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sweave.lyx: completely revised example file by Yihui Xie
git-svn-id: svn://svn.lyx.org/lyx/lyx-devel/trunk@40744 a592a061-630c-0410-9148-cb99ea01b6c8
This commit is contained in:
Uwe Stöhr
parent
dfee6bc359
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e0436370b6
@ -260,7 +260,7 @@ PATH
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\family sans
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PATH
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\family default
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under Windows, you may use the R script
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under Windows, you may either use the R script
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\family sans
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add-R-path-win.R
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\family default
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@ -275,15 +275,64 @@ https://github.com/yihui/lyx
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\end_inset
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to change it automatically (we recommend you to learn
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to change it automatically (not recommended; you should learn
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\family sans
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PATH
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\family default
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anyway).
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anyway), or go to
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\family sans
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Tools\SpecialChar \menuseparator
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Preferences\SpecialChar \menuseparator
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Paths\SpecialChar \menuseparator
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PATH prefix
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\family default
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to add the bin path of R (recommended), which is often like
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\family sans
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C:
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\backslash
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Program Files
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\backslash
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R
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\backslash
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R-x.x.x
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\backslash
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bin
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\family default
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and you can find it in R:
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\end_layout
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\begin_layout Standard
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If
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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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<<where-is-R-bin,eval=FALSE>>=
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\end_layout
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\begin_layout Plain Layout
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R.home('bin')
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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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After you have done these changes, you need to reconfigure LyX by
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\family sans
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Tools\SpecialChar \menuseparator
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Reconfigure
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\family default
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.
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If
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\family typewriter
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Rscript
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\family default
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@ -739,14 +788,12 @@ name "tab:xtable-demo"
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\end_layout
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\begin_layout Plain Layout
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\align center
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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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\backslash
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begin{center}
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\end_layout
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\begin_layout Plain Layout
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@ -775,13 +822,6 @@ print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
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@
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\end_layout
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\begin_layout Plain Layout
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\backslash
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end{center}
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\end_layout
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\end_inset
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@ -854,18 +894,12 @@ sideways false
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status open
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\begin_layout Plain Layout
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\align center
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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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\backslash
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begin{center}
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\end_layout
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\begin_layout Plain Layout
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<<iris-pairs,fig=TRUE,width=4.5,height=4.5>>=
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\end_layout
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@ -879,13 +913,6 @@ pairs(iris, col = iris$Species)
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@
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\end_layout
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\begin_layout Plain Layout
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\backslash
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end{center}
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\end_layout
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\end_inset
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@ -926,18 +953,12 @@ sideways false
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status open
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\begin_layout Plain Layout
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\align center
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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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\backslash
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begin{center}
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\end_layout
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\begin_layout Plain Layout
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<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F>>=
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\end_layout
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@ -956,13 +977,6 @@ boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
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@
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\end_layout
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\begin_layout Plain Layout
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\backslash
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end{center}
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\end_layout
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\end_inset
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@ -1347,6 +1361,79 @@ label=
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immediately.
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\end_layout
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\begin_layout Standard
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Another known issue is the Sweave code chunk may fail when we change the
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alignment of the chunk paragraph in LyX (using
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\family sans
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Paragraph settings
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\family default
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), because LyX may add a macro like
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\family typewriter
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\backslash
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centering{}
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\family default
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before the code chunk without adding a new line, which will lead to a code
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chunk like this:
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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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\backslash
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begin{verbatim}
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\end_layout
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\begin_layout Plain Layout
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\backslash
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centering{}<<xtable-demo,results=tex,echo=FALSE>>=
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\end_layout
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\begin_layout Plain Layout
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\backslash
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end{verbatim}
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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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This is not a legitimate Sweave code chunk, since
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\family typewriter
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<<>>=
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\family default
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must start in a new line with nothing before it.
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Therefore we recommend you to double check the real source code via
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\family sans
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View\SpecialChar \menuseparator
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View Source
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\family default
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when changing the alignment of a chunk paragraph, and make sure
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\family typewriter
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<<>>=
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\family default
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appears in a new line.
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This explains why we manually added an empty line in the code chunk in
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Table
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\begin_inset CommandInset ref
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LatexCommand ref
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reference "tab:xtable-demo"
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\end_inset
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.
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\end_layout
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\begin_layout Section
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Resources
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\end_layout
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@ -1516,29 +1603,16 @@ lyxsweave.R
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\end_layout
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\begin_layout Standard
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Beside the support for the official Sweave in R, we have a few customized
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R scripts to unofficially support other R packages under
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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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https://github.com/yihui/lyx
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\end_layout
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\end_inset
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, e.g., the
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\series bold
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pgfSweave
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\series default
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and the
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Beside the support for the official Sweave in R, the
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\series bold
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knitr
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\series default
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package.
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The former supports cache and tikz graphics in R, and the latter is an
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alternative literate programming engine to Sweave which has even more features.
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package is also supported, which is an alternative tool to Sweave; the
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corresponding module is 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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\end_body
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