Author: lasgouttes
Date: Sat Jan 28 11:50:12 2012
New Revision: 40684
URL: http://www.lyx.org/trac/changeset/40684
Log:
backport support for knitr
Added:
lyx-devel/branches/BRANCH_2_0_X/lib/examples/knitr.lyx (props changed)
- copied unchanged from r40674, lyx-devel/trunk/lib/examples/knitr.lyx
lyx-devel/branches/BRANCH_2_0_X/lib/layouts/knitr.module (props changed)
- copied unchanged from r40674, lyx-devel/trunk/lib/layouts/knitr.module
lyx-devel/branches/BRANCH_2_0_X/lib/scripts/lyxknitr.R (props changed)
- copied unchanged from r40674, lyx-devel/trunk/lib/scripts/lyxknitr.R
Modified:
lyx-devel/branches/BRANCH_2_0_X/lib/Makefile.am
lyx-devel/branches/BRANCH_2_0_X/lib/configure.py
lyx-devel/branches/BRANCH_2_0_X/status.20x
Modified: lyx-devel/branches/BRANCH_2_0_X/lib/Makefile.am
==============================================================================
--- lyx-devel/branches/BRANCH_2_0_X/lib/Makefile.am Fri Jan 27 22:44:30
2012 (r40683)
+++ lyx-devel/branches/BRANCH_2_0_X/lib/Makefile.am Sat Jan 28 11:50:12
2012 (r40684)
@@ -258,6 +258,7 @@
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 @@
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 @@
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.
Modified: lyx-devel/branches/BRANCH_2_0_X/lib/configure.py
==============================================================================
--- lyx-devel/branches/BRANCH_2_0_X/lib/configure.py Fri Jan 27 22:44:30
2012 (r40683)
+++ lyx-devel/branches/BRANCH_2_0_X/lib/configure.py Sat Jan 28 11:50:12
2012 (r40684)
@@ -581,6 +581,7 @@
\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"
@@ -708,9 +709,18 @@
\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 "%%" ""' ])
Copied: lyx-devel/branches/BRANCH_2_0_X/lib/examples/knitr.lyx (from r40674,
lyx-devel/trunk/lib/examples/knitr.lyx)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ lyx-devel/branches/BRANCH_2_0_X/lib/examples/knitr.lyx Sat Jan 28
11:50:12 2012 (r40684, copy of r40674,
lyx-devel/trunk/lib/examples/knitr.lyx)
@@ -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 "[email protected]"
+target "[email protected]"
+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
Copied: lyx-devel/branches/BRANCH_2_0_X/lib/layouts/knitr.module (from r40674,
lyx-devel/trunk/lib/layouts/knitr.module)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ lyx-devel/branches/BRANCH_2_0_X/lib/layouts/knitr.module Sat Jan 28
11:50:12 2012 (r40684, copy of r40674,
lyx-devel/trunk/lib/layouts/knitr.module)
@@ -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
+
Copied: lyx-devel/branches/BRANCH_2_0_X/lib/scripts/lyxknitr.R (from r40674,
lyx-devel/trunk/lib/scripts/lyxknitr.R)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ lyx-devel/branches/BRANCH_2_0_X/lib/scripts/lyxknitr.R Sat Jan 28
11:50:12 2012 (r40684, copy of r40674,
lyx-devel/trunk/lib/scripts/lyxknitr.R)
@@ -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
+
Modified: lyx-devel/branches/BRANCH_2_0_X/status.20x
==============================================================================
--- lyx-devel/branches/BRANCH_2_0_X/status.20x Fri Jan 27 22:44:30 2012
(r40683)
+++ lyx-devel/branches/BRANCH_2_0_X/status.20x Sat Jan 28 11:50:12 2012
(r40684)
@@ -24,7 +24,11 @@
* 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.
