lyx_mirror/lib/examples/sweave.lyx

#LyX 2.0 created this file. For more info see http://www.lyx.org/
\lyxformat 413
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\begin_modules
sweave
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\begin_body

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

%
\backslash
SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

%% 
\backslash
maxwidth was defined in the preamble; see document settings
\end_layout

\begin_layout Plain Layout


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

\end_inset


\end_layout

\begin_layout Title
Using Sweave 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

 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\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 LaTeX document, and will be executed in R when
 the document is compiled; the results are written into the TeX output.
\end_layout

\begin_layout Standard
Since LyX 2.0, Sweave can be used out of the box with any document class
 using the 
\family sans
Sweave
\family default
 module, which means we no longer need to modify the 
\family sans
preferences
\family default
 file manually or add special layouts such as 
\family sans
literate-article.layout
\family default
 and 
\family sans
literate-book.layout
\family default
 like we did before.
 We can add the 
\family sans
Sweave
\family default
 module to a 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

.
\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 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 (we recommend you to learn 
\family sans
PATH
\family default
 anyway).
\end_layout

\begin_layout Standard
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 LaTeX style file 
\family sans
Sweave.sty
\family default
 which is shipped with R under this path (it is not on CTAN):
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<sweave-sty,eval=FALSE>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
MikTeX users may add the texmf directory to the list of root directories
 in MikTeX through MikTeX 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 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 LyX document by 
\family sans
Insert\SpecialChar \menuseparator
Custom Insets\SpecialChar \menuseparator
Sweave Options
\family default
, or just use TeX code to write it (
\family sans
Insert\SpecialChar \menuseparator
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 LaTeX document).
 
\end_layout

\begin_layout Standard
To write R code in LyX, you can first switch to the 
\family typewriter
Chunk
\family default
 environment in the layout styles list (droplist in the top-left corner
 in the toolbar), or you can simply open a TeX code environment and write
 Sweave code chunks in it.
 The latter approach is recommended since it is more stable.
\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
\begin_inset ERT
status open

\begin_layout Plain Layout

<<setup, keep.source=TRUE>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

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

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<print-integers, keep.source=TRUE>>=
\end_layout

\begin_layout Plain Layout

## the integers from 1 to 10 are
\end_layout

\begin_layout Plain Layout

1:10 
\end_layout

\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout

<<hide-results, results=hide>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

print(1:20)
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

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

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<calculator>>=
\end_layout

\begin_layout Plain Layout

1 + pi
\end_layout

\begin_layout Plain Layout

sin(pi/6)
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

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

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<rnorm>>=
\end_layout

\begin_layout Plain Layout

set.seed(123)  # for reproducibility
\end_layout

\begin_layout Plain Layout

x <- rnorm(20)
\end_layout

\begin_layout Plain Layout

print(x)
\end_layout

\begin_layout Plain Layout

t1 <- t.test(x)
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\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 LyX menu is 
\family sans
Insert\SpecialChar \menuseparator
Custom Insets\SpecialChar \menuseparator
S/R expression
\family default
, or alternatively just use 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
\begin_inset ERT
status open

\begin_layout Plain Layout

<<iris-summary>>=
\end_layout

\begin_layout Plain Layout

summary(iris[,-5])
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

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

\begin_layout Plain Layout
\begin_inset Caption

\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


\end_layout

\begin_layout Plain Layout
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{center}
\end_layout

\begin_layout Plain Layout

<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout


\backslash
end{center}
\end_layout

\end_inset


\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 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
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{center}
\end_layout

\begin_layout Plain Layout

<<iris-pairs,fig=TRUE,width=4.5,height=4.5>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout


\backslash
end{center}
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption

\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
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{center}
\end_layout

\begin_layout Plain Layout

<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F>>=
\end_layout

\begin_layout Plain Layout

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

\begin_layout Plain Layout

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

\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout


\backslash
end{center}
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption

\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
.
\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 LyX document contains literate programming components
 with R, so that LyX will handle such documents according to the specific
 converters (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 LyX.
 This script takes an 
\family sans
Rnw
\family default
 document from LyX and call Sweave to process it to a TeX document, then
 LyX takes care of the rest of work.
\end_layout

\begin_layout Standard
The converter from the 
\family sans
sweave
\family default
 format to 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 LyX library directory 
\family typewriter
$$s
\family default
 can be found from the menu 
\family sans
Help\SpecialChar \menuseparator
About LyX
\family default
.
 All the rest of options passed to R are explained in the R script, and
 the LyX Customization manual also has detailed explanations about 
\family typewriter
$$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 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 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 LaTeX cannot find 
\family sans
Sweave.sty
\family default
, this R script will copy it to the temporary directory automatically where
 the 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"

\end_inset

) is that if the filename (without extension) contains dots, 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
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 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 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 LyX and Sweave can be posted to the LyX mailing list (
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

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

\end_inset

).
 More 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 LaTeX errors if you use Sweave in beamer slides in
 LyX; the reason is the beamer frame that contains verbatim R code and output
 must have the 
\family typewriter
fragile
\family default
 option.
 However, currently there is no straightforward way to do this.
 One way is to write raw TeX code, and the other is to use the 
\family sans
beamer-fragile.module
\family default
 discussed in 
\begin_inset CommandInset href
LatexCommand href
name "#7273"
target "http://www.lyx.org/trac/ticket/7273"

\end_inset

 (put this file under the 
\family sans
layouts
\family default
 directory of LyX user directory and reconfigure LyX).
 After including this module in your document, you should be able to use
 
\family sans
Insert\SpecialChar \menuseparator
Custom Insets\SpecialChar \menuseparator
FragileFrame
\family default
, which is essentially 
\family typewriter

\backslash
begin{frame}[fragile]
\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 LyX
\family default
).
 Note 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 LyX library directory
 directly, since updating 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, we have a few customized
 R scripts to unofficially support other R packages under 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

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

\end_inset

, e.g., the 
\series bold
pgfSweave
\series default
 and the 
\series bold
knitr
\series default
 package.
 The former supports cache and tikz graphics in R, and the latter is an
 alternative literate programming engine to Sweave which has even more features.
\end_layout

\end_body
\end_document