Browse Source

Trying to write a project overview at top of rorg.org

Dan Davison 16 years ago
parent
commit
cf31c1f134

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existing_tools/RweaveOrg/testing-004.pdf

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+ 1 - 0
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, ...)

+ 73 - 0
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

+ 25 - 0
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}{}}

+ 612 - 0
existing_tools/RweaveOrg/testing.log

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+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 <v3.8h> 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
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+   defining Unicode char U+0143 (decimal 323)
+   defining Unicode char U+0144 (decimal 324)
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+   defining Unicode char U+0148 (decimal 328)
+   defining Unicode char U+014A (decimal 330)
+   defining Unicode char U+014B (decimal 331)
+   defining Unicode char U+0150 (decimal 336)
+   defining Unicode char U+0151 (decimal 337)
+   defining Unicode char U+0152 (decimal 338)
+   defining Unicode char U+0153 (decimal 339)
+   defining Unicode char U+0154 (decimal 340)
+   defining Unicode char U+0155 (decimal 341)
+   defining Unicode char U+0158 (decimal 344)
+   defining Unicode char U+0159 (decimal 345)
+   defining Unicode char U+015A (decimal 346)
+   defining Unicode char U+015B (decimal 347)
+   defining Unicode char U+015E (decimal 350)
+   defining Unicode char U+015F (decimal 351)
+   defining Unicode char U+0160 (decimal 352)
+   defining Unicode char U+0161 (decimal 353)
+   defining Unicode char U+0162 (decimal 354)
+   defining Unicode char U+0163 (decimal 355)
+   defining Unicode char U+0164 (decimal 356)
+   defining Unicode char U+0165 (decimal 357)
+   defining Unicode char U+016E (decimal 366)
+   defining Unicode char U+016F (decimal 367)
+   defining Unicode char U+0170 (decimal 368)
+   defining Unicode char U+0171 (decimal 369)
+   defining Unicode char U+0178 (decimal 376)
+   defining Unicode char U+0179 (decimal 377)
+   defining Unicode char U+017A (decimal 378)
+   defining Unicode char U+017B (decimal 379)
+   defining Unicode char U+017C (decimal 380)
+   defining Unicode char U+017D (decimal 381)
+   defining Unicode char U+017E (decimal 382)
+   defining Unicode char U+200C (decimal 8204)
+   defining Unicode char U+2013 (decimal 8211)
+   defining Unicode char U+2014 (decimal 8212)
+   defining Unicode char U+2018 (decimal 8216)
+   defining Unicode char U+2019 (decimal 8217)
+   defining Unicode char U+201A (decimal 8218)
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+   defining Unicode char U+2031 (decimal 8241)
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+)
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+
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+   defining Unicode char U+00A3 (decimal 163)
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+   defining Unicode char U+00C6 (decimal 198)
+   defining Unicode char U+00D8 (decimal 216)
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+   defining Unicode char U+00E6 (decimal 230)
+   defining Unicode char U+00EC (decimal 236)
+   defining Unicode char U+00ED (decimal 237)
+   defining Unicode char U+00EE (decimal 238)
+   defining Unicode char U+00EF (decimal 239)
+   defining Unicode char U+00F8 (decimal 248)
+   defining Unicode char U+0131 (decimal 305)
+   defining Unicode char U+0141 (decimal 321)
+   defining Unicode char U+0142 (decimal 322)
+   defining Unicode char U+0152 (decimal 338)
+   defining Unicode char U+0153 (decimal 339)
+   defining Unicode char U+2013 (decimal 8211)
+   defining Unicode char U+2014 (decimal 8212)
+   defining Unicode char U+2018 (decimal 8216)
+   defining Unicode char U+2019 (decimal 8217)
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+)
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+   defining Unicode char U+00A7 (decimal 167)
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+)
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+   defining Unicode char U+00AA (decimal 170)
+   defining Unicode char U+00AE (decimal 174)
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+   defining Unicode char U+02C6 (decimal 710)
+   defining Unicode char U+02DC (decimal 732)
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+   defining Unicode char U+2026 (decimal 8230)
+   defining Unicode char U+2122 (decimal 8482)
+   defining Unicode char U+2423 (decimal 9251)
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+)
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+)
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+Package: Sweave 
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+
+No file fancyvrb.cfg.
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+atim and verb
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+
+(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def
+File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
+Now handling font encoding TS1 ...
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+
