+++ /dev/null
-#+OPTIONS: H:3 num:nil toc:2 \n:nil @: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) noexport(n)
-#+TITLE: LaTeX Code Blocks in Babel
-#+AUTHOR: Tom Dye
-#+EMAIL: tsd at tsdye dot com
-#+LANGUAGE: en
-#+STYLE: <style type="text/css">#outline-container-introduction{ clear:both; }</style>
-#+BABEL: :exports code
-
-#+begin_html
- <div id="subtitle" style="float: center; text-align: center;">
- <p>
- Babel support for LaTeX
- </p>
- <p>
- </div>
-#+end_html
-
-* Notes :noexport:
-** Queries
-** Comments
-* Requirements and Enhancements
-** [[http://www.gnu.org/software/auctex/][AucTeX]]
- Strongly recommended for editing .tex files. Add the following
- line to .emacs:
-
-#+begin_src emacs-lisp
-(load "auctex.el" nil t t)
-#+end_src
-
-** [[http://www.gnu.org/software/auctex/reftex.html][RefTeX]]
- This cross-reference, bibliography, glossary, and index manager is
- indispensable. Add the following line to .emacs:
-#+begin_src emacs-lisp
-(add-hook 'LaTeX-mode-hook 'turn-on-reftex)
-#+end_src
-
-*** Recommended RefTeX Setting
- - It can be helpful to name a default bibliography when editing
- source code in Babel. Add the following lines, edited to
- conform to your setup, to .emacs:
-
-
-#+begin_src emacs-lisp
- (setq reftex-default-bibliography
- (quote
- ("default.bib" "other-default.bib")))
-#+end_src
-
-*** Enhanced RefTeX Support
- - You can give RefTeX access to information in other LaTeX code
- blocks with the following code
-
- - Add the following lines to your .emacs (adapted from Kevin Brubeck Unhammer's [[http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/][Reftex Setup]])
-#+begin_src emacs-lisp
- (defun org-mode-article-modes ()
- (reftex-mode t)
- (and (buffer-file-name)
- (file-exists-p (buffer-file-name))
- (reftex-parse-all)))
-
- (add-hook 'org-mode-hook
- (lambda ()
- (if (member "REFTEX" org-todo-keywords-1)
- (org-mode-article-modes))))
-#+end_src
-
- - Add the following line to the top of an org-mode file that
- contains LaTeX code blocks
-#+begin_src latex
- #+TODO: REFTEX
-#+end_src
-
- - When you open an org-mode file with this line, RefTeX will prompt
- for the master .tex file
-
-* Configuration in Babel
-** Activate LaTeX Evaluation
- - Add the commented line to .emacs
-#+begin_src emacs-lisp :tangle yes
- (org-babel-do-load-languages
- 'org-babel-load-languages
- '((R . t)
- (ditaa . t)
- (dot . t)
- (emacs-lisp . t)
- (gnuplot . nil)
- (haskell . nil)
- (latex . t) ; this is the entry to activate LaTeX
- (ocaml . nil)
- (perl . t)
- (python . t)
- (ruby . t)
- (screen . nil)
- (sh . t)
- (sql . nil)
- (sqlite . nil)))
-#+end_src
-
-* Language-specific Conventions
- - Babel returns raw LaTeX code on evaluation, unless a =:file=
- header argument is present
- - The default value for the =:exports= header argument is
- =results=[fn:1]
- - The default value for the =:results= header argument is =latex=
-* Header Arguments
- - Babel's LaTeX support uses the =:file= and =:buffer= header
- arguments in language-specific ways
- - It adds these header arguments: =:pdfheight=, =:pdfwidth=,
- =:packages=, =:fit=, and =:border=
-
-** Language Specific Header Arguments
-- The =:file= header argument accepts a file name ending in =.png= or
- =.pdf=
-- When =:file FILENAME.png= is set, =:buffer no= specifies that buffer
- colors won't be used in the =.png= file
-- When =:file FILENAME.pdf= is set, =:pdfheight= and =:pdfwidth=
- header arguments can be used to specify the size of the pdf image in
- LaTeX lengths, e.g., =1in=, =6em=, =48pt=, etc.
-- The =:packages= header argument can be passed an assoc-list that
- temporarily adds one or more packages to
- =org-export-latex-packages-alist=
-- =:fit= will use the LaTeX [[http://www.ctan.org/tex-archive/macros/latex/contrib/preview/][preview]] package for neatly fitting the
- size of the generated pdf file to the size of the figure or text
- resulting from the code block. This is only useful when a =.pdf=
- file type is in use.
