lyx_mirror/lib/examples/sweave.lyx

#LyX 2.3 created this file. For more info see http://www.lyx.org/
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\options nogin
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\begin_modules
sweave
\end_modules
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\language english
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\author 2047637253 "Guillaume Munch"
\end_header

\begin_body

\begin_layout Standard

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\begin_inset Note Note
status open

\begin_layout Plain Layout

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\begin_inset Flex Sweave Options
status open

\begin_layout Plain Layout

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prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
\end_layout

\end_inset


\end_layout

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\backslash
setkeys{Gin}{width=
\backslash
maxwidth}
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\end_inset


\end_layout

\begin_layout Title
Using Sweave with \SpecialChar 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:"
literal "false"

\end_inset


\end_layout

\end_inset

 
\begin_inset ERT
status collapsed

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\backslash
and
\end_layout

\end_inset

 Gregor Gorjanc 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
and
\end_layout

\end_inset

 Jean-Marc Lasgouttes
\end_layout

\begin_layout Standard
Sweave is a tool in the R language (
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://www.r-project.org
\end_layout

\end_inset

) for dynamic report generation using the ideas of literate programming.
 R code can be mixed into a \SpecialChar LaTeX
 document, and will be executed in R when the
 document is compiled; the results are written into the \SpecialChar TeX
 output.
\end_layout

\begin_layout Standard
Since \SpecialChar LyX
 2.0, Sweave can be used out of the box with any document class using
 the 
\family sans
Sweave
\family default
 module.
 We can add the 
\family sans
Sweave
\family default
 module to a \SpecialChar LyX
 document from 
\family sans
Document\SpecialChar menuseparator
Settings\SpecialChar menuseparator
Modules
\family default
.
 In this manual, we demonstrate some common features of Sweave and explain
 how the module works.
 A PDF version of this manual can be found at 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://github.com/downloads/yihui/lyx/sweave.pdf
\end_layout

\end_inset

.
\change_inserted 2047637253 1483898587

\end_layout

\begin_layout Standard

\change_inserted 2047637253 1483899123
Since \SpecialChar LyX
 2.3, it is necessary to enable the use of 
\emph on
needauth
\emph default
 converters in
\family sans
 Preferences\SpecialChar menuseparator
File Handling\SpecialChar menuseparator
Converters
\family default
 in order to compile with Sweave.
\change_unchanged

\end_layout

\begin_layout Section
System Requirements
\end_layout

\begin_layout Standard
The 
\family sans
Sweave
\family default
 module depends on the executable 
\family typewriter
Rscript
\family default
, so it has to be in the 
\family sans
PATH
\family default
 variable of the system.
 It is usually not a problem for Linux and Mac OS users, but may be confusing
 to Windows users; if you do not understand what is 
\family sans
PATH
\family default
 under Windows, you may either use the R script 
\family sans
add-R-path-win.R
\family default
 in the repository 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://github.com/yihui/lyx
\end_layout

\end_inset

 to change it automatically (not recommended; you should learn 
\family sans
PATH
\family default
 anyway), or go to 
\family sans
Tools\SpecialChar menuseparator
Preferences\SpecialChar menuseparator
Paths\SpecialChar menuseparator
PATH prefix
\family default
 to add the bin path of R (recommended), which is often like 
\family sans
C:
\backslash
Program Files
\backslash
R
\backslash
R-x.x.x
\backslash
bin
\family default
 and you can find it in R:
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\begin_layout Standard

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status open

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status open

\begin_layout Plain Layout

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where-is-R-bin,eval=FALSE
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

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R.home('bin')
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
After you have done these changes, you need to reconfigure \SpecialChar LyX
 by 
\family sans
Tools\SpecialChar menuseparator
Reconfigure
\family default
.
 If 
\family typewriter
Rscript
\family default
 is not present in 
\family sans
PATH
\family default
, the 
\family sans
Sweave
\family default
 module will be unavailable.
 It is recommended to use the latest version of R, since Sweave is still
 being updated.
 Another dependency is introduced by the \SpecialChar LaTeX
 style file 
\family sans
Sweave.sty
\family default
 which is shipped with R under this path (it is not on CTAN):
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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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sweave-sty,eval=FALSE
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

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file.path(R.home('share'), 'texmf', 'tex', 'latex')
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
Mik\SpecialChar TeX
 users may add the texmf directory to the list of root directories in
 Mik\SpecialChar TeX
 through Mik\SpecialChar TeX
 settings.
 Further note that 
\family sans
Sweave.sty
\family default
 depends on the 
\series bold
fancyvrb
\series default
 package and 
\emph on
may
\emph default
 depend on 
\series bold
ae
\series default
.
 If \SpecialChar LyX
 cannot find 
\family sans
Sweave.sty
\family default
, it will directly copy from R, so the Sweave module works even if you do
 not know where is this style file.
\end_layout

