Trying to write a project overview at top of rorg.org
This commit is contained in:
Dan Davison
parent
bdae433d69
commit
cf31c1f134
|
|
@ -0,0 +1,252 @@
|
|||
%PDF-1.1
|
||||
%<25>â<EFBFBD>ã<EFBFBD>Ï<EFBFBD>Ó\r
|
||||
1 0 obj
|
||||
<<
|
||||
/CreationDate (D:20090208111729)
|
||||
/ModDate (D:20090208111729)
|
||||
/Title (R Graphics Output)
|
||||
/Producer (R 2.7.2)
|
||||
/Creator (R)
|
||||
>>
|
||||
endobj
|
||||
2 0 obj
|
||||
<<
|
||||
/Type /Catalog
|
||||
/Pages 3 0 R
|
||||
>>
|
||||
endobj
|
||||
5 0 obj
|
||||
<<
|
||||
/Type /Font
|
||||
/Subtype /Type1
|
||||
/Name /F1
|
||||
/BaseFont /ZapfDingbats
|
||||
>>
|
||||
endobj
|
||||
6 0 obj
|
||||
<<
|
||||
/Type /Page
|
||||
/Parent 3 0 R
|
||||
/Contents 7 0 R
|
||||
/Resources 4 0 R
|
||||
>>
|
||||
endobj
|
||||
7 0 obj
|
||||
<<
|
||||
/Length 8 0 R
|
||||
>>
|
||||
stream
|
||||
q
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
BT
|
||||
0.000 0.000 0.000 rg
|
||||
/F2 1 Tf 12.00 0.00 -0.00 12.00 219.53 18.00 Tm (dist) Tj
|
||||
ET
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
BT
|
||||
0.000 0.000 0.000 rg
|
||||
/F2 1 Tf 0.00 12.00 -12.00 0.00 20.62 210.55 Tm (speed) Tj
|
||||
ET
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
0.000 0.000 0.000 RG
|
||||
0.75 w
|
||||
[] 0 d
|
||||
1 J
|
||||
1 j
|
||||
10.00 M
|
||||
70.95 396.99 m 70.95 402.66 l S
|
||||
122.73 396.99 m 122.73 402.66 l S
|
||||
174.50 396.99 m 174.50 402.66 l S
|
||||
226.28 396.99 m 226.28 402.66 l S
|
||||
278.06 396.99 m 278.06 402.66 l S
|
||||
329.83 396.99 m 329.83 402.66 l S
|
||||
381.61 396.99 m 381.61 402.66 l S
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
0.000 0.000 0.000 RG
|
||||
0.75 w
|
||||
[] 0 d
|
||||
1 J
|
||||
1 j
|
||||
10.00 M
|
||||
54.74 91.90 m 49.07 91.90 l S
|
||||
54.74 162.95 m 49.07 162.95 l S
|
||||
54.74 234.00 m 49.07 234.00 l S
|
||||
54.74 305.05 m 49.07 305.05 l S
|
||||
54.74 376.10 m 49.07 376.10 l S
|
||||
BT
|
||||
0.000 0.000 0.000 rg
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 37.85 88.31 Tm (5) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 32.29 159.36 Tm (10) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 32.29 230.41 Tm (15) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 32.29 301.46 Tm (20) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 32.29 372.51 Tm (25) Tj
|
||||
ET
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
0.000 0.000 0.000 RG
|
||||
0.75 w
|
||||
[] 0 d
|
||||
1 J
|
||||
1 j
|
||||
10.00 M
|
||||
70.95 56.80 m 70.95 51.13 l S
|
||||
122.73 56.80 m 122.73 51.13 l S
|
||||
174.50 56.80 m 174.50 51.13 l S
|
||||
226.28 56.80 m 226.28 51.13 l S
|
||||
278.06 56.80 m 278.06 51.13 l S
|
||||
329.83 56.80 m 329.83 51.13 l S
|
||||
381.61 56.80 m 381.61 51.13 l S
|
||||
BT
|
||||
0.000 0.000 0.000 rg
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 68.17 38.29 Tm (0) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 117.17 38.29 Tm (20) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 168.94 38.29 Tm (40) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 220.72 38.29 Tm (60) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 272.50 38.29 Tm (80) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 321.49 38.29 Tm (100) Tj
|
||||
/F2 1 Tf 10.00 0.00 -0.00 10.00 373.27 38.29 Tm (120) Tj
|
||||
ET
|
||||
402.99 91.90 m 408.66 91.90 l S
|
||||
402.99 162.95 m 408.66 162.95 l S
|
||||
402.99 234.00 m 408.66 234.00 l S
|
||||
402.99 305.05 m 408.66 305.05 l S
|
||||
402.99 376.10 m 408.66 376.10 l S
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q 54.74 56.80 348.25 340.19 re W n
|
||||
0.000 0.502 1.000 RG
|
||||
0.75 w
|
||||
[] 0 d
|
||||
1 J
|
||||
1 j
|
||||
10.00 M
|
||||
BT