-- the results of the =:fit= header argument mentioned above may seem
- too tight. The =:border= header argument is exactly like =:fit=
- only it takes an argument specifying the size of border to place
- around the image (e.g. =:border 1em=)
-- the height and width of the generated =.pdf= file can also be
- specified manually using the =:pdfheight= and =:pdfwidth= header
- arguments, which take LaTeX length arguments (e.g. =:pdfwidth 3in=)
-- LaTeX source code blocks do not support the =:session= header
- argument
-
-** Examples of Use
-*** Display the LaTeX logo in the Emacs buffer
-
-: #+begin_src latex :file latex-logo.png
-: \LaTeX
-: #+end_src
-
-#+begin_src latex :file latex-logo.png :exports none
- \LaTeX
-#+end_src
-
-*** Generate a complex figure
-This example uses the excellent [[http://sourceforge.net/projects/pgf/][pgf/tikz]] package
-: #+begin_src latex :file fsa.pdf :packages '(("" "tikz")) :border 1em
-: % Define block styles
-: \usetikzlibrary{shapes,arrows}
-: \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, fill=blue!25]
-: \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, fill=red!25]
-:
-: \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node distance=2.8cm, semithick]
-: \node [astate] (1) at (0,0) {1};
-: \node [astate] (2) at (1,0) {2};
-: \node [rstate] (3) at (2,0) {3};
-: \path (1) edge [bend left] node {b} (2)
-: (2) edge node {b} (3)
-: (2) edge [bend left] node {a} (1)
-: (3) edge [loop above] node {(a, b)} (3);
-: \end{tikzpicture}
-: #+end_src
-
-* Common Idioms
-
- - Org-mode can export its outline structure to LaTeX, yielding a
- serviceable document independent of Babel, see the [[http://orgmode.org/worg/org-tutorials/org-latex-export.html][LaTeX export tutorial]]
-
-** Creating and Including Graphics
- - This example creates a graph in R, then inserts it into a LaTeX
- clode block with a noweb reference
-
-: #+name: r-complete-weight-histogram
-: #+begin_src R :session adze :file r/adze_wt_log.pdf
-: adze.wt <- ggplot(whole.adze, aes(x = weight))
-: adze.wt + geom_histogram() + scale_x_log10()
-: ggsave(file = "adze_wt_log.pdf", width = 5, height = 3)
-: #+end_src
-
-: #+begin_src latex :tangle graphics-document.tex
-: \begin{figure}[htb!]
-: \centering
-: \includegraphics[width=5in]{<<r-complete-weight-histogram()>>}
-: \caption[Weight of complete adzes]{Weight of complete adzes on a
-: logarithmic scale.}
-: \label{fig:complete-weight}
-: \end{figure}
-: #+end_src
-
-
-
-** Passing an Org-mode table to a LaTeX code block
-
-Tables are difficult to set in type. This was true when lead type was
-set manually and it is still true with a sophisticated type-setting
-engine like LaTeX. One way to make a LaTeX table is to write it out
-using an Org-mode table and then "export" the table into the LaTeX
-code block using the function =orgtbl-to-generic=.
-
-This Emacs lisp function, slightly modified from one written by Eric
-Schulte, inserts an Org-mode table into a LaTeX code block. It
-depends on the [[http://www.ctan.org/tex-archive/macros/latex/contrib/booktabs/][LaTeX booktabs package]], which draws horizontal rules of
-appropriate widths at the top and bottom of a table, as well as within
-the table.
-
-: #+name: booktabs-2
-: #+begin_src emacs-lisp :var table='((:head) hline (:body))
-: (flet ((to-tab (tab)
-: (orgtbl-to-generic
-: (mapcar (lambda (lis)
-: (if (listp lis)
-: (mapcar (lambda (el)
-: (if (stringp el)
-: el
-: (format "%S" el))) lis)
-: lis)) tab)
-: (list :lend " \\\\" :sep " & " :hline "\\hline"))))
-: (org-fill-template
-: "
-: \\toprule
-: %table
-: \\bottomrule\n"
-: (list
-: (cons "table"
-: ;; only use \midrule if it looks like there are column headers
-: (if (equal 'hline (second table))
-: (concat (to-tab (list (first table)))
-: "\n\\midrule\n"
-: (to-tab (cddr table)))
-: (to-tab table))))))
-: #+end_src
-
-The function can be called using noweb syntax, like this:
-
-: #+begin_src latex :noweb yes
-: \begin{table}[htb!]