\begin_layout Section
Sweave Examples
\end_layout

\begin_layout Standard
Before we write an Sweave document, we can set some Sweave options; the
 command is 
\family typewriter

\backslash
SweaveOpts{}
\family default
 in Sweave and it can be inserted in a \SpecialChar LyX
 document by 
\family sans
Insert\SpecialChar menuseparator
Custom Insets\SpecialChar menuseparator
Sweave Options
\family default
, or just use \SpecialChar TeX
 code to write it (
\family sans
Insert\SpecialChar menuseparator
\SpecialChar TeX
 Code
\family default
).
 For example, we can set a global option 
\family typewriter
echo=FALSE
\family default
 in the beginning of a document to suppress all R code (by default, both
 R code and its output will show up in the \SpecialChar LaTeX
 document).
 
\end_layout

\begin_layout Standard
To write R code in \SpecialChar LyX
, you can first 
\change_inserted 2047637253 1483898412
insert 
\change_deleted 2047637253 1483898419
switch to the 
\change_unchanged

\family typewriter
Chunk
\family default
 
\change_inserted 2047637253 1483898437
insets from 
\family sans
Insert\SpecialChar menuseparator
Custom Insets\SpecialChar menuseparator
Chunk
\change_deleted 2047637253 1483898459

\family default
environment in the layout styles list (droplist in the top-left corner in
 the toolbar)
\change_unchanged
, or you can simply open a \SpecialChar TeX
 code environment and write Sweave code chunks
 in it.
 
\change_deleted 2047637253 1483898024
The latter approach is recommended since it is more stable.
\change_inserted 2047637253 1483961753
However, \SpecialChar LyX
 provides a summary of all the 
\family typewriter
Chunk
\family default
 insets in the document in the 
\family sans
Navigate\SpecialChar menuseparator
Literate Programming
\family default
 and 
\family sans
View\SpecialChar menuseparator
Outline Pane
\family default
 menus.
\change_unchanged

\end_layout

\begin_layout Standard
Some R options can be useful to the Sweave output as well, e.g.
 
\family typewriter
width
\family default
 and 
\family typewriter
useFancyQuotes
\family default
.
 The former option can adjust the width of the output, and the latter can
 avoid a common problem with quotes.
 Users are encouraged to read the Sweave manual in R for more details.
\end_layout

\begin_layout Standard

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status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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setup, keep.source=TRUE
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

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## the option 'digits' can set the (approximate) number of digits
\end_layout

\begin_layout Plain Layout

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options(width = 70, useFancyQuotes = FALSE, digits = 4)
\end_layout

\end_inset


\end_layout

\begin_layout Standard

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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sweave-manual, eval=FALSE, keep.source=TRUE
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897653

## view the Sweave vignette (requires R >= 2.13.0)
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897653

vignette("Sweave", package = "utils")
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
A simple example that will run in any S engine: 
\end_layout

\begin_layout Standard

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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print-integers, keep.source=TRUE
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897659

## the integers from 1 to 10 are
\end_layout

\begin_layout Plain Layout

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1:10
\end_layout

\end_inset


\end_layout

\begin_layout Standard

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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hide-results, results=hide
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897659

## intentionally hide the output by setting results=hide
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897659

print(1:20)
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
We can also emulate a simple calculator: 
\end_layout

\begin_layout Standard

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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calculator
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

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1 + pi
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897665

sin(pi/6)
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
Now we look at some Gaussian data:
\end_layout

\begin_layout Standard

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status open

\begin_layout Plain Layout

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\begin_inset Argument 1
status open

\begin_layout Plain Layout

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rnorm
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

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set.seed(123)  # for reproducibility
\end_layout

\begin_layout Plain Layout

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x <- rnorm(20)
\end_layout

\begin_layout Plain Layout

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print(x)
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897670

t1 <- t.test(x)
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
Note that we can easily integrate some numbers into standard text; this
 is done with the command 
\family typewriter

\backslash
Sexpr{}
\family default
, and the corresponding \SpecialChar LyX
 menu is 
\family sans
Insert\SpecialChar menuseparator
Custom Insets\SpecialChar menuseparator
S/R expression
\family default
, or alternatively just use \SpecialChar TeX
 code.
 For example, the third element of the vector 
\family typewriter
x
\family default
 is 
\begin_inset Flex S/R expression
status collapsed

\begin_layout Plain Layout

x[3]
\end_layout

\end_inset

 (i.e.
 