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 73.49 75.39 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 94.21 75.39 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 78.67 118.02 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 125.27 118.02 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 109.74 132.23 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 94.21 146.44 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 114.92 160.65 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 135.63 160.65 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 156.34 160.65 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 112.33 174.86 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 140.80 174.86 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 104.56 189.07 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 120.09 189.07 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 130.45 189.07 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 140.80 189.07 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 135.63 203.28 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 156.34 203.28 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 156.34 203.28 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 187.40 203.28 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 135.63 217.49 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 161.51 217.49 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 223.65 217.49 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 275.42 217.49 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 120.09 231.70 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 135.63 231.70 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 208.11 231.70 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 151.16 245.91 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 171.87 245.91 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 151.16 260.12 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 171.87 260.12 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 197.76 260.12 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 177.05 274.33 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 213.29 274.33 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 265.07 274.33 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 285.78 274.33 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 161.51 288.54 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 187.40 288.54 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 244.36 288.54 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 151.16 302.75 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 192.58 302.75 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 202.94 302.75 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 213.29 302.75 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 234.00 302.75 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 239.18 331.17 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 208.11 345.38 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 249.53 359.59 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 306.49 359.59 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 309.08 359.59 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 378.98 359.59 Tm (l) Tj 0 Tr
|
||||
/F1 1 Tf 1 Tr 6.65 0 0 6.65 288.37 373.80 Tm (l) Tj 0 Tr
|
||||
0.000 0.000 0.000 RG
|
||||
ET
|
||||
54.74 63.48 m 402.99 63.48 l S
|
||||
86.48 56.80 m 86.48 396.99 l S
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
0.000 0.000 0.000 RG
|
||||
0.75 w
|
||||
[] 0 d
|
||||
1 J
|
||||
1 j
|
||||
10.00 M
|
||||
54.74 56.80 348.25 340.19 re S
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q q -216.00 -216.00 864.00 864.00 re W n
|
||||
Q
|
||||
endstream
|
||||
endobj
|
||||
8 0 obj
|
||||
5554
|
||||
endobj
|
||||
3 0 obj
|
||||
<<
|
||||
/Type /Pages
|
||||
/Kids [
|
||||
6 0 R
|
||||
]
|
||||
/Count 1
|
||||
/MediaBox [0 0 432 432]
|
||||
>>
|
||||
endobj
|
||||
4 0 obj
|
||||
<<
|
||||
/ProcSet [/PDF /Text]
|
||||
/Font << /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
|
||||
|
|
@ -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, ...)