-: \centering
-: \caption{A test table}
-: \label{tab:test}
-: \begin{tabular}{rl}
-: <<booktabs-2(table=months)>>
-: \end{tabular}
-: \end{table}
-: #+end_src
-
-
-* Footnotes
-
-[fn:1] *Note:* The default value of the =:exports= header argument
- alters the expected behavior of Org-mode export to HTML and LaTeX.
- LaTeX code blocks will require an explicit =:exports code= header
- argument to export as described in the Org-mode manual.
+++ /dev/null
-#+OPTIONS: H:3 num:nil toc:2 \n:nil @: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) noexport(n)
-#+TITLE: Org-babel-R
-#+AUTHOR: Eric Schulte, Dan Davison, Tom Dye
-#+EMAIL: schulte.eric at gmail dot com, davison at stats dot ox dot ac dot uk
-#+LANGUAGE: en
-#+STYLE: <style type="text/css">#outline-container-introduction{ clear:both; }</style>
-
-#+begin_html
- <div id="subtitle" style="float: center; text-align: center;">
- <p>
- Org-babel support for
- <a href="http://www.r-project.org/">R</a>
- </p>
- <p>
- <a href="http://www.r-project.org/">
- <img src="http://www.r-project.org/Rlogo.jpg"/>
- </a>
- </p>
- </div>
-#+end_html
-
-* Notes :noexport:
-** Template Design
- - What the user wants to know:
- - Required software
- - How to install it
- - How to configure it in Org-babel
- - Org-babel conventions that might affect the language
- - How it modifies Org-babel
- - Common ways to use it
-** Queries
- - Eric, I think you should name your starter kit Literate Emacs
- Starter Kit (LESK). I've taken the liberty of labeling the link
- to it that way below. Is that OK?
- - I think LESK is a couple of steps away from being useful to Lisp
- illiterates (like me). I'm thinking of LESK for Lisp
- IlliteraTEs, or LESK LITE. Is that anathema?
-
-** Comments
- - I'm not sure how you two use tags. I've used :Fix on Dan's
- Graphical output, because I think it should be parceled out to
- various sections of the template, and not because I think it
- needs fixing in and of itself.
-
-* Requirements :Update:
-** [[http://ess.r-project.org/][Emacs Speaks Statistics]]
- Required for session-based evaluation.
-*** Installation using [[http://github.com/eschulte/emacs-starter-kit/tree/master][Literate Emacs Starter Kit]] :noexport::Write:
- - unpack ess-VERSION.tgz in .emacs.d/src
- - for me, this created ess-5.6, need an alias named ess?
- - where to put (require 'ess-site)?
-* Examples
- :PROPERTIES:
- :CUSTOM_ID: examples
- :END:
-Examples demonstrating the use of R code within Org-mode.
-
-- [[file:R/RBabelExample.org][RBabelExample]] ([[http://orgmode.org/w/?p%3Dworg.git%3Ba%3Dblob_plain%3Bf%3Dorg-contrib/babel/languages/R/RBabelExample.org%3Bhb%3DHEAD][.org]], [[http://orgmode.org/w/?p%3Dworg.git%3Ba%3Dblob_plain%3Bf%3Dorg-contrib/babel/languages/R/RBabelExample.pdf%3Bhb%3DHEAD][.pdf]]) -- a short introductory example
-- [[file:../uses.org::#foo][foo.org]] ([[http://orgmode.org/w/?p%3Dworg.git%3Ba%3Dblob_plain%3Bf%3Dorg-contrib/babel/examples/foo.org%3Bh%3Dff77d114bd79eb600139d23338910b1948c06332%3Bhb%3DHEAD][.org]], [[http://orgmode.org/w/?p%3Dworg.git%3Ba%3Dblob%3Bf%3Dorg-contrib/babel/examples/foo.pdf%3Bh%3D15d4233e6561b99216c768a9f94ddcbd0c052524%3Bhb%3DHEAD][.pdf]], [[http://orgmode.org/w/?p%3Dworg.git%3Ba%3Dblob_plain%3Bf%3Dorg-contrib/babel/examples/foo.org.html%3Bh%3D3d157d2ac1b361eea9afc71436a3b0a23a5f1070%3Bhb%3DHEAD][preview]]) -- a more complex example
-
-* Configuration in Org-babel :Write:noexport:
-** Variables
-* Language-specific Features :Write:
-** Graphical output :Fix:
- If a =:file filename.ext= header argument is provided to an R
- source block, then the output from the source block will go to the
- named file. What that output is depends on the value of the
- =:results= header argument.
