From cf31c1f13423d24095f8808db07f84c8f1e2798e Mon Sep 17 00:00:00 2001 From: Dan Davison Date: Sun, 8 Feb 2009 13:11:22 -0500 Subject: [PATCH] Trying to write a project overview at top of rorg.org --- existing_tools/RweaveOrg/testing-004.pdf | 252 +++++++++ existing_tools/RweaveOrg/testing.Rorg | 1 + existing_tools/RweaveOrg/testing.Rorg.org | 73 +++ existing_tools/RweaveOrg/testing.aux | 25 + existing_tools/RweaveOrg/testing.log | 612 ++++++++++++++++++++++ existing_tools/RweaveOrg/testing.org | 86 +++ existing_tools/RweaveOrg/testing.out | 6 + existing_tools/RweaveOrg/testing.pdf | Bin 0 -> 38835 bytes existing_tools/RweaveOrg/testing.tex | 82 +++ existing_tools/RweaveOrg/testing.toc | 6 + nogit-rorg-dan.org | 113 ++++ rorg.html | 344 ++++++++++++ rorg.org | 63 ++- 13 files changed, 1662 insertions(+), 1 deletion(-) create mode 100644 existing_tools/RweaveOrg/testing-004.pdf create mode 100644 existing_tools/RweaveOrg/testing.Rorg.org create mode 100644 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/F1 5 0 R /F2 10 0 R >> +/ExtGState << >> +>> +endobj +9 0 obj +<< +/Type /Encoding +/BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +10 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F2 +/BaseFont /Helvetica +/Encoding 9 0 R +>> endobj +xref +0 11 +0000000000 65535 f +0000000021 00000 n +0000000163 00000 n +0000006002 00000 n +0000006085 00000 n +0000000212 00000 n +0000000295 00000 n +0000000375 00000 n +0000005982 00000 n +0000006178 00000 n +0000006435 00000 n +trailer +<< +/Size 11 +/Info 1 0 R +/Root 2 0 R +>> +startxref +6532 +%%EOF diff --git a/existing_tools/RweaveOrg/testing.Rorg b/existing_tools/RweaveOrg/testing.Rorg index 51cf2c643..39ed91a81 100644 --- a/existing_tools/RweaveOrg/testing.Rorg +++ b/existing_tools/RweaveOrg/testing.Rorg @@ -64,6 +64,7 @@ #+CAPTION: speed by distance #+LABEL: fig:speed_by_distance #+BEGIN_R fig=TRUE, eps=FALSE, pdf=TRUE +require(lattice) print(xyplot(speed ~ dist, cars, panel = function (x, y, ...) { panel.xyplot(x, y, ...) diff --git a/existing_tools/RweaveOrg/testing.Rorg.org b/existing_tools/RweaveOrg/testing.Rorg.org new file mode 100644 index 000000000..51cf2c643 --- /dev/null +++ b/existing_tools/RweaveOrg/testing.Rorg.org @@ -0,0 +1,73 @@ +# -*- mode: org -*- +#+OPTIONS: LaTeX:t + +* Sweave and org-mode + If you're reading a PDF version of this document, you should also + look at [[file:testing.Rorg][testing.Rorg]] (the source file) and [[file:testing.org][testing.org]] (the output + of the Sweave process). + + Keep in mind that one of the advantages of a block-based approach is + using \texttt{C-'} to edit code in its native mode. + +** Use the Sweave package for latex formatting + Org allows us to issue commands to be included in \{LaTeX} export. +#+LATEX_HEADER: \usepackage{Sweave} + +** R blocks + The first argument to an R block when using Sweave is the label for + that block. + + Not all R blocks are printed. Sweave options allow the printing of + the evaluated code, the output of the code, both, or neither. + +*** R code that is not printed +#+BEGIN_R: hidden_block, echo=FALSE, results=HIDE + a <- 3 + b <- 6 +#+END_R + +*** R code that is printed +#+BEGIN_R: visible_block + c <- 4 +#+END_R + + We can use block labels to embed blocks by reference (even if they + weren't printed before). +*** R code that references other blocks +#+BEGIN_R: combined_block +#+R_CODEREF: hidden_block +#+R_CODEREF: visible_block + a + b +c +#+END_R + +** Inline references to R data + We can evaluate R code inline. +*** Used in text + The value of =a= is \R{a}. + +*** Used in a table + | a | b | c | TOTAL | + |-------+-------+-------+---------------| + | \R{a} | \R{b} | \R{c} | \R{a + b + c} | + +** Single-line R commands + If we want a line of R code to be evaluated but not printed, + there's a convenient shorthand. This only works for single lines + of R code, but you can have more than one in a row. +#+R: library(lattice) +#+R: data(cars) + +** Graphics + We use values defined elsewhere