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -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}{}}
|
||||
|
|
@ -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 <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
|
||||
\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 inputenc
|
||||
defining Unicode char U+00A1 (decimal 161)
|
||||
defining Unicode char U+00A3 (decimal 163)
|
||||
defining Unicode char U+00AB (decimal 171)
|
||||
defining Unicode char U+00BB (decimal 187)
|
||||
defining Unicode char U+00BF (decimal 191)
|
||||
defining Unicode char U+00C0 (decimal 192)
|
||||
defining Unicode char U+00C1 (decimal 193)
|
||||
defining Unicode char U+00C2 (decimal 194)
|
||||
defining Unicode char U+00C3 (decimal 195)
|
||||
defining Unicode char U+00C4 (decimal 196)
|
||||
defining Unicode char U+00C5 (decimal 197)
|
||||
defining Unicode char U+00C6 (decimal 198)
|
||||
defining Unicode char U+00C7 (decimal 199)
|
||||
defining Unicode char U+00C8 (decimal 200)
|
||||
defining Unicode char U+00C9 (decimal 201)
|
||||
defining Unicode char U+00CA (decimal 202)
|
||||
defining Unicode char U+00CB (decimal 203)
|
||||
defining Unicode char U+00CC (decimal 204)
|
||||
defining Unicode char U+00CD (decimal 205)
|
||||
defining Unicode char U+00CE (decimal 206)
|
||||
defining Unicode char U+00CF (decimal 207)
|
||||
defining Unicode char U+00D0 (decimal 208)
|
||||
defining Unicode char U+00D1 (decimal 209)
|
||||
defining Unicode char U+00D2 (decimal 210)
|
||||
defining Unicode char U+00D3 (decimal 211)
|
||||
defining Unicode char U+00D4 (decimal 212)
|
||||
defining Unicode char U+00D5 (decimal 213)
|
||||
defining Unicode char U+00D6 (decimal 214)
|
||||
defining Unicode char U+00D8 (decimal 216)
|
||||
defining Unicode char U+00D9 (decimal 217)
|
||||
defining Unicode char U+00DA (decimal 218)
|
||||
defining Unicode char U+00DB (decimal 219)
|
||||
defining Unicode char U+00DC (decimal 220)
|
||||
defining Unicode char U+00DD (decimal 221)
|
||||
defining Unicode char U+00DE (decimal 222)
|
||||
defining Unicode char U+00DF (decimal 223)
|
||||
defining Unicode char U+00E0 (decimal 224)
|
||||
defining Unicode char U+00E1 (decimal 225)
|
||||
defining Unicode char U+00E2 (decimal 226)
|
||||
defining Unicode char U+00E3 (decimal 227)
|
||||
defining Unicode char U+00E4 (decimal 228)
|
||||
defining Unicode char U+00E5 (decimal 229)
|
||||
defining Unicode char U+00E6 (decimal 230)
|
||||
defining Unicode char U+00E7 (decimal 231)
|
||||
defining Unicode char U+00E8 (decimal 232)
|
||||
defining Unicode char U+00E9 (decimal 233)
|
||||
defining Unicode char U+00EA (decimal 234)
|
||||
defining Unicode char U+00EB (decimal 235)
|
||||
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+00F0 (decimal 240)
|
||||
defining Unicode char U+00F1 (decimal 241)
|
||||
defining Unicode char U+00F2 (decimal 242)
|
||||
defining Unicode char U+00F3 (decimal 243)
|
||||
defining Unicode char U+00F4 (decimal 244)
|
||||
defining Unicode char U+00F5 (decimal 245)
|
||||
defining Unicode char U+00F6 (decimal 246)
|
||||
defining Unicode char U+00F8 (decimal 248)
|
||||
defining Unicode char U+00F9 (decimal 249)
|
||||
defining Unicode char U+00FA (decimal 250)
|
||||
defining Unicode char U+00FB (decimal 251)
|
||||
defining Unicode char U+00FC (decimal 252)
|
||||
defining Unicode char U+00FD (decimal 253)
|
||||
defining Unicode char U+00FE (decimal 254)
|
||||
defining Unicode char U+00FF (decimal 255)
|
||||
defining Unicode char U+0102 (decimal 258)
|
||||
defining Unicode char U+0103 (decimal 259)
|
||||
defining Unicode char U+0104 (decimal 260)
|
||||
defining Unicode char U+0105 (decimal 261)
|
||||
defining Unicode char U+0106 (decimal 262)
|
||||
defining Unicode char U+0107 (decimal 263)
|
||||
defining Unicode char U+010C (decimal 268)
|
||||
defining Unicode char U+010D (decimal 269)
|
||||
defining Unicode char U+010E (decimal 270)
|
||||
defining Unicode char U+010F (decimal 271)
|
||||
defining Unicode char U+0110 (decimal 272)
|
||||
defining Unicode char U+0111 (decimal 273)
|
||||
defining Unicode char U+0118 (decimal 280)
|
||||
defining Unicode char U+0119 (decimal 281)
|
||||
defining Unicode char U+011A (decimal 282)
|
||||