-
- If the value is =:results graphics= then "base" graphics output is
- captured on disk, and a link to the graphics file is inserted into
- the Org-mode buffer (as is also the case with the graphics-only
- languages such as gnuplot, ditaa, dot, and asymptote.) An attempt
- is made to find an R graphics device corresponding to the file
- extension. Currently, the following extensions are recognized:
- .png, .jpg, .jpeg, .tiff, .bmp, .pdf, .ps, .postscript, and .svg.
- If the extension of the file name passed to =:file= is not
- recognized, png format output is created by default.
-
-
- For further clarification of =:file= and =:results=, see [[http://thread.gmane.org/gmane.emacs.orgmode/35396/focus=35766][this
- thread]].
-
-# <<r-dev-header-args>>
- Additionally, values for several arguments to the R graphics
- device can be passed using header args:
-
-#+begin_example
- :width :height :bg :fg :units :pointsize :antialias :quality :compression :res :type :family
- :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal
-#+end_example
-
- See the R help page for the graphics devices (e.g. using =?png=,
- =?pdf=) for explanations of these arguments.
-
- Arguments to the R graphics device can also be passed as a string
- in R argument syntax, using the header arg =:R-dev-args=. This is
- useful for graphics device arguments that don't have an Org-babel
- header argument counterpart.
-
- The following example source block illustrates use of
- =:R-dev-args= to pass background and foreground colors. Note that
- both of these arguments can also be passed directly as
- header args, using =:fg= and =:bg=.
-
-#+begin_src org
- ,#+header: :width 8 :height 8 :R-dev-args bg="olivedrab", fg="hotpink"
- ,#+begin_src R :file z.pdf :results graphics
- ,plot(matrix(rnorm(100), ncol=2), type="l")
- ,#+end_src
-#+end_src
-
-If "base" graphics aren't begin generated, then additional header
-arguments might be needed. For example, with the =ggplot2= package,
-graphics output requires =:results output graphics=. The following
-example writes the graphics output to the file specified in the
-=:file= header argument.
-
-#+begin_example
- ,#+name: r-edge-angle-histogram
- ,#+begin_src R :results output graphics :var x=whole-adzes :file r/adze_edge_angle.png :width 400 :height 300
- library(ggplot2)
- adze.edge.angle <- ggplot(x, aes(edge_angle))
- adze.edge.angle + geom_histogram(aes(y=..density..)) +
- geom_density(weight=2) + xlab("Measured cutting edge angle (degrees)")
- ,#+end_src
-
- ,#+results:
- [[file:r/adze_edge_angle.png]]
-#+end_example
-
-** Missing Values :Write:noexport:
-* Additions to Org-babel :Write:
-** Header Arguments
-R support introduces a large number of header arguments to Org-babel.
-Most of these set parameters of R graphic devices, as described [[r-dev-header-args][above]].
-
-It is also possible to include column names during export of data
-frames.
-
-| Header arg | Meaning |
-|---------------+--------------------------------|
-| :colnames yes | Include column names in output |
-
-* Common Idioms :Write:noexport:
-* Tips for usage
-** Debugging
- This section contains some tips on how to proceed if your R code is
- not doing what you had hoped.
-*** Use =:session=
- Evaluate your code using the =:session= header argument, then
- visit the R buffer (i.e. the buffer containing the "inferior ESS"
- process). Then you can inspect the objects that have been created,
- and try out some lines of code. Useful R functions for inspecting
- objects include (as always in R, type a "?" followed by the name
- of the function to get help with the function)
- - str
- - dim
- - summary
-*** Use ESS to step through evaluation line-by-line
- 1. Use C-c ' to visit the edit buffer for your code block
- 2. Use ess-eval-line-and-step to evaluate each line in turn
-
-In addition to ess-eval-line-and-step, there are several other ESS
-functions with names beginning ess-eval-*. They evaluate lines and
-regions in different ways; it's worth looking at their descriptions
-(C-h f).
