-headline-levels)) (setq umax-toc (if (integerp org=
-export-with-toc) (min org-export-with-toc umax) umax)) (unless body-only (=
insert (format "%s\n\=
n\n\n%s\n\n\n\n\n\n\n%s\n%s\n\n\n=
%s\n" (format (or (and ... org-export-html-xml-declaration) (cdr ...) (cdr =
...) "") (or charset "iso-8859-1")) language language title (or charset "is=
o-8859-1") date author description keywords style mathjax (if (or link-up l=
ink-home) (concat (format org-export-html-home/up-format ... ...) "\n") "")=
)) (when (plist-get opt-plist :html-preamble) (let ((html-pre (plist-get op=
t-plist :html-preamble))) (insert "