defining Unicode char U+011B (decimal 283)
|
||||
defining Unicode char U+011E (decimal 286)
|
||||
defining Unicode char U+011F (decimal 287)
|
||||
defining Unicode char U+0130 (decimal 304)
|
||||
defining Unicode char U+0131 (decimal 305)
|
||||
defining Unicode char U+0132 (decimal 306)
|
||||
defining Unicode char U+0133 (decimal 307)
|
||||
defining Unicode char U+0139 (decimal 313)
|
||||
defining Unicode char U+013A (decimal 314)
|
||||
defining Unicode char U+013D (decimal 317)
|
||||
defining Unicode char U+013E (decimal 318)
|
||||
defining Unicode char U+0141 (decimal 321)
|
||||
defining Unicode char U+0142 (decimal 322)
|
||||
defining Unicode char U+0143 (decimal 323)
|
||||
defining Unicode char U+0144 (decimal 324)
|
||||
defining Unicode char U+0147 (decimal 327)
|
||||
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)
|
||||
defining Unicode char U+201C (decimal 8220)
|
||||
defining Unicode char U+201D (decimal 8221)
|
||||
defining Unicode char U+201E (decimal 8222)
|
||||
defining Unicode char U+2030 (decimal 8240)
|
||||
defining Unicode char U+2031 (decimal 8241)
|
||||
defining Unicode char U+2039 (decimal 8249)
|
||||
defining Unicode char U+203A (decimal 8250)
|
||||
defining Unicode char U+2423 (decimal 9251)
|
||||
)
|
||||
Now handling font encoding OT1 ...
|
||||
... processing UTF-8 mapping file for font encodingOT1
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu
|
||||
File: ot1enc.dfu 2006/03/30 v1.1i UTF-8 support for inputenc
|
||||
defining Unicode char U+00A1 (decimal 161)
|
||||
defining Unicode char U+00A3 (decimal 163)
|
||||
defining Unicode char U+00B8 (decimal 184)
|
||||
defining Unicode char U+00BF (decimal 191)
|
||||
defining Unicode char U+00C5 (decimal 197)
|
||||
defining Unicode char U+00C6 (decimal 198)
|
||||
defining Unicode char U+00D8 (decimal 216)
|
||||
defining Unicode char U+00DF (decimal 223)
|
||||
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)
|
||||
defining Unicode char U+201C (decimal 8220)
|
||||
defining Unicode char U+201D (decimal 8221)
|
||||
)
|
||||
Now handling font encoding OMS ...
|
||||
... processing UTF-8 mapping file for font encodingOMS
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu
|
||||
File: omsenc.dfu 2006/03/30 v1.1i UTF-8 support for inputenc
|
||||
defining Unicode char U+00A7 (decimal 167)
|
||||
defining Unicode char U+00B6 (decimal 182)
|
||||
defining Unicode char U+00B7 (decimal 183)
|
||||
defining Unicode char U+2020 (decimal 8224)
|
||||
defining Unicode char U+2021 (decimal 8225)
|
||||
defining Unicode char U+2022 (decimal 8226)
|
||||
)
|
||||
Now handling font encoding OMX ...
|
||||
... no UTF-8 mapping file for font encoding OMX
|
||||
Now handling font encoding U ...
|
||||
... no UTF-8 mapping file for font encoding U
|
||||
defining Unicode char U+00A9 (decimal 169)
|
||||
defining Unicode char U+00AA (decimal 170)
|
||||
defining Unicode char U+00AE (decimal 174)
|
||||
defining Unicode char U+00BA (decimal 186)
|
||||
defining Unicode char U+02C6 (decimal 710)
|
||||
defining Unicode char U+02DC (decimal 732)
|
||||
defining Unicode char U+200C (decimal 8204)
|
||||
defining Unicode char U+2026 (decimal 8230)
|
||||
defining Unicode char U+2122 (decimal 8482)
|
||||
defining Unicode char U+2423 (decimal 9251)
|
||||
))
|
||||
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
|
||||
Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def
|
||||
File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
|
||||
LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
|
||||
))
|
||||
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
|
||||
Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty
|
||||
Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
|
||||
\KV@toks@=\toks16
|
||||
)
|
||||
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
|
||||
Package: graphics 2006/02/20 v1.0o Standard LaTeX Graphics (DPC,SPQR)
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty
|
||||
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
|
||||
)
|
||||
(/etc/texmf/tex/latex/config/graphics.cfg
|
||||
File: graphics.cfg 2007/01/18 v1.5 graphics configuration of teTeX/TeXLive
|
||||
)
|
||||
Package graphics Info: Driver file: pdftex.def on input line 90.