in the buffer to produce this + graph. The new CAPTION and LABEL arguments work just fine. + +#+CAPTION: speed by distance +#+LABEL: fig:speed_by_distance +#+BEGIN_R fig=TRUE, eps=FALSE, pdf=TRUE +print(xyplot(speed ~ dist, cars, + panel = function (x, y, ...) { + panel.xyplot(x, y, ...) + panel.abline(h=a) + panel.abline(v=b) + })) +#+END_R diff --git a/existing_tools/RweaveOrg/testing.aux b/existing_tools/RweaveOrg/testing.aux new file mode 100644 index 000000000..173d0d06c --- /dev/null +++ b/existing_tools/RweaveOrg/testing.aux @@ -0,0 +1,25 @@ +\relax +\ifx\hyper@anchor\@undefined +\global \let \oldcontentsline\contentsline +\gdef \contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global \let \oldnewlabel\newlabel +\gdef \newlabel#1#2{\newlabelxx{#1}#2} +\gdef \newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\let \contentsline\oldcontentsline +\let \newlabel\oldnewlabel} +\else +\global \let \hyper@last\relax +\fi + +\@writefile{toc}{\contentsline {section}{\numberline {1}Sweave and org-mode}{1}{section.1}} +\newlabel{sec-1}{{1}{1}{Sweave and org-mode\relax }{section.1}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}R code that is not printed}{1}{subsection.1.1}} +\newlabel{sec-1.3}{{1.1}{1}{R code that is not printed\relax }{subsection.1.1}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}R code that is printed}{1}{subsection.1.2}} +\newlabel{sec-1.4}{{1.2}{1}{R code that is printed\relax }{subsection.1.2}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}R code that references other blocks}{1}{subsection.1.3}} +\newlabel{sec-1.5}{{1.3}{1}{R code that references other blocks\relax }{subsection.1.3}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}Used in text}{2}{subsection.1.4}} +\newlabel{sec-1.7}{{1.4}{2}{Used in text\relax }{subsection.1.4}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.5}Used in a table}{2}{subsection.1.5}} +\newlabel{sec-1.8}{{1.5}{2}{Used in a table\relax }{subsection.1.5}{}} diff --git a/existing_tools/RweaveOrg/testing.log b/existing_tools/RweaveOrg/testing.log new file mode 100644 index 000000000..a03a90d80 --- /dev/null +++ b/existing_tools/RweaveOrg/testing.log @@ -0,0 +1,612 @@ +This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) (format=pdflatex 2008.10.27) 8 FEB 2009 11:19 +entering extended mode + %&-line parsing enabled. +**testing.tex +(./testing.tex +LaTeX2e <2005/12/01> +Babel and hyphenation patterns for english, usenglishmax, dumylang, noh +yphenation, croatian, ukrainian, russian, bulgarian, czech, slovak, danish, dut +ch, finnish, basque, french, german, ngerman, ibycus, greek, monogreek, ancient +greek, hungarian, italian, latin, mongolian, norsk, icelandic, interlingua, tur +kish, coptic, romanian, welsh, serbian, slovenian, estonian, esperanto, upperso +rbian, indonesian, polish, portuguese, spanish, catalan, galician, swedish, loa +ded. +(/usr/share/texmf-texlive/tex/latex/base/article.cls +Document Class: article 2005/09/16 v1.4f Standard LaTeX document class +(/usr/share/texmf-texlive/tex/latex/base/size11.clo +File: size11.clo 2005/09/16 v1.4f Standard LaTeX file (size option) +) +\c@part=\count79 +\c@section=\count80 +\c@subsection=\count81 +\c@subsubsection=\count82 +\c@paragraph=\count83 +\c@subparagraph=\count84 +\c@figure=\count85 +\c@table=\count86 +\abovecaptionskip=\skip41 +\belowcaptionskip=\skip42 +\bibindent=\dimen102 +) +(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty +Package: inputenc 2006/05/05 v1.1b Input encoding file +\inpenc@prehook=\toks14 +\inpenc@posthook=\toks15 + +(/usr/share/texmf-texlive/tex/latex/base/utf8.def +File: utf8.def 2006/03/30 v1.1i UTF-8 support for inputenc +Now handling font encoding OML ... +... no UTF-8 mapping file for font encoding OML +Now handling font encoding T1 ... +... processing UTF-8 mapping file for font encodingT1 + +(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu +File: t1enc.dfu 2006/03/30 v1.1i UTF-8 support for 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line 