+(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu
+File: ts1enc.dfu 2006/03/30 v1.1i UTF-8 support for inputenc
+   defining Unicode char U+00A2 (decimal 162)
+   defining Unicode char U+00A3 (decimal 163)
+   defining Unicode char U+00A4 (decimal 164)
+   defining Unicode char U+00A5 (decimal 165)
+   defining Unicode char U+00A6 (decimal 166)
+   defining Unicode char U+00A7 (decimal 167)
+   defining Unicode char U+00A8 (decimal 168)
+   defining Unicode char U+00A9 (decimal 169)
+   defining Unicode char U+00AA (decimal 170)
+   defining Unicode char U+00AC (decimal 172)
+   defining Unicode char U+00AE (decimal 174)
+   defining Unicode char U+00AF (decimal 175)
+   defining Unicode char U+00B0 (decimal 176)
+   defining Unicode char U+00B1 (decimal 177)
+   defining Unicode char U+00B2 (decimal 178)
+   defining Unicode char U+00B3 (decimal 179)
+   defining Unicode char U+00B4 (decimal 180)
+   defining Unicode char U+00B5 (decimal 181)
+   defining Unicode char U+00B6 (decimal 182)
+   defining Unicode char U+00B7 (decimal 183)
+   defining Unicode char U+00B9 (decimal 185)
+   defining Unicode char U+00BA (decimal 186)
+   defining Unicode char U+00BC (decimal 188)
+   defining Unicode char U+00BD (decimal 189)
+   defining Unicode char U+00BE (decimal 190)
+   defining Unicode char U+00D7 (decimal 215)
+   defining Unicode char U+00F7 (decimal 247)
+   defining Unicode char U+0192 (decimal 402)
+   defining Unicode char U+02C7 (decimal 711)
+   defining Unicode char U+02D8 (decimal 728)
+   defining Unicode char U+02DD (decimal 733)
+   defining Unicode char U+0E3F (decimal 3647)
+   defining Unicode char U+2016 (decimal 8214)
+   defining Unicode char U+2020 (decimal 8224)
+   defining Unicode char U+2021 (decimal 8225)
+   defining Unicode char U+2022 (decimal 8226)
+   defining Unicode char U+2030 (decimal 8240)
+   defining Unicode char U+2031 (decimal 8241)
+   defining Unicode char U+203B (decimal 8251)
+   defining Unicode char U+203D (decimal 8253)
+   defining Unicode char U+2044 (decimal 8260)
+   defining Unicode char U+204E (decimal 8270)
+   defining Unicode char U+2052 (decimal 8274)
+   defining Unicode char U+20A1 (decimal 8353)
+   defining Unicode char U+20A4 (decimal 8356)
+   defining Unicode char U+20A6 (decimal 8358)
+   defining Unicode char U+20A9 (decimal 8361)
+   defining Unicode char U+20AB (decimal 8363)
+   defining Unicode char U+20AC (decimal 8364)
+   defining Unicode char U+20B1 (decimal 8369)
+   defining Unicode char U+2103 (decimal 8451)
+   defining Unicode char U+2116 (decimal 8470)
+   defining Unicode char U+2117 (decimal 8471)
+   defining Unicode char U+211E (decimal 8478)
+   defining Unicode char U+2120 (decimal 8480)
+   defining Unicode char U+2122 (decimal 8482)
+   defining Unicode char U+2126 (decimal 8486)
+   defining Unicode char U+2127 (decimal 8487)
+   defining Unicode char U+212E (decimal 8494)
+   defining Unicode char U+2190 (decimal 8592)
+   defining Unicode char U+2191 (decimal 8593)
+   defining Unicode char U+2192 (decimal 8594)
+   defining Unicode char U+2193 (decimal 8595)
+   defining Unicode char U+2329 (decimal 9001)
+   defining Unicode char U+232A (decimal 9002)
+   defining Unicode char U+2422 (decimal 9250)
+   defining Unicode char U+25E6 (decimal 9702)
+   defining Unicode char U+25EF (decimal 9711)
+   defining Unicode char U+266A (decimal 9834)
+))
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+)
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+
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+File: t1aer.fd 1997/11/16 Font definitions for T1/aer.
+))))
+No file testing.aux.
+\openout1 = `testing.aux'.
+
+LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 14.
+LaTeX Font Info:    ... okay on input line 14.
+LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 14.
+LaTeX Font Info:    ... okay on input line 14.
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+LaTeX Font Info:    ... okay on input line 14.
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+LaTeX Font Info:    ... okay on input line 14.
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+LaTeX Font Info:    Try loading font information for TS1+cmr on input 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.
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+
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+
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+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'.
+
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+LaTeX Font Info:    External font `cmex10' loaded for size
+(Font)              <8> on input line 17.
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+\openout5 = `testing.toc'.
+
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+
+(/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
+</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb></usr/share/texmf
+-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1
+/bluesky/cm/cmr12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr17.pf
+b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/tex
+mf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb>
+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)
+