\family typewriter
x[3]
\family default
) and the 
\begin_inset Formula $p$
\end_inset

-value of the test is 
\begin_inset Flex S/R expression
status collapsed

\begin_layout Plain Layout

format.pval(t1$p.value)
\end_layout

\end_inset

.
 You can round these numbers using functions like 
\emph on
round()
\emph default
 in R.
 
\end_layout

\begin_layout Standard

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
Now we look at a summary of the 
\family typewriter
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
iris
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
 dataset:
\end_layout

\begin_layout Standard

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897677

\begin_inset Argument 1
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897677
iris-summary
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897677

summary(iris[,-5])
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Standard
\begin_inset Float table
wide false
sideways false
status open

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout
Quantiles of the first four variables in the 
\family typewriter
iris
\family default
 data.
\begin_inset CommandInset label
LatexCommand label
name "tab:xtable-demo"

\end_inset


\end_layout

\end_inset


\change_inserted 2047637253 1483897685

\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897698

\begin_inset Argument 1
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897692
xtable-demo,results=tex,echo=FALSE
\change_unchanged

\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897699

if (require('xtable')) {
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897699

print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897699

} else cat('the xtable package is not available! please install.packages("xtable"
)')
\change_unchanged

\end_layout

\end_inset


\change_unchanged

\end_layout

\end_inset


\end_layout

\begin_layout Standard
Usually people do not like such 
\begin_inset Quotes eld
\end_inset

raw
\begin_inset Quotes erd
\end_inset

 output, and we can polish these messy numbers with the 
\series bold
xtable
\series default
 package.
 Table 
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:xtable-demo"

\end_inset

 is an example demonstrating how to use the 
\series bold
xtable
\series default
 package with Sweave; note the chunk option 
\family typewriter
results=tex
\family default
 makes sure that the R output is written out as raw \SpecialChar LaTeX
 code instead of being
 wrapped in a special environment (
\family typewriter
Soutput
\family default
).
\end_layout

\begin_layout Standard
Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:iris-pairs"

\end_inset

 and 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:iris-boxplots"

\end_inset

 are two simple examples of producing graphics output with Sweave.
\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Note Note
status open

\begin_layout Plain Layout
Both eps and pdf are set to true so that both latex and pdflatex work.
 In practice, you would probably just choose one.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout
\align center

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\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897772

\begin_inset Argument 1
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897770
iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
\change_unchanged

\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897776

pairs(iris, col = iris$Species)
\change_unchanged

\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout
Scatter plot matrix of the 
\family typewriter
iris
\family default
 data.
\begin_inset CommandInset label
LatexCommand label
name "fig:iris-pairs"

\end_inset


\end_layout

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center

\change_inserted 2047637253 1483897883
\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897883

\begin_inset Argument 1
status open

\begin_layout Plain Layout

\change_inserted 2047637253 1483897883
iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897883

par(mar=c(4,5,.1,.3), las=1)
\end_layout

\begin_layout Plain Layout

\change_inserted 2047637253 1483897883

boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
\end_layout

\end_inset


\change_unchanged

\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout
Boxplots of sepal length grouped by species.
\begin_inset CommandInset label
LatexCommand label
name "fig:iris-boxplots"

\end_inset


\end_layout

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
We can also export all the R code in an Sweave document as a single R script
 (
\family sans
File\SpecialChar menuseparator
Export\SpecialChar menuseparator
R/S code
\family default
), which is done via 
\family typewriter
R CMD Stangle
\family default
.
\change_inserted 2047637253 1483898877

\end_layout

\begin_layout Section
The 
\family sans
Sweave
\family default
 Module
\end_layout

\begin_layout Standard
The 
\family sans
Sweave
\family default
 module declares that a \SpecialChar LyX
 document contains literate programming components
 with R, so that \SpecialChar LyX
 will handle such documents according to the specific converter
s (see the Customization manual).
 The 
\family sans
Sweave
\family default
 module uses the 
\family sans
sweave
\family default
 converter, which essentially consists of an R script 
\family sans
lyxsweave.R
\family default
 under the 
\family sans
scripts
\family default
 directory of \SpecialChar LyX
.
 This script takes an 
\family sans
Rnw
\family default
 document from \SpecialChar LyX
 and call Sweave to process it to a \SpecialChar TeX
 document, then \SpecialChar LyX
 takes
 care of the rest of work.
\end_layout