14. +(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd +File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions +) +LaTeX Font Info: ... okay on input line 14. +Package hyperref Info: Link coloring OFF on input line 14. + +(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty +Package: nameref 2006/12/27 v2.28 Cross-referencing by name of section + +(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty +Package: refcount 2006/02/20 v3.0 Data extraction from references (HO) +) +\c@section@level=\count103 +) +LaTeX Info: Redefining \ref on input line 14. +LaTeX Info: Redefining \pageref on input line 14. +\@outlinefile=\write4 +\openout4 = `testing.out'. + +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <12> on input line 17. +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <8> on input line 17. +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <6> on input line 17. +\tf@toc=\write5 +\openout5 = `testing.toc'. + +LaTeX Font Info: Try loading font information for T1+aett on input line 30. + +(/usr/share/texmf-texlive/tex/latex/ae/t1aett.fd +File: t1aett.fd 1997/11/16 Font definitions for T1/aett. +) [1 + +{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <10.95> on input line 72. + [2] (./testing.aux) + +LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. + + ) +Here is how much of TeX's memory you used: + 3994 strings out of 94101 + 54395 string characters out of 1165809 + 105369 words of memory out of 1500000 + 7194 multiletter control sequences out of 10000+50000 + 24855 words of font info for 58 fonts, out of 1200000 for 2000 + 637 hyphenation exceptions out of 8191 + 35i,6n,36p,243b,336s stack positions out of 5000i,500n,6000p,200000b,5000s + +Output written on testing.pdf (2 pages, 38835 bytes). +PDF statistics: + 54 PDF objects out of 1000 (max. 8388607) + 10 named destinations out of 1000 (max. 131072) + 17 words of extra memory for PDF output out of 10000 (max. 10000000) + diff --git a/existing_tools/RweaveOrg/testing.org b/existing_tools/RweaveOrg/testing.org new file mode 100644 index 000000000..df6c88124 --- /dev/null +++ b/existing_tools/RweaveOrg/testing.org @@ -0,0 +1,86 @@ +# -*- mode: org -*- +#+OPTIONS: LaTeX:t + +* Sweave and org-mode + If you're reading a PDF version of this document, you should also + look at [[file:testing.Rorg][testing.Rorg]] (the source file) and [[file:testing.org][testing.org]] (the output + of the Sweave process). + + Keep in mind that one of the advantages of a block-based approach is + using \texttt{C-'} to edit code in its native mode. + +** Use the Sweave package for latex formatting + Org allows us to issue commands to be included in \{LaTeX} export. +#+LATEX_HEADER: \usepackage{Sweave} + +** R blocks + The first argument to an R block when using Sweave is the label for + that block. + + Not all R blocks are printed. Sweave options allow the printing of + the evaluated code, the output of the code, both, or neither. + +*** R code that is not printed + +*** R code that is printed +#+BEGIN_LaTeX +\begin{Schunk} +\begin{Sinput} +> c <- 4 +\end{Sinput} +\end{Schunk} +#+END_LaTeX + + We can use block labels to embed blocks by reference (even if they + weren't printed before). +*** R code that references other blocks +#+BEGIN_LaTeX +\begin{Schunk} +\begin{Sinput} +> a <- 3 +> b <- 6 +> c <- 4 +> a + b + c +\end{Sinput} +\begin{Soutput} +[1] 13 +\end{Soutput} +\end{Schunk} +#+END_LaTeX + +** Inline references to R data + We can evaluate R code inline. +*** Used in text + The value of =a= is 3. + +*** Used in a table + | a | b | c | TOTAL | + |-------+-------+-------+---------------| + | 3 | 6 | 4 | 13 | + +** Single-line R commands + If we want a line of R code to be evaluated but not printed, + there's a convenient shorthand. This only works for single lines + of R code, but you can have more than one in a row. +#+R: library(lattice) +#+R: data(cars) + +** Graphics + We use values defined elsewhere in the buffer to produce this + graph. The new CAPTION