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backport support for knitr

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git-svn-id: svn://svn.lyx.org/lyx/lyx-devel/branches/BRANCH_2_0_X@40684 a592a061-630c-0410-9148-cb99ea01b6c8
This commit is contained in:
Jean-Marc Lasgouttes 2012-01-28 10:50:12 +00:00
parent 8016aebdf1
commit 881d6bc268
6 changed files with 394 additions and 1 deletions
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3
lib/Makefile.am
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@ -258,6 +258,7 @@ dist_examples_DATA = \
examples/iecc07.fen \
examples/iecc12.fen \
examples/instant_preview.lyx \
examples/knitr.lyx \
examples/landslide.lyx \
examples/lilypond.lyx \
examples/linguistics.lyx \
@ -1397,6 +1398,7 @@ dist_layouts_DATA =\
layouts/jsbook.layout \
layouts/jss.layout \
layouts/kluwer.layout \
layouts/knitr.module \
layouts/latex8.layout \
layouts/letter.layout \
layouts/lettre.layout \
@ -1498,6 +1500,7 @@ dist_layouts_DATA =\
scriptsdir = $(pkgdatadir)/scripts
dist_scripts_DATA = \
scripts/bash_completion \
scripts/lyxknitr.R \
scripts/lyxstangle.R \
scripts/lyxsweave.R
# We use DATA now instead of PYTHON because automake 1.11.2 complains.

10
lib/configure.py
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@ -581,6 +581,7 @@ def checkFormatEntries(dtl_tools):
\Format literate nw NoWeb N "" "%%" "document,menu=export"
\Format sweave Rnw "Sweave" S "" "%%" "document,menu=export"
\Format r R "R/S code" "" "" "%%" "document,menu=export"
\Format knitr Rnw "Rnw (knitr)" "" "" "%%" "document,menu=export"
\Format lilypond ly "LilyPond music" "" "" "%%" "vector"
\Format lilypond-book lytex "LilyPond book (LaTeX)" "" "" "%%" "document,menu=export"
\Format latex tex "LaTeX (plain)" L "" "%%" "document,menu=export"
@ -707,10 +708,19 @@ def checkConverterEntries():
\converter sweave pdflatex "%%" ""
\converter sweave xetex "%%" ""
\converter sweave luatex "%%" ""'''])
#
checkProg('a knitr -> LaTeX converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r'],
rc_entry = [r'''\converter knitr latex "%%" ""
\converter knitr pdflatex "%%" ""
\converter knitr xetex "%%" ""
\converter knitr luatex "%%" ""'''])
#
checkProg('a Sweave -> R/S code converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxstangle.R $$i $$e $$r'],
rc_entry = [ r'\converter sweave r "%%" ""' ])
#
checkProg('a knitr -> R/S code converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r tangle'],
rc_entry = [ r'\converter knitr r "%%" ""' ])
#
checkProg('an HTML -> LaTeX converter', ['html2latex $$i', 'gnuhtml2latex $$i',
'htmltolatex -input $$i -output $$o', 'htmltolatex.jar -input $$i -output $$o'],
rc_entry = [ r'\converter html latex "%%" ""' ])

246
lib/examples/knitr.lyx Normal file
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@ -0,0 +1,246 @@
#LyX 2.1 created this file. For more info see http://www.lyx.org/
\lyxformat 424
\begin_document
\begin_header
\textclass article
\use_default_options true
\begin_modules
knitr
\end_modules
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding auto
\fontencoding global
\font_roman palatino
\font_sans lmss
\font_typewriter lmtt
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize default
\use_geometry true
\use_package amsmath 1
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 0
\use_package mhchem 1
\use_package undertilde 1
\cite_engine basic
\cite_engine_type numerical
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 2.5cm
\topmargin 2.5cm
\rightmargin 2.5cm
\bottommargin 2.5cm
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header
\begin_body
\begin_layout Title
Using knitr with LyX
\end_layout
\begin_layout Author
Yihui Xie
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
Department of Statistics, Iowa State University.
Email:
\begin_inset CommandInset href
LatexCommand href
name "xie@yihui.name"
target "xie@yihui.name"
type "mailto:"
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The R (
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://www.r-project.org
\end_layout
\end_inset
) package
\series bold
knitr
\series default
is an alternative tool to Sweave based on a different design with more
features.
LyX has native support to Sweave since version 2.0.0, and the support to
\series bold
knitr
\series default
was also added since 2.0.3.
The usage is basically the same as the
\family sans
Sweave
\family default
module
\begin_inset Foot
status open
\begin_layout Plain Layout
read the LyX/Sweave manual from
\family sans
Help\SpecialChar \menuseparator
Specific Manuals
\end_layout
\end_inset
:
\end_layout
\begin_layout Enumerate
Open a new LyX document;
\end_layout
\begin_layout Enumerate
Go to
\family sans
Document\SpecialChar \menuseparator
Settings\SpecialChar \menuseparator
Modules
\family default
and insert the module named
\family sans
Rnw (knitr)
\family default
;
\end_layout
\begin_layout Enumerate
Then insert R code in the document with either
\family sans
Insert\SpecialChar \menuseparator
TeX Code
\family default
or the
\family sans
Chunk
\family default
environment;
\end_layout
\begin_layout Standard
The package website
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://yihui.github.com/knitr
\end_layout
\end_inset
has full documentation and demos of
\series bold
knitr
\series default
; many of the examples have links to the LyX source documents.
\end_layout
\begin_layout Standard
Note the
\series bold
knitr
\series default
package requires R >= 2.14.1, so you need to update R if you are using an
old version of R.
Here we show one chunk as a simple example:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<show-off>>=
\end_layout
\begin_layout Plain Layout
rnorm(5)
\end_layout
\begin_layout Plain Layout
df=data.frame(y=rnorm(100), x=1:100)
\end_layout
\begin_layout Plain Layout
summary(lm(y~x, data=df))
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Please contact the package author in case of any problems.
\end_layout
\end_body
\end_document

