From fc64b49c3324941f53a9f7ae7418b4091eedae23 Mon Sep 17 00:00:00 2001 From: Thomas Dye Date: Sun, 23 Sep 2012 14:35:50 -1000 Subject: [PATCH] Removed .old files --- org-contrib/babel/languages/ob-doc-LaTeX.org.old | 257 -------------------- org-contrib/babel/languages/ob-doc-R.org.old | 280 ---------------------- 2 files changed, 0 insertions(+), 537 deletions(-) delete mode 100644 org-contrib/babel/languages/ob-doc-LaTeX.org.old delete mode 100644 org-contrib/babel/languages/ob-doc-R.org.old diff --git a/org-contrib/babel/languages/ob-doc-LaTeX.org.old b/org-contrib/babel/languages/ob-doc-LaTeX.org.old deleted file mode 100644 index 8a39157..0000000 --- a/org-contrib/babel/languages/ob-doc-LaTeX.org.old +++ /dev/null @@ -1,257 +0,0 @@ -#+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: -#+BABEL: :exports code - -#+begin_html -
-

- Babel support for LaTeX -

-

-

-#+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]{<>} -: \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} -: <> -: \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. diff --git a/org-contrib/babel/languages/ob-doc-R.org.old b/org-contrib/babel/languages/ob-doc-R.org.old deleted file mode 100644 index f04b8c6..0000000 --- a/org-contrib/babel/languages/ob-doc-R.org.old +++ /dev/null @@ -1,280 +0,0 @@ -#+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: - -#+begin_html -
-

- Org-babel support for - R -

-

- - - -

-
-#+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]]. - -# <> - 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. -- 1.7.2.5