and LABEL arguments work just fine. + +#+CAPTION: speed by distance +#+LABEL: fig:speed_by_distance +#+BEGIN_LaTeX +\begin{Schunk} +\begin{Sinput} +> require(lattice) +> print(xyplot(speed ~ dist, cars, panel = function(x, y, ...) { ++ panel.xyplot(x, y, ...) ++ panel.abline(h = a) ++ panel.abline(v = b) ++ })) +\end{Sinput} +\end{Schunk} +#+END_LaTeX +[[./testing-004.pdf]] diff --git a/existing_tools/RweaveOrg/testing.out b/existing_tools/RweaveOrg/testing.out new file mode 100644 index 000000000..eb59ff2ab --- /dev/null +++ b/existing_tools/RweaveOrg/testing.out @@ -0,0 +1,6 @@ +\BOOKMARK [1][-]{section.1}{Sweave and org-mode}{} +\BOOKMARK [2][-]{subsection.1.1}{R code that is not printed}{section.1} +\BOOKMARK [2][-]{subsection.1.2}{R code that is printed}{section.1} +\BOOKMARK [2][-]{subsection.1.3}{R code that references other blocks}{section.1} +\BOOKMARK [2][-]{subsection.1.4}{Used in text}{section.1} +\BOOKMARK [2][-]{subsection.1.5}{Used in a table}{section.1} 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+\documentclass[11pt]{article} +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} +\usepackage{graphicx} +\usepackage{longtable} +\usepackage{hyperref} +\usepackage{Sweave} + +\title{testing} +\author{Dan} +\date{08 February 2009} + +\begin{document} + +\maketitle + +\setcounter{tocdepth}{3} +\tableofcontents +\vspace*{1cm} + +\section{Sweave and org-mode} +\label{sec-1} + + If you're reading a PDF version of this document, you should also + look at \href{file:///home/dan/src/rorg/existing_tools/RweaveOrg/testing.Rorg}{testing.Rorg} (the source file) and \href{file:///home/dan/src/rorg/existing_tools/RweaveOrg/testing.org}{testing.org} (the output + of the Sweave process). + + Keep in mind that one of the advantages of a block-based approach is + using \texttt{C-'} to edit code in its native mode. + +\subsection{R code that is not printed} +\label{sec-1.3} + + +\subsection{R code that is printed} +\label{sec-1.4} + +\begin{Schunk} +\begin{Sinput} +> c <- 4 +\end{Sinput} +\end{Schunk} + + We can use block labels to embed blocks by reference (even if they + weren't printed before). +\subsection{R code that references other blocks} +\label{sec-1.5} + +\begin{Schunk} +\begin{Sinput} +> a <- 3 +> b <- 6 +> c <- 4 +> a + b + c +\end{Sinput} +\begin{Soutput} +[1] 13 +\end{Soutput} +\end{Schunk} + +\subsection{Used in text} +\label{sec-1.7} + + The value of \verb=a= is 3. + +\subsection{Used in a table} +\label{sec-1.8} + + +\begin{center} +\begin{tabular}{rrrr} + a & b & c & TOTAL \\ +\hline + 3 & 6 & 4 & 13 \\ +\end{tabular} +\end{center} + + + + +\end{document} diff --git a/existing_tools/RweaveOrg/testing.toc b/existing_tools/RweaveOrg/testing.toc new file mode 100644 index 000000000..7a8d78760 --- /dev/null +++ b/existing_tools/RweaveOrg/testing.toc @@ -0,0 +1,6 @@ +\contentsline {section}{\numberline {1}Sweave and org-mode}{1}{section.1} +\contentsline {subsection}{\numberline {1.1}R code that is not printed}{1}{subsection.1.1} +\contentsline {subsection}{\numberline {1.2}R code that is printed}{1}{subsection.1.2} +\contentsline {subsection}{\numberline {1.3}R code that references other blocks}{1}{subsection.1.3} +\contentsline {subsection}{\numberline {1.4}Used in text}{2}{subsection.1.4} +\contentsline {subsection}{\numberline {1.5}Used in a table}{2}{subsection.1.5} diff --git a/nogit-rorg-dan.org b/nogit-rorg-dan.org new file mode 100644 index 000000000..e72f2fa9c --- /dev/null +++ b/nogit-rorg-dan.org @@ -0,0 +1,113 @@ +#+TITLE: rorg --- R and org-mode + +* Objectives +** Send data to R from org + Org-mode includes orgtbl-mode, an extremely convenient way of using + tabular data in a plain text file. Currently, spreadsheet + functionality is available in org tables using the emacs package + calc. It would be a boon both to org users and R users to allow + org tables to be manipulated with the R programming language. Org + tables give R users an easy way to enter and display data; R gives + org users a powerful