82
lib/layouts/knitr.module Normal file
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@ -0,0 +1,82 @@
#\DeclareLyXModule[knitr->latex]{Rnw (knitr)}
#DescriptionBegin
#Uses the knitr package in R for dynamic report generation. This R package has to be installed for this module to work: install.packages('knitr'). Note it depends on R >= 2.14.1.
#For more info see http://yihui.github.com/knitr
#DescriptionEnd
#Category: literate
#Excludes: lilypond | sweave
Format 35
OutputType literate
OutputFormat knitr
Style Chunk
Category Sweave
LatexType Paragraph
LatexName dummy
Margin static
Align Left
AlignPossible Block, Left, Right, Center
TopSep 0.7
BottomSep 0.7
NewLine 0
FreeSpacing 1
PassThru 1
ParbreakIsNewline 1
Spellcheck 0
## What is LabelType used for?
LabelType Static
TextFont
Color latex
Family Typewriter
EndFont
End
Style Scrap
ObsoletedBy Chunk
End
InsetLayout "Flex:Sweave Options"
LabelString "Sweave opts"
LatexType Command
LaTexName SweaveOpts
LyXType Custom
Decoration Classic
Font
Color latex
Family typewriter
EndFont
LabelFont
Color latex
Size Small
EndFont
MultiPar false
PassThru 1
ParbreakIsNewline 1
Spellcheck 0
FreeSpacing true
ForceLTR true
End
InsetLayout "Flex:S/R expression"
LabelString "S/R expr"
LatexType Command
LaTexName Sexpr
LyXType Custom
Decoration Conglomerate
Font
Color latex
Family typewriter
EndFont
LabelFont
Color latex
Size Small
EndFont
MultiPar false
PassThru 1
ParbreakIsNewline 1
Spellcheck 0
FreeSpacing true
ForceLTR true
End

48
lib/scripts/lyxknitr.R Normal file
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@ -0,0 +1,48 @@
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## This program is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
## author Yihui Xie
## knitr is an alternative package to Sweave, and has more features
## and flexibility; see https://yihui.github.com/knitr
## Rscript $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r
## $$p the path of the output (temp dir)
## $$i the file name of the input Rnw
## $$o the tex output
## $$r path to the original input file (the lyx document)
## $$e encoding (e.g. 'UTF-8')
library(knitr)
.cmdargs = commandArgs(TRUE)
.orig.enc = getOption("encoding")
options(encoding = .cmdargs[3])
## the working directory is the same with the original .lyx file; you
## can put your data files there and functions like read.table() can
## work correctly without specifying the full path
setwd(.cmdargs[4])
## copy the Rnw file to the current working directory if it does not exist
.tmp.file = tempfile(); .rnw.file = basename(.cmdargs[1])
.rnw.exists = file.exists(.rnw.file)
if (.rnw.exists) file.rename(.rnw.file, .tmp.file)
file.copy(.cmdargs[1], '.')
## run knit() to get .tex or .R
knit(.rnw.file, tangle = 'tangle' %in% .cmdargs)
setwd(.cmdargs[4])
## remove the copied .Rnw if it did not exist, otherwise move the original one back
if (.rnw.exists) file.rename(.tmp.file, .rnw.file) else unlink(.rnw.file)
file.rename(basename(.cmdargs[2]), .cmdargs[2]) # move .tex to the temp dir
rm(.tmp.file, .rnw.file, .rnw.exists) # clean up these variables

6
status.20x
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@ -24,7 +24,11 @@ What's new
* DOCUMENT INPUT/OUTPUT
- Fix Sweave support for document encoding with R >= 2.13.1 (bug 7876).
- Fix Sweave support for document encoding with R >= 2.13.1 (bug
7876).
- Add support for `knitr', an alternative for Sweave on R >= 2.14.1
(bug 7887).
- Improved output of Comment notes for XHTML. These are now div's that are
hidden by the default CSS.