\begin_layout Standard
The converter from the 
\family sans
sweave
\family default
 format to \SpecialChar LaTeX
 is a call to R via the command line as:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout

Rscript --no-save --no-restore $$s/scripts/lyxsweave.R $$p$$i $$p$$o $$e
 $$r
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The \SpecialChar LyX
 library directory 
\family typewriter
$$s
\family default
 can be found from the menu 
\family sans
Help\SpecialChar menuseparator
About \SpecialChar LyX

\family default
.
 All the rest of options passed to R are explained in the R script, and
 the \SpecialChar LyX
 Customization manual also has detailed explanations about 
\family typewriter
$$i
\family default
, 
\family typewriter
$$o
\family default
, 
\family typewriter
$$e
\family default
 and 
\family typewriter
$$r
\family default
.
 General users do not need to know clearly what they mean, but here we need
 to explain a few issues in the R code:
\end_layout

\begin_layout Enumerate
the encoding string of the \SpecialChar LyX
 document is passed to R as an command line option;
 possible values are 
\family typewriter
ISO-8859-15
\family default
 and 
\family typewriter
UTF-8
\family default
, etc.
 The encoding is used for R to read the 
\family sans
Rnw
\family default
 document correctly.
\end_layout

\begin_layout Enumerate
the R code chunks in the Sweave document are executed under the directory
 of the \SpecialChar LyX
 document (if you are not sure, put 
\family typewriter
getwd()
\family default
 in a code chunk to see what is the current working directory).
 In this case, you can put data files under the same directory and use relative
 paths in R to guarantee reproducibility, i.e.
 we do not need to write hard-coded paths which may not exist in other systems.
\end_layout

\begin_layout Enumerate
if \SpecialChar LaTeX
 cannot find 
\family sans
Sweave.sty
\family default
, this R script will copy it to the temporary directory automatically where
 the \SpecialChar LaTeX
 compilation takes place.
\end_layout

\begin_layout Enumerate
Sweave will use the filename of the Rnw file as the prefix string for the
 graphics output by default; one known issue (
\begin_inset CommandInset href
LatexCommand href
name "#7551"
target "http://www.lyx.org/trac/ticket/7551"
literal "false"

\end_inset

) is that if the filename (without extension) contains dots, \SpecialChar LaTeX
 can fail to
 deal with such files in 
\family typewriter

\backslash
includegraphics{}
\family default
.
 Therefore, we have set the default value of the prefix to be the filename
 with all the dots being replaced by 
\begin_inset Quotes eld
\end_inset

-
\begin_inset Quotes erd
\end_inset

.
 We can also solve this problem in Sweave directly: set the Sweave option
 
\family typewriter
prefix.string
\family default
 to be a character string without dots, and this option will override the
 default value.
\end_layout

\begin_layout Standard
We have pre-specified an option 
\family typewriter
noae
\family default
 for the Sweave package.
 This option stops Sweave from loading these two packages:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout


\backslash
RequirePackage[T1]{fontenc}  
\end_layout

\begin_layout Plain Layout


\backslash
RequirePackage{ae}
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\SpecialChar LyX
 can deal with the font encoding by default, so there is no need to ask
 Sweave to do this (furthermore, this may bring clashes of package options);
 besides, the users can load the 
\series bold
ae
\series default
 package by themselves in the preamble if needed.
\end_layout

\begin_layout Section
Trouble Shooting
\end_layout

\begin_layout Standard
Since \SpecialChar LyX
 2.0, we can see the detailed information during compilation via 
\family sans
View\SpecialChar menuseparator
View Messages
\family default
.
 This is extremely helpful for trouble shooting – the process of R will
 be shown in the message panel, and we will be able to know which chunk
 goes wrong in cases of errors.
 For example, when you compile this document, you can see messages like
 below:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout

17:58:47.868: Processing code chunks with options ...
\end_layout

\begin_layout Plain Layout

17:58:47.885:  1 : echo keep.source term verbatim (label=setup)
\end_layout

\begin_layout Plain Layout

17:58:47.889:  2 : echo keep.source (label=sweave-manual)
\end_layout

\begin_layout Plain Layout

17:58:47.908:  3 : echo keep.source term verbatim (label=print-integers)
\end_layout