way to perform vector operations, statistical + tests, and visualization on their tables. + +*** Implementations +**** naive + Naive implementation would be to use =(org-export-table "tmp.csv")= + and =(ess-execute "read.csv('tmp.csv')")=. +**** org-R + org-R passes data to R from two sources: org tables, or csv + files. Org tables are first exported to a temporary csv file + using [[file:existing_tools/org-R.el::defun%20org%20R%20export%20to%20csv%20csv%20file%20options][org-R-export-to-csv]]. +**** org-exp-blocks +**** RweaveOrg + NA + +** Evaluate R code in org and deal with output appropriately +*** vector output + When R code evaluation generates vectors and 2-dimensional arrays, + this should be formatted appropriately in org buffers + (orgtbl-mode) as well as in export targets (html, latex). Values + assigned to in the global environment should be available to + blocks of R code elsewhere in the org buffer. +**** Implementations +***** org-R + org-R converts R output (vectors, or matrices / 2d-arrays) to an + org table and stores it in the org buffer, or in a separate org + file (csv output would also be perfectly possible). +***** org-exp-blocks +***** RweaveOrg +*** graphical output + R can generate graphical output on a screen graphics device + (e.g. X11, quartz), and in various standard image file formats + (png, jpg, ps, pdf, etc). When graphical output is generated by + evaluation of R code in Org, at least the following two things are desirable: + 1. output to screen for immediate viewing is possible + 2. graphical output to file is linked to appropriately from the + org file This should have the automatic consequence that it is + included appropriately in subsequent export targets (html, + latex). +**** Implementations +***** org-R + org-R does (1) if no output file is specified and (2) otherwise +***** org-exp-blocks +***** RweaveOrg + + +* Notes +** Special editing and evaluation of source code in R blocks + Unfortunately org-mode how two different block types, both useful. + In developing RweaveOrg, a third was introduced. + + Eric is leaning towards using the =#+begin_src= blocks, as that is + really what these blocks contain: source code. Austin believes + that specifying export options at the beginning of a block is + useful functionality, to be preserved if possible. + + Note that upper and lower case are not relevant in block headings. + +*** Source code blocks + Org has an extremely useful method of editing source code and + examples in their native modes. In the case of R code, we want to + be able to use the full functionality of ESS mode, including + interactive evaluation of code. + + Source code blocks look like the following and allow for the + special editing of code inside of the block through + `org-edit-special'. + +#+BEGIN_SRC r + +,## hit C-c ' within this block to enter a temporary buffer in r-mode. + +,## while in the temporary buffer, hit C-c C-c on this comment to +,## evaluate this block +a <- 3 +a + +,## hit C-c ' to exit the temporary buffer +#+END_SRC + +*** dblocks + dblocks are useful because org-mode will automatically call + `org-dblock-write:dblock-type' where dblock-type is the string + following the =#+BEGIN:= portion of the line. + + dblocks look like the following and allow for evaluation of the + code inside of the block by calling =\C-c\C-c= on the header of + the block. + +#+BEGIN: dblock-type +#+END: + +*** R blocks + In developing RweaveOrg, Austin created [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]]. This + allows for the kind of blocks shown in [[file:existing_tools/RweaveOrg/testing.Rorg][testing.Rorg]]. These blocks + have the advantage of accepting options to the Sweave preprocessor + following the #+BEGIN_R declaration. + + +* tasks + +* buffer dictionary + LocalWords: DBlocks dblocks diff --git a/rorg.html b/rorg.html new file mode 100644 index 000000000..abe08acf1 --- /dev/null +++ b/rorg.html @@ -0,0 +1,344 @@ + + + +rorg — R and org-mode + + + + + + + +

