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https://git.lyx.org/repos/lyx.git
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Add support for R package knitr (a Sweave alternative)
This fixes #7887. git-svn-id: svn://svn.lyx.org/lyx/lyx-devel/trunk@40674 a592a061-630c-0410-9148-cb99ea01b6c8
This commit is contained in:
Jean-Marc Lasgouttes
parent
99c8eecaf9
commit
7335b3193b
@ -252,8 +252,9 @@ dist_examples_DATA = \
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examples/iecc05.fen \
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examples/iecc07.fen \
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examples/iecc12.fen \
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examples/instant_preview.lyx \
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examples/landslide.lyx \
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examples/instant_preview.lyx \
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examples/knitr.lyx \
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examples/lilypond.lyx \
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examples/linguistics.lyx \
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examples/listerrors.lyx \
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@ -1468,6 +1469,7 @@ dist_layouts_DATA =\
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layouts/svmult.layout \
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layouts/svprobth.layout \
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layouts/sweave.module \
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layouts/knitr.module \
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layouts/tabs-within-sections.module \
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layouts/tarticle.layout \
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layouts/tbook.layout \
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@ -1502,6 +1504,7 @@ dist_layouts_DATA =\
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scriptsdir = $(pkgdatadir)/scripts
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dist_scripts_DATA = \
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scripts/bash_completion \
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scripts/lyxknitr.R \
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scripts/lyxstangle.R \
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scripts/lyxsweave.R
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# We use DATA now instead of PYTHON because automake 1.11.2 complains.
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@ -548,6 +548,7 @@ def checkFormatEntries(dtl_tools):
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\Format literate nw NoWeb N "" "%%" "document,menu=export"
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\Format sweave Rnw "Sweave" S "" "%%" "document,menu=export"
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\Format r R "R/S code" "" "" "%%" "document,menu=export"
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\Format knitr Rnw "Rnw (knitr)" "" "" "%%" "document,menu=export"
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\Format lilypond ly "LilyPond music" "" "" "%%" "vector"
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\Format lilypond-book lytex "LilyPond book (LaTeX)" "" "" "%%" "document,menu=export"
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\Format latex tex "LaTeX (plain)" L "" "%%" "document,menu=export"
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@ -669,10 +670,19 @@ def checkConverterEntries():
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\converter sweave pdflatex "%%" ""
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\converter sweave xetex "%%" ""
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\converter sweave luatex "%%" ""'''])
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#
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checkProg('a knitr -> LaTeX converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r'],
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rc_entry = [r'''\converter knitr latex "%%" ""
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\converter knitr pdflatex "%%" ""
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\converter knitr xetex "%%" ""
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\converter knitr luatex "%%" ""'''])
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#
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checkProg('a Sweave -> R/S code converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxstangle.R $$i $$e $$r'],
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rc_entry = [ r'\converter sweave r "%%" ""' ])
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#
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checkProg('a knitr -> R/S code converter', ['Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r tangle'],
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rc_entry = [ r'\converter knitr r "%%" ""' ])
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#
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checkProg('an HTML -> LaTeX converter', ['html2latex $$i', 'gnuhtml2latex $$i',
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'htmltolatex -input $$i -output $$o', 'htmltolatex.jar -input $$i -output $$o'],
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rc_entry = [ r'\converter html latex "%%" ""' ])
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246
lib/examples/knitr.lyx
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246
lib/examples/knitr.lyx
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@ -0,0 +1,246 @@
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#LyX 2.1 created this file. For more info see http://www.lyx.org/
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\lyxformat 424
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\begin_document
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\begin_header
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\textclass article
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\use_default_options true
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\begin_modules
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knitr
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\end_modules
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\maintain_unincluded_children false
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\language english
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\language_package default
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\inputencoding auto
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\fontencoding global
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\font_roman palatino
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\font_sans lmss
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\font_typewriter lmtt
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\font_default_family default
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\use_non_tex_fonts false
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\font_sc false
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\font_osf false
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\font_sf_scale 100
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\font_tt_scale 100
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\graphics default
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\default_output_format default
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\output_sync 0
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\bibtex_command default
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\index_command default
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\paperfontsize default
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\spacing single
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\use_hyperref false
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\papersize default
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\use_geometry true
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\use_package amsmath 1
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\use_package esint 1
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\use_package mathdots 1
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\use_package mathtools 0
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\use_package mhchem 1
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\use_package undertilde 1
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\cite_engine basic
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\cite_engine_type numerical
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\biblio_style plain
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\use_bibtopic false
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\use_indices false
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\paperorientation portrait
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\suppress_date false
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\justification true
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\use_refstyle 1
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\index Index
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\shortcut idx
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\color #008000
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\end_index
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\leftmargin 2.5cm
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\topmargin 2.5cm
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\rightmargin 2.5cm