+ 86 - 0
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]]

+ 6 - 0
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}

BIN
existing_tools/RweaveOrg/testing.pdf


+ 82 - 0
existing_tools/RweaveOrg/testing.tex

@@ -0,0 +1,82 @@
+% Created 2009-02-08 Sun 11:18
+\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}

+ 6 - 0
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}

+ 113 - 0
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

+ 344 - 0
rorg.html

@@ -0,0 +1,344 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+               "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+lang="en" xml:lang="en">
+<head>
+<title>rorg &mdash; R and org-mode</title>
+<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"/>
+<meta name="generator" content="Org-mode"/>
+<meta name="generated" content="2009-02-05 21:16:20 EST"/>
+<meta name="author" content="Dan"/>
+<style type="text/css">
+ <!--/*--><![CDATA[/*><!--*/
+  html { font-family: Times, serif; font-size: 12pt; }
+  .title  { text-align: center; }
+  .todo   { color: red; }
+  .done   { color: green; }
+  .tag    { background-color:lightblue; font-weight:normal }
+  .target { }
+  .timestamp { color: grey }
+  .timestamp-kwd { color: CadetBlue }
+  p.verse { margin-left: 3% }
+  pre {
+	border: 1pt solid #AEBDCC;
+	background-color: #F3F5F7;
+	padding: 5pt;
+	font-family: courier, monospace;
+        font-size: 90%;
+        overflow:auto;
+  }
+  table { border-collapse: collapse; }
+  td, th { vertical-align: top; }
+  dt { font-weight: bold; }
+  div.figure { padding: 0.5em; }
+  div.figure p { text-align: center; }
+  .linenr { font-size:smaller }
+  .code-highlighted {background-color:#ffff00;}
+  .org-info-js_info-navigation { border-style:none; }
+  #org-info-js_console-label { font-size:10px; font-weight:bold;
+                               white-space:nowrap; }
+  .org-info-js_search-highlight {background-color:#ffff00; color:#000000;
+                                 font-weight:bold; }
+  /*]]>*/-->
+</style>
+<script type="text/javascript">
+<!--/*--><![CDATA[/*><!--*/
+ function CodeHighlightOn(elem, id)
+ {
+   var target = document.getElementById(id);
+   if(null != target) {
+     elem.cacheClassElem = elem.className;
+     elem.cacheClassTarget = target.className;
+     target.className = "code-highlighted";
+     elem.className   = "code-highlighted";
+   }
+ }
+ function CodeHighlightOff(elem, id)
+ {
+   var target = document.getElementById(id);
+   if(elem.cacheClassElem)
+     elem.className = elem.cacheClassElem;
+   if(elem.cacheClassTarget)
+     target.className = elem.cacheClassTarget;
+ }
+/*]]>*/-->
+</script>
+</head><body>
+<h1 class="title">rorg &mdash; R and org-mode</h1>
+
+
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#sec-1">1 Objectives </a>
+<ul>
+<li><a href="#sec-1.1">1.1 Send data to R from org </a>
+<ul>
+<li><a href="#sec-1.1.1">1.1.1 Implementations </a></li>
+</ul>
+</li>
+<li><a href="#sec-1.2">1.2 evaluate R code from org and deal with output appropriately </a>
