#LyX 2.1 created this file. For more info see http://www.lyx.org/ \lyxformat 445 \begin_document \begin_header \textclass article \begin_preamble %% maxwidth is the original width if it's less than linewidth %% otherwise use linewidth (to make sure the graphics do not exceed the margin) \def\maxwidth{% \ifdim\Gin@nat@width>\linewidth \linewidth \else \Gin@nat@width \fi } \end_preamble \options nogin \use_default_options true \begin_modules sweave \end_modules \maintain_unincluded_children false \language english \language_package auto \inputencoding default \fontencoding global \font_roman palatino \font_sans lmss \font_typewriter lmtt \font_math auto \font_default_family default \use_non_tex_fonts false \font_sc false \font_osf false \font_sf_scale 100 \font_tt_scale 100 \graphics default \default_output_format default \output_sync 0 \bibtex_command default \index_command default \paperfontsize default \spacing single \use_hyperref false \papersize default \use_geometry true \use_package amsmath 1 \use_package amssymb 1 \use_package esint 1 \use_package mathdots 1 \use_package mathtools 0 \use_package mhchem 1 \use_package undertilde 0 \cite_engine basic \cite_engine_type numerical \biblio_style plain \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false \justification true \use_refstyle 0 \index Index \shortcut idx \color #008000 \end_index \leftmargin 3cm \topmargin 3cm \rightmargin 3cm \bottommargin 3cm \secnumdepth 3 \tocdepth 3 \paragraph_separation indent \paragraph_indentation default \quotes_language english \papercolumns 1 \papersides 1 \paperpagestyle default \tracking_changes false \output_changes false \html_math_output 0 \html_css_as_file 0 \html_be_strict false \end_header \begin_body \begin_layout 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. 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 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: \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout R.home('bin') \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard After you have done these changes, you need to reconfigure 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 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 <>= \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 <>= \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 <>= \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 <>= \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 <>= \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 <>= \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 <>= \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 <>= \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 \align center \begin_inset ERT status open \begin_layout Plain Layout \end_layout \begin_layout Plain Layout <>= \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 \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 \align center \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout pairs(iris, col = iris$Species) \end_layout \begin_layout Plain Layout @ \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 \align center \begin_inset ERT status open \begin_layout Plain Layout <>= \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 \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 Standard Another known issue is the Sweave code chunk may fail when we change the alignment of the chunk paragraph in LyX (using \family sans Paragraph settings \family default ), because 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{}<>= \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. 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 . \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, 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