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\bottommargin 2.5cm
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\secnumdepth 3
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\tocdepth 3
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\paragraph_separation indent
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\paragraph_indentation default
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\quotes_language english
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\papercolumns 1
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\papersides 1
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\paperpagestyle default
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\tracking_changes false
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\output_changes false
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\html_math_output 0
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\html_css_as_file 0
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\html_be_strict false
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\end_header
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\begin_body
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\begin_layout Title
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Using knitr with LyX
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\end_layout
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\begin_layout Author
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Yihui Xie
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\begin_inset Foot
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status collapsed
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\begin_layout Plain Layout
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Department of Statistics, Iowa State University.
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Email:
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\begin_inset CommandInset href
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LatexCommand href
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name "xie@yihui.name"
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target "xie@yihui.name"
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type "mailto:"
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\end_inset
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Standard
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The R (
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\begin_inset Flex URL
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status collapsed
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\begin_layout Plain Layout
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http://www.r-project.org
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\end_layout
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\end_inset
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) package
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\series bold
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knitr
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\series default
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is an alternative tool to Sweave based on a different design with more
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features.
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LyX has native support to Sweave since version 2.0.0, and the support to
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\series bold
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knitr
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\series default
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was also added since 2.0.3.
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The usage is basically the same as the
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\family sans
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Sweave
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\family default
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module
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\begin_inset Foot
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status open
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\begin_layout Plain Layout
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read the LyX/Sweave manual from
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\family sans
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Help\SpecialChar \menuseparator
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Specific Manuals
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\end_layout
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\end_inset
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:
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\end_layout
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\begin_layout Enumerate
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Open a new LyX document;
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\end_layout
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\begin_layout Enumerate
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Go to
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\family sans
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Document\SpecialChar \menuseparator
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Settings\SpecialChar \menuseparator
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Modules
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\family default
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and insert the module named
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\family sans
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Rnw (knitr)
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\family default
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;
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\end_layout
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\begin_layout Enumerate
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Then insert R code in the document with either
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\family sans
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Insert\SpecialChar \menuseparator
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TeX Code
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\family default
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or the
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\family sans
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Chunk
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\family default
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environment;
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\end_layout
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\begin_layout Standard
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The package website
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\begin_inset Flex URL
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status collapsed
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\begin_layout Plain Layout
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http://yihui.github.com/knitr
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\end_layout
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\end_inset
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has full documentation and demos of
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\series bold
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knitr
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\series default
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; many of the examples have links to the LyX source documents.
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\end_layout
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\begin_layout Standard
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Note the
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\series bold
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knitr
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\series default
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package requires R >= 2.14.1, so you need to update R if you are using an
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old version of R.
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Here we show one chunk as a simple example:
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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status open
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\begin_layout Plain Layout
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<<show-off>>=
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\end_layout
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\begin_layout Plain Layout
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rnorm(5)
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\end_layout
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\begin_layout Plain Layout
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df=data.frame(y=rnorm(100), x=1:100)
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\end_layout
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\begin_layout Plain Layout
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summary(lm(y~x, data=df))
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\end_layout
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\begin_layout Plain Layout
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@
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Standard
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Please contact the package author in case of any problems.