+<ul>
+<li><a href="#sec-1.2.1">1.2.1 vector output </a></li>
+<li><a href="#sec-1.2.2">1.2.2 graphical output </a></li>
+</ul></li>
+</ul>
+</li>
+<li><a href="#sec-2">2 Notes </a>
+<ul>
+<li><a href="#sec-2.1">2.1 Special editing and evaluation of source code in R blocks </a>
+<ul>
+<li><a href="#sec-2.1.1">2.1.1 Source code blocks </a></li>
+<li><a href="#sec-2.1.2">2.1.2 dblocks </a></li>
+<li><a href="#sec-2.1.3">2.1.3 R blocks </a></li>
+</ul></li>
+</ul>
+</li>
+<li><a href="#sec-3">3 tasks </a></li>
+<li><a href="#sec-4">4 buffer dictionary </a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-1" class="outline-2">
+<h2 id="sec-1">1 Objectives </h2>
+<div id="text-1">
+
+
+</div>
+
+<div id="outline-container-1.1" class="outline-3">
+<h3 id="sec-1.1">1.1 Send data to R from org </h3>
+<div id="text-1.1">
+
+<p>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.
+</p>
+
+</div>
+
+<div id="outline-container-1.1.1" class="outline-4">
+<h4 id="sec-1.1.1">1.1.1 Implementations </h4>
+<div id="text-1.1.1">
+
+<ul>
+<li id="sec-1.1.1.1">naive <br/>
+Naive implementation would be to use <code>(org-export-table "tmp.csv")</code>
+and <code>(ess-execute "read.csv('tmp.csv')")</code>.  
+</li>
+<li id="sec-1.1.1.2">org-R <br/>
+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 <a href="existing_tools/org-R.el">org-R-export-to-csv</a>.
+</li>
+<li id="sec-1.1.1.3">org-exp-blocks <br/>
+</li>
+<li id="sec-1.1.1.4">RweaveOrg <br/>
+NA
+
+</li>
+</ul>
+</div>
+</div>
+
+</div>
+
+<div id="outline-container-1.2" class="outline-3">
+<h3 id="sec-1.2">1.2 evaluate R code from org and deal with output appropriately </h3>
+<div id="text-1.2">
+
+
+</div>
+
+<div id="outline-container-1.2.1" class="outline-4">
+<h4 id="sec-1.2.1">1.2.1 vector output </h4>
+<div id="text-1.2.1">
+
+<p>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)
+</p><ul>
+<li id="sec-1.2.1.1">Implementations <br/>
+<ul>
+<li id="sec-1.2.1.1.1">org-R <br/>
+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).
+</li>
+<li id="sec-1.2.1.1.2">org-exp-blocks <br/>
+</li>
+<li id="sec-1.2.1.1.3">RweaveOrg <br/>
+</li>
+</ul>
+</li>
+</ul>
+</div>
+
+</div>
+
+<div id="outline-container-1.2.2" class="outline-4">
+<h4 id="sec-1.2.2">1.2.2 graphical output </h4>
+<div id="text-1.2.2">
+
+<p>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:
+</p><ol>
+<li>
+output to screen for immediate viewing is possible
+</li>
+<li>
+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).
+</li>
+</ol>
+<ul>
+<li id="sec-1.2.2.1">Implementations <br/>
+<ul>
+<li id="sec-1.2.2.1.1">org-R <br/>
+org-R does (1) if no output file is specified and (2) otherwise
+</li>
+<li id="sec-1.2.2.1.2">org-exp-blocks <br/>
+</li>
+<li id="sec-1.2.2.1.3">RweaveOrg <br/>
+
+
+</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+</div>
+
+<div id="outline-container-2" class="outline-2">
+<h2 id="sec-2">2 Notes </h2>
+<div id="text-2">
+
+
+</div>
+
+<div id="outline-container-2.1" class="outline-3">