rorg — R and org-mode

+ + + + +
+

1 Objectives

+
+ + +
+ +
+

1.1 Send data to R from org

+
+ +

Org-mode includes orgtbl-mode, an extremely convenient way of using +tabular data in a plain text file. Currently, spreadsheet +functionality is available in org tables using the emacs package +calc. It would be a boon both to org users and R users to allow +org tables to be manipulated with the R programming language. Org +tables give R users an easy way to enter and display data; R gives +org users a powerful way to perform vector operations, statistical +tests, and visualization on their tables. +

+ +
+ +
+

1.1.1 Implementations

+
+ +
    +
  • naive
    +Naive implementation would be to use (org-export-table "tmp.csv") +and (ess-execute "read.csv('tmp.csv')"). +
    • +
  • org-R
    +org-R passes data to R from two sources: org tables, or csv +files. Org tables are first exported to a temporary csv file +using org-R-export-to-csv. +
    • +
  • org-exp-blocks
    +
    • +
  • RweaveOrg
    +NA + +
    • +
+
+
+ +
+ +
+

1.2 evaluate R code from org and deal with output appropriately

+
+ + +
+ +
+

1.2.1 vector output

+
+ +

When R code evaluation generates vectors and 2-dimensional arrays, +this should be formatted appropriately in org buffers (orgtbl-mode) as well +as in export targets (html, latex) +

    +
  • Implementations
    +
      +
    • org-R
      +org-R converts R output (vectors, or matrices / 2d-arrays) to an +org table and stores it in the org buffer, or in a separate org +file (csv output would also be perfectly possible). +
      • +
    • org-exp-blocks
      +
      • +
    • RweaveOrg
      +
      • +
    +
    • +
+
+ +
+ +
+

1.2.2 graphical output

+
+ +

R can generate graphical output on a screen graphics device +(e.g. X11, quartz), and in various standard image file formats +(png, jpg, ps, pdf, etc). When graphical output is generated by +evaluation of R code in Org, at least the following two things are desirable: +

    +
  1. +output to screen for immediate viewing is possible +
    2. +
  2. +graphical output to file is linked to appropriately from the +org file This should have the automatic consequence that it is +included appropriately in subsequent export targets (html, +latex). +
    3. +
+
    +
  • Implementations
    +
      +
    • org-R
      +org-R does (1) if no output file is specified and (2) otherwise +
      • +
    • org-exp-blocks
      +
      • +
    • RweaveOrg
      + + +
      • +
    +
    • +
+
+
+
+ +
+ +
+

2 Notes

+
+ + +
+ +
+

2.1 Special editing and evaluation of source code in R blocks

+
+ +

Unfortunately org-mode how two different block types, both useful. +In developing RweaveOrg, a third was introduced. +

+

+Eric is leaning towards using the #+begin_src blocks, as that is +really what these blocks contain: source code. Austin believes +that specifying export options at the beginning of a block is +useful functionality, to be preserved if possible. +

+

+Note that upper and lower case are not relevant in block headings. +

+ +
+ +
+

2.1.1 Source code blocks

+
+ +

Org has an extremely useful method of editing source code and +examples in their native modes. In the case of R code, we want to +be able to use the full functionality of ESS mode, including +interactive evaluation of code. +