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def
|
||||
File: pdftex.def 2007/01/08 v0.04d Graphics/color for pdfTeX
|
||||
\Gread@gobject=\count87
|
||||
))
|
||||
\Gin@req@height=\dimen103
|
||||
\Gin@req@width=\dimen104
|
||||
)
|
||||
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty
|
||||
Package: longtable 2004/02/01 v4.11 Multi-page Table package (DPC)
|
||||
\LTleft=\skip43
|
||||
\LTright=\skip44
|
||||
\LTpre=\skip45
|
||||
\LTpost=\skip46
|
||||
\LTchunksize=\count88
|
||||
\LTcapwidth=\dimen105
|
||||
\LT@head=\box26
|
||||
\LT@firsthead=\box27
|
||||
\LT@foot=\box28
|
||||
\LT@lastfoot=\box29
|
||||
\LT@cols=\count89
|
||||
\LT@rows=\count90
|
||||
\c@LT@tables=\count91
|
||||
\c@LT@chunks=\count92
|
||||
\LT@p@ftn=\toks17
|
||||
)
|
||||
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
|
||||
Package: hyperref 2007/02/07 v6.75r Hypertext links for LaTeX
|
||||
\@linkdim=\dimen106
|
||||
\Hy@linkcounter=\count93
|
||||
\Hy@pagecounter=\count94
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def
|
||||
File: pd1enc.def 2007/02/07 v6.75r Hyperref: PDFDocEncoding definition (HO)
|
||||
Now handling font encoding PD1 ...
|
||||
... no UTF-8 mapping file for font encoding PD1
|
||||
)
|
||||
(/etc/texmf/tex/latex/config/hyperref.cfg
|
||||
File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
|
||||
)
|
||||
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
|
||||
Package: kvoptions 2006/08/22 v2.4 Connects package keyval with LaTeX options (
|
||||
HO)
|
||||
)
|
||||
Package hyperref Info: Hyper figures OFF on input line 2288.
|
||||
Package hyperref Info: Link nesting OFF on input line 2293.
|
||||
Package hyperref Info: Hyper index ON on input line 2296.
|
||||
Package hyperref Info: Plain pages OFF on input line 2303.
|
||||
Package hyperref Info: Backreferencing OFF on input line 2308.
|
||||
|
||||
Implicit mode ON; LaTeX internals redefined
|
||||
Package hyperref Info: Bookmarks ON on input line 2444.
|
||||
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty
|
||||
\Urlmuskip=\muskip10
|
||||
Package: url 2005/06/27 ver 3.2 Verb mode for urls, etc.
|
||||
)
|
||||
LaTeX Info: Redefining \url on input line 2599.
|
||||
\Fld@menulength=\count95
|
||||
\Field@Width=\dimen107
|
||||
\Fld@charsize=\dimen108
|
||||
\Choice@toks=\toks18
|
||||
\Field@toks=\toks19
|
||||
Package hyperref Info: Hyper figures OFF on input line 3102.
|
||||
Package hyperref Info: Link nesting OFF on input line 3107.
|
||||
Package hyperref Info: Hyper index ON on input line 3110.
|
||||
Package hyperref Info: backreferencing OFF on input line 3117.
|
||||
Package hyperref Info: Link coloring OFF on input line 3122.
|
||||
\Hy@abspage=\count96
|
||||
\c@Item=\count97
|
||||
\c@Hfootnote=\count98
|
||||
)
|
||||
*hyperref using default driver hpdftex*
|
||||
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def
|
||||
File: hpdftex.def 2007/02/07 v6.75r Hyperref driver for pdfTeX
|
||||
\Fld@listcount=\count99
|
||||
)
|
||||
(/usr/share/texmf/tex/latex/R/Sweave.sty
|
||||
Package: Sweave
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty
|
||||
Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
|
||||
)
|
||||
(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
|
||||
Package: fancyvrb 1998/07/17
|
||||
|
||||
Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
|
||||
\FV@CodeLineNo=\count100
|
||||
\FV@InFile=\read1
|
||||
\FV@TabBox=\box30
|
||||
\c@FancyVerbLine=\count101
|
||||
\FV@StepNumber=\count102
|
||||
\FV@OutFile=\write3
|
||||
|
||||
No file fancyvrb.cfg.