+<h3 id="sec-2.1">2.1 Special editing and evaluation of source code in R blocks </h3>
+<div id="text-2.1">
+
+<p>Unfortunately org-mode how two different block types, both useful.
+In developing RweaveOrg, a third was introduced.
+</p>
+<p>
+Eric is leaning towards using the <code>#+begin_src</code> 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.
+</p>
+<p>
+Note that upper and lower case are not relevant in block headings.
+</p>
+
+</div>
+
+<div id="outline-container-2.1.1" class="outline-4">
+<h4 id="sec-2.1.1">2.1.1 Source code blocks </h4>
+<div id="text-2.1.1">
+
+<p>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.
+</p>
+<p>
+Source code blocks look like the following and allow for the
+special editing of code inside of the block through
+`org-edit-special'.
+</p>
+
+
+
+<pre class="src src-r">
+
+,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">hit C-c ' within this block to enter a temporary buffer in r-mode.
+</span>
+,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">while in the temporary buffer, hit C-c C-c on this comment to
+</span>,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">evaluate this block
+</span>a <span style="color: #98fb98;">&lt;-</span> 3
+a
+
+,<span style="color: #add8e6;">## </span><span style="color: #add8e6;">hit C-c ' to exit the temporary buffer
+</span></pre>
+
+
+
+
+</div>
+
+</div>
+
+<div id="outline-container-2.1.2" class="outline-4">
+<h4 id="sec-2.1.2">2.1.2 dblocks </h4>
+<div id="text-2.1.2">
+
+<p>dblocks are useful because org-mode will automatically call
+`org-dblock-write:dblock-type' where dblock-type is the string
+following the <code>#+BEGIN:</code> portion of the line.
+</p>
+<p>
+dblocks look like the following and allow for evaluation of the
+code inside of the block by calling <code>\C-c\C-c</code> on the header of
+the block.  
+</p>
+
+</div>
+
+</div>
+
+<div id="outline-container-2.1.3" class="outline-4">
+<h4 id="sec-2.1.3">2.1.3 R blocks </h4>
+<div id="text-2.1.3">
+
+<p>In developing RweaveOrg, Austin created <a href="existing_tools/RweaveOrg/org-sweave.el">org-sweave.el</a>.  This
+allows for the kind of blocks shown in <a href="existing_tools/RweaveOrg/testing.Rorg">testing.Rorg</a>.  These blocks
+have the advantage of accepting options to the Sweave preprocessor
+following the #+BEGIN<sub>R</sub> declaration.
+</p>
+
+</div>
+</div>
+</div>
+
+</div>
+
+<div id="outline-container-3" class="outline-2">
+<h2 id="sec-3">3 tasks </h2>
+<div id="text-3">
+
+
+</div>
+
+</div>
+
+<div id="outline-container-4" class="outline-2">
+<h2 id="sec-4">4 buffer dictionary </h2>
+<div id="text-4">
+
+<p>LocalWords:  DBlocks dblocks
+</p></div>
+</div>
+<div id="postamble"><p class="author"> Author: Dan
+<a href="mailto:dan@Tichodroma">&lt;dan@Tichodroma&gt;</a>
+</p>
+<p class="date"> Date: 2009-02-05 21:16:20 EST</p>
+<p>HTML generated by org-mode 6.20f in emacs 22</p>
+</div></body>
+</html>

+ 62 - 1
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