-
-** LaTeX code from R
-This example summarises a linear regression fit. Usually the org-babel
-user should not have to be involved in latex code generation, as this
-is the responsibility of org-mode's latex export engine. But in this
-example, neither the printed representation nor the value of
-summary(lm(y ~ x)) is at all tabular, and it would therefore require
-some work to get the information in to an org table. However, the
-xtable package can be used to output a latex table. Using ':results
-latex' in org-babel ensures that this is stored as a latex block in
-the org buffer and thus can be included correctly in latex-based
-export targets.
-
-#+begin_src R :results output latex
-library(xtable)
-x <- rnorm(100)
-y <- x + rnorm(100)
-xtable(summary(lm(y ~ x)))
-#+end_src
-
-#+results:
-#+BEGIN_LaTeX
-% latex table generated in R 2.9.2 by xtable 1.5-5 package
-% Wed Dec 9 17:17:53 2009
-\begin{table}[ht]
-\begin{center}
-\begin{tabular}{rrrrr}
- \hline
- & Estimate & Std. Error & t value & Pr($>$$|$t$|$) \\
- \hline
-(Intercept) & -0.0743 & 0.0969 & -0.77 & 0.4454 \\
- x & 1.0707 & 0.0923 & 11.60 & 0.0000 \\
- \hline
-\end{tabular}
-\end{center}
-\end{table}
-#+END_LaTeX
-** Org output from R
-David Hajage's [[http://cran.r-project.org/web/packages/ascii/index.html][ascii]] R package creates appropriate plain text
-representations of many R objects, and features an option to specify
-that the plain text representations should be in Org format. This can
-be particularly useful for retrieving non-tabular R data structures in
-Org.
-
-In R:
-#+begin_example
-> library(ascii)
-> options(asciiType = "org")
-> library(Hmisc)
-> ascii(describe(esoph))
-#+CAPTION: esoph
-- 5 Variable
-- 88 Observations
-
-*agegp*
-| n | missing | unique |
-| 88 | 0 | 6 |
-
-| | 25-34 | 35-44 | 45-54 | 55-64 | 65-74 | 75+ |
-| Frequency | 15 | 15 | 16 | 16 | 15 | 11 |
-| % | 17 | 17 | 18 | 18 | 17 | 12 |
-
-*alcgp*
-| n | missing | unique |
-| 88 | 0 | 4 |
-
- 0-39g/day (23, 26%), 40-79 (23, 26%), 80-119 (21, 24%), 120+ (21, 24%)
-
-*tobgp*
-| n | missing | unique |
-| 88 | 0 | 4 |
-
- 0-9g/day (24, 27%), 10-19 (24, 27%), 20-29 (20, 23%), 30+ (20, 23%)
-
-*ncases*
-| n | missing | unique | Mean | .05 | .10 | .25 | .50 | .75 | .90 | .95 |
-| 88 | 0 | 10 | 2.273 | 0.0 | 0.0 | 0.0 | 1.0 | 4.0 | 5.3 | 6.0 |
-
-| | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 8 | 9 | 17 |
-| Frequency | 29 | 16 | 11 | 9 | 8 | 6 | 5 | 1 | 2 | 1 |
-| % | 33 | 18 | 12 | 10 | 9 | 7 | 6 | 1 | 2 | 1 |
-
-*ncontrols*
-| n | missing | unique | Mean | .05 | .10 | .25 | .50 | .75 | .90 | .95 |
-| 88 | 0 | 30 | 11.08 | 1.0 | 1.0 | 3.0 | 6.0 | 14.0 | 29.1 | 40.0 |
-
- lowest: 1 2 3 4 5, highest: 40 46 48 49 60
-#+end_example
-
-
- From Org-babel:
-#+begin_src R :results output org
- library(ascii)
- options(asciiType="org")
- ascii(summary(table(1:4, 1:4)))
-#+end_src
-
-#+results:
-Loading required package: proto
-- Number of cases in table: 4
-- Number of factors: 2
-- Test for independence of all factors:
- - Chisq = 12, df = 9, p-value = 0.2133
- - Chi-squared approximation may be incorrect
-
-** ess-switch-to-end-of-ESS
- When in an org mode R code edit buffer with an associated R
- session, ess-switch-to-end-of-ESS will bring the R session buffer
- into view and place point at the prompt. ESS binds this to C-c C-z
- and C-M-r by default.
projects / worg.git / commitdiff