|
||||
) (/usr/share/texmf/tex/latex/R/upquote.sty
|
||||
Package: upquote 2003/08/11 v1.1 Covington's upright-quote modification to verb
|
||||
atim and verb
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
|
||||
Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
|
||||
Package textcomp Info: Sub-encoding information:
|
||||
(textcomp) 5 = only ISO-Adobe without \textcurrency
|
||||
(textcomp) 4 = 5 + \texteuro
|
||||
(textcomp) 3 = 4 + \textohm
|
||||
(textcomp) 2 = 3 + \textestimated + \textcurrency
|
||||
(textcomp) 1 = TS1 - \textcircled - \t
|
||||
(textcomp) 0 = TS1 (full)
|
||||
(textcomp) Font families with sub-encoding setting implement
|
||||
(textcomp) only a restricted character set as indicated.
|
||||
(textcomp) Family '?' is the default used for unknown fonts.
|
||||
(textcomp) See the documentation for details.
|
||||
Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
|
||||
|
||||
(/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 ...
|
||||
... processing UTF-8 mapping file for font encoding TS1
|
||||
|
||||
(/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)
|
||||
))
|
||||
LaTeX Info: Redefining \oldstylenums on input line 266.
|
||||
Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
|
||||
Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
|
||||
Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
|
||||
Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
|
||||
Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
|
||||
Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
|
||||
Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
|
||||
Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
|
||||
Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
|
||||
Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
|
||||
Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
|
||||
Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
|
||||
Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
|
||||
Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
|
||||
Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
|
||||
Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
|
||||
Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
|
||||
Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
|
||||
Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
|
||||
Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
|
||||
Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
|
||||
Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
|
||||
Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
|
||||
Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
|
||||
|
||||
Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
|
||||
Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
|
||||
Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
|
||||
Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
|
||||
Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
|
||||
Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
|
||||
Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 311.
|
||||
Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 312.
|
||||
Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 313.
|
||||
Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 314.
|
||||
Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 315.
|
||||
Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 316.
|
||||
Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 317.
|
||||
Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 318.
|
||||
Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 319.
|
||||
Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 320.
|
||||
Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 321.
|
||||
Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 322.
|
||||
Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 323.
|
||||
Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 324.
|
||||
Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 325.
|
||||
Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 326.
|
||||
))
|
||||
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
|
||||
Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def
|
||||
File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
|
||||
LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
|
||||
))
|
||||
(/usr/share/texmf-texlive/tex/latex/ae/ae.sty
|
||||
Package: ae 2001/02/12 1.3 Almost European Computer Modern
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
|
||||
Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def
|
||||
File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
|
||||
LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
|
||||
)
|
||||
LaTeX Font Info: Try loading font information for T1+aer on input line 100.
|
||||
|
||||
(/usr/share/texmf-texlive/tex/latex/ae/t1aer.fd
|
||||
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.
|
||||
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 14.
|
||||
LaTeX Font Info: ... okay on input line 14.
|
||||
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 14.
|
||||
LaTeX Font Info: ... okay on input line 14.
|
||||
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 14.
|
||||
LaTeX Font Info: ... okay on input line 14.
|
||||
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 14.
|
||||
LaTeX Font Info: ... okay on input line 14.
|
||||
LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 14.
|
||||
LaTeX Font Info: ... okay on input line 14.
|
||||
LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 14.
|
||||
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.
|
||||
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
|
||||
</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)
|
||||
|
||||
|
|
@ -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]]
|
||||
|
|
@ -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}
|
||||
Binary file not shown.
|
|
@ -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}
|
||||
|
|
@ -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}
|
||||
|
|
@ -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
|
||||
|
|
@ -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 — 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 — 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;"><-</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"><dan@Tichodroma></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>
|
||||
63
rorg.org
63
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
|
||||
|
|
|
|||
Loading…
Reference in New Issue