+

+Source code blocks look like the following and allow for the +special editing of code inside of the block through +`org-edit-special'. +

+ + + +
+
+,## hit C-c ' within this block to enter a temporary buffer in r-mode.
+
+,## while in the temporary buffer, hit C-c C-c on this comment to
+,## evaluate this block
+a <- 3
+a
+
+,## hit C-c ' to exit the temporary buffer
+
+ + + + +
+ +
+ +
+

2.1.2 dblocks

+
+ +

dblocks are useful because org-mode will automatically call +`org-dblock-write:dblock-type' where dblock-type is the string +following the #+BEGIN: portion of the line. +

+

+dblocks look like the following and allow for evaluation of the +code inside of the block by calling \C-c\C-c on the header of +the block. +

+ +
+ +
+ +
+

2.1.3 R blocks

+
+ +

In developing RweaveOrg, Austin created org-sweave.el. This +allows for the kind of blocks shown in testing.Rorg. These blocks +have the advantage of accepting options to the Sweave preprocessor +following the #+BEGINR declaration. +

+ +
+
+
+ +
+ +
+

3 tasks

+
+ + +
+ +
+ +
+

4 buffer dictionary

+
+ +

LocalWords: DBlocks dblocks +

+
+

Author: Dan +<dan@Tichodroma> +

+

Date: 2009-02-05 21:16:20 EST

+

HTML generated by org-mode 6.20f in emacs 22

+
+ diff --git a/rorg.org b/rorg.org index 34b893e2b..9cbbad785 100644 --- a/rorg.org +++ b/rorg.org @@ -1,5 +1,66 @@ #+TITLE: rorg --- R and org-mode #+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE +#+STARTUP: oddeven + +* Overview + +** Dan [2009-02-08 Sun] +This project is basically about putting source code into org +files. This isn't just code to look pretty as a source code example, +but code to be evaluated. Org files have 3 main export targets: org, +html and latex. Thus the aim of this project is to produce files in +those formats that have benefitted in some way from the evaluation of +source code that is present in the source org file. We have a current +focus on R code, but we are regarding that more as a working example +than as a defining feature of the project. + +The following are three important questions: + + 1. How is the code placed in the org file? + 2. When is the code evaluated? + 3. What happens when the code is evaluated? + +Let's take them in reverse order, as 1 and 2 can be viewed as +details of the implementation of 3. + +*** What happens when the code is evaluated? +Code evaluation can have three relevant consequences + 1. It produces text/numeric output + 2. It produces graphical output + 3. It alters the environment by side effect in some other way + +I think our aims here are fairly straightforward to specify: in the +case of (1) we (optionally) incorporate the text output as text in the +target document. In the case of (2) we either place a link to the +graphics or (html/latex) include them inline. We don't need to do anything +about (3), except bear in mind that it's a possibility. + +*** When is the code evaluated? +Let's take the three export targets in turn +**** Latex + Here we have some options. I'll use an asterisk to indicate + content which includes the *result* of code evaluation, rather + than the code itself. + +***** org \to org* \to latex + This is what RweaveOrg does, e.g. +: Sweave("testing.Rorg", driver=RweaveOrg, syntax=SweaveSyntaxOrg) +Here testing.Rorg is an org file, and Sweave generates another org +file, but with the code evaluated. + +This is also what org-R does. + +***** org \to latex \to \latex* + This seems like a possibility to me, but AFAIK we don't have it + working. So in the case of R, here you would use something like + `org-export-as-latex', and then from R, run Sweave (with the + RweaveLatex driver) on the exported latex to generate the latex* + file with evaluation results. Since Sweave with RweaveLatex is + an established technology that is heavily used in the R + community, it would be nice to provide this route as an option, + so at any point users can `bail out' and enter a workflow where + they treat the latex/noweb as source code to be edited directly + (rather than editing a org buffer). * Commentary @@ -202,7 +263,7 @@ different components which have to interactive with R including: - automatic evaluation on export - evaluation of \R{} snippets - evaluation of single source code lines -- sending/recieving vector data +- sending/receiving vector data I think we currently have two implementation of interaction with R processes; [[file:existing_tools/org-R.el][org-R.el]] and [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]]. We should be sure to take