\begin_layout Plain Layout

....
\end_layout

\begin_layout Plain Layout

17:58:47.941: Loading required package: xtable
\end_layout

\begin_layout Plain Layout

17:58:47.976:  9 : echo term verbatim pdf (label=iris-pairs)
\end_layout

\begin_layout Plain Layout

....
\end_layout

\begin_layout Plain Layout

17:58:48.116: You can now run (pdf)latex on 'sweave.tex'
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The string after 
\family typewriter
label=
\family default
 is the chunk label.
 If any chunk causes an error in R, you will see the error message here
 immediately.
\end_layout

\begin_layout Standard
Another 
\change_deleted 2047637253 1483899012
known
\change_unchanged
 issue 
\change_inserted 2047637253 1483898966
with the \SpecialChar TeX
 code environment 
\change_unchanged
is the Sweave code chunk may fail when we change the alignment of the chunk
 paragraph in \SpecialChar LyX
 (using 
\family sans
Paragraph settings
\family default
), because \SpecialChar LyX
 may add a macro like 
\family typewriter

\backslash
centering{}
\family default
 before the code chunk without adding a new line, which will lead to a code
 chunk like this:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout


\backslash
centering{}<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
This is not a legitimate Sweave code chunk, since 
\family typewriter
<<>>=
\family default
 must start in a new line with nothing before it.

\change_inserted 2047637253 1483899083
 This does not happen when using the Chunk inset instead of the \SpecialChar TeX
 code environmen
t.

\change_unchanged
 
\change_deleted 2047637253 1483898988
Therefore we recommend you to double check the real source code via 
\family sans
View\SpecialChar menuseparator
View Source
\family default
 when changing the alignment of a chunk paragraph, and make sure 
\family typewriter
<<>>=
\family default
 appears in a new line.
 This explains why we manually added an empty line in the code chunk in
 Table 
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:xtable-demo"

\end_inset

.
\change_unchanged

\end_layout

\begin_layout Section
Resources
\end_layout

\begin_layout Standard
The homepage of Sweave is at 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://www.stat.uni-muenchen.de/~leisch/Sweave/
\end_layout

\end_inset

.
 The CRAN task view on 
\begin_inset Quotes eld
\end_inset

Reproducible Research
\begin_inset Quotes erd
\end_inset

 has a list of Sweave-related packages which can be potentially useful;
 see 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://cran.r-project.org/web/views/ReproducibleResearch.html
\end_layout

\end_inset

.
 Questions about \SpecialChar LyX
 and Sweave can be posted to the \SpecialChar LyX
 mailing list (
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://www.lyx.org/MailingLists
\end_layout

\end_inset

).
 More \SpecialChar LyX
 examples are provided at 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://github.com/yihui/lyx
\end_layout

\end_inset

.
\end_layout

\begin_layout Section
FAQ
\end_layout

\begin_layout Subsection
How to use Sweave with beamer?
\end_layout

\begin_layout Standard
You will end up with \SpecialChar LaTeX
 errors if you use Sweave in normal beamer slides in
 \SpecialChar LyX
; the reason is the beamer frame that contains verbatim R code.
 The solution is to use a 
\emph on
FragileFrame
\emph default
 instead of a normal 
\emph on
Frame
\emph default
, or to pass the option 
\family typewriter
fragile
\family default
 to the frame title via 
\family sans
Insert\SpecialChar menuseparator
Frame Options
\family default
.
\end_layout

\begin_layout Subsection
Can I define my own R script to compile the Rnw document?
\end_layout

\begin_layout Standard
Yes, of course.
 First you need to understand how the R script 
\family typewriter
$$s
\family sans
/scripts/lyxsweave.R
\family default
 works, which was introduced previously, and we recommend you to read the
 R source code as well (on how R takes the paths and uses 
\emph on
Sweave()
\emph default
 to handle the Rnw document).
 Then you put your customized 
\family sans
lyxsweave.R
\family default
 under the 
\family sans
scripts
\family default
 directory of your 
\emph on
user directory
\emph default
 (again, see 
\family sans
Help\SpecialChar menuseparator
About \SpecialChar LyX

\family default
).
 Note \SpecialChar LyX
 will check the 
\emph on
user directory
\emph default
 before going to its own 
\emph on
library directory
\emph default
; if an R script 
\family sans
lyxsweave.R
\family default
 is found in the user directory, it will be used.
 It is not recommended to hack the script under the \SpecialChar LyX
 library directory directly,
 since updating \SpecialChar LyX
 will override you modified script (the user directory will
 not be affected).
\end_layout

\begin_layout Standard
Beside the support for the official Sweave in R, the 
\series bold
knitr
\series default
 package is also supported, which is an alternative tool to Sweave; the
 corresponding module is named 
\family sans
Rnw (knitr)
\family default
.
\end_layout

\end_body
\end_document