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\end_layout
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\end_body
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\end_document
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82
lib/layouts/knitr.module
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82
lib/layouts/knitr.module
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@ -0,0 +1,82 @@
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#\DeclareLyXModule[knitr->latex]{Rnw (knitr)}
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#DescriptionBegin
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#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.
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#For more info see http://yihui.github.com/knitr
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#DescriptionEnd
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#Category: literate
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#Excludes: lilypond | sweave
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Format 35
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OutputType literate
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OutputFormat knitr
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Style Chunk
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Category Sweave
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LatexType Paragraph
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LatexName dummy
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Margin static
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Align Left
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AlignPossible Block, Left, Right, Center
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TopSep 0.7
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BottomSep 0.7
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NewLine 0
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FreeSpacing 1
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PassThru 1
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ParbreakIsNewline 1
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Spellcheck 0
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## What is LabelType used for?
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LabelType Static
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TextFont
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Color latex
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Family Typewriter
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EndFont
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End
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Style Scrap
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ObsoletedBy Chunk
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End
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InsetLayout "Flex:Sweave Options"
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LabelString "Sweave opts"
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LatexType Command
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LaTexName SweaveOpts
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LyXType Custom
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Decoration Classic
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Font
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Color latex
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Family typewriter
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EndFont
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LabelFont
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Color latex
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Size Small
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EndFont
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MultiPar false
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PassThru 1
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ParbreakIsNewline 1
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Spellcheck 0
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FreeSpacing true
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ForceLTR true
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End
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InsetLayout "Flex:S/R expression"
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LabelString "S/R expr"
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LatexType Command
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LaTexName Sexpr
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LyXType Custom
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Decoration Conglomerate
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Font
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Color latex
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Family typewriter
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EndFont
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LabelFont
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Color latex
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Size Small
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EndFont
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MultiPar false
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PassThru 1
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ParbreakIsNewline 1
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Spellcheck 0
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FreeSpacing true
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ForceLTR true
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End
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48
lib/scripts/lyxknitr.R
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48
lib/scripts/lyxknitr.R
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@ -0,0 +1,48 @@
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## This program is free software; you can redistribute it and/or
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## modify it under the terms of the GNU General Public License as
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## published by the Free Software Foundation; either version 2 of the
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## License, or (at your option) any later version.
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##
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## This program is distributed in the hope that it will be useful, but
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## WITHOUT ANY WARRANTY; without even the implied warranty of
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## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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## General Public License for more details.
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## author Yihui Xie
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## knitr is an alternative package to Sweave, and has more features
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## and flexibility; see https://yihui.github.com/knitr
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## Rscript $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r
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## $$p the path of the output (temp dir)
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## $$i the file name of the input Rnw
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## $$o the tex output
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## $$r path to the original input file (the lyx document)
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## $$e encoding (e.g. 'UTF-8')
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library(knitr)
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.cmdargs = commandArgs(TRUE)
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.orig.enc = getOption("encoding")
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options(encoding = .cmdargs[3])
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## the working directory is the same with the original .lyx file; you
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## can put your data files there and functions like read.table() can
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## work correctly without specifying the full path
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setwd(.cmdargs[4])
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## copy the Rnw file to the current working directory if it does not exist
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.tmp.file = tempfile(); .rnw.file = basename(.cmdargs[1])
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.rnw.exists = file.exists(.rnw.file)
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if (.rnw.exists) file.rename(.rnw.file, .tmp.file)
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file.copy(.cmdargs[1], '.')
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## run knit() to get .tex or .R
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knit(.rnw.file, tangle = 'tangle' %in% .cmdargs)
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setwd(.cmdargs[4])
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## remove the copied .Rnw if it did not exist, otherwise move the original one back
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if (.rnw.exists) file.rename(.tmp.file, .rnw.file) else unlink(.rnw.file)
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file.rename(basename(.cmdargs[2]), .cmdargs[2]) # move .tex to the temp dir
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rm(.tmp.file, .rnw.file, .rnw.exists) # clean up these variables
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