-#LyX 2.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 462
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
+\lyxformat 544
\begin_document
\begin_header
+\save_transient_properties true
+\origin /systemlyxdir/examples/
\textclass article
\begin_preamble
%% maxwidth is the original width if it's less than linewidth
\language_package auto
\inputencoding default
\fontencoding global
-\font_roman palatino
-\font_sans lmss
-\font_typewriter lmtt
-\font_math auto
+\font_roman "palatino" "default"
+\font_sans "lmss" "default"
+\font_typewriter "lmtt" "default"
+\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
+\font_sf_scale 100 100
+\font_tt_scale 100 100
+\use_microtype false
+\use_dash_ligatures false
\graphics default
\default_output_format default
\output_sync 0
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
+\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
-\use_package mathtools 0
+\use_package mathtools 1
\use_package mhchem 1
-\use_package stackrel 0
-\use_package stmaryrd 0
-\use_package undertilde 0
+\use_package stackrel 1
+\use_package stmaryrd 1
+\use_package undertilde 1
\cite_engine basic
-\cite_engine_type numerical
+\cite_engine_type default
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
-\suppress_date false
+\suppress_date true
\justification true
\use_refstyle 0
+\use_minted 0
\index Index
\shortcut idx
\color #008000
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
-\quotes_language english
+\is_math_indent 0
+\math_numbering_side default
+\quotes_style english
+\dynamic_quotes 0
\papercolumns 1
\papersides 1
\paperpagestyle default
\begin_body
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Note Note
status open
\begin_layout Plain Layout
+\begin_inset Flex Sweave Options
+status open
+
+\begin_layout Plain Layout
+
+prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
+\end_layout
+
+\end_inset
+
-%
-\backslash
-SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
\end_layout
\end_inset
\end_layout
\begin_layout Title
-Using Sweave with LyX
+Using Sweave with \SpecialChar LyX
+
\end_layout
\begin_layout Author
name "xie@yihui.name"
target "xie@yihui.name"
type "mailto:"
+literal "false"
\end_inset
\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.
+ 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 LyX 2.0, Sweave can be used out of the box with any document class
- using the
+Since \SpecialChar LyX
+ 2.0, Sweave can be used out of the box with any document class using
+ the
\family sans
Sweave
\family default
\family sans
Sweave
\family default
- module to a LyX document from
+ module to a \SpecialChar LyX
+ document from
\family sans
-Document\SpecialChar \menuseparator
-Settings\SpecialChar \menuseparator
+Document\SpecialChar menuseparator
+Settings\SpecialChar menuseparator
Modules
\family default
.
.
\end_layout
+\begin_layout Standard
+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.
+\end_layout
+
\begin_layout Section
System Requirements
\end_layout
\family default
anyway), or go to
\family sans
-Tools\SpecialChar \menuseparator
-Preferences\SpecialChar \menuseparator
-Paths\SpecialChar \menuseparator
+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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<where-is-R-bin,eval=FALSE>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-R.home('bin')
+where-is-R-bin,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+R.home('bin')
\end_layout
\end_inset
\end_layout
\begin_layout Standard
-After you have done these changes, you need to reconfigure LyX by
+After you have done these changes, you need to reconfigure \SpecialChar LyX
+ by
\family sans
-Tools\SpecialChar \menuseparator
+Tools\SpecialChar menuseparator
Reconfigure
\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
+ Another dependency is introduced by the \SpecialChar LaTeX
+ style file
\family sans
Sweave.sty
\family default
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<sweave-sty,eval=FALSE>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-file.path(R.home('share'), 'texmf', 'tex', 'latex')
+sweave-sty,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+file.path(R.home('share'), 'texmf', 'tex', 'latex')
\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.
+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
ae
\series default
.
- If LyX cannot find
+ If \SpecialChar LyX
+ cannot find
\family sans
Sweave.sty
\family default
\backslash
SweaveOpts{}
\family default
- in Sweave and it can be inserted in a LyX document by
+ in Sweave and it can be inserted in a \SpecialChar LyX
+ document by
\family sans
-Insert\SpecialChar \menuseparator
-Custom Insets\SpecialChar \menuseparator
+Insert\SpecialChar menuseparator
+Custom Insets\SpecialChar menuseparator
Sweave Options
\family default
-, or just use TeX code to write it (
+, or just use \SpecialChar TeX
+ code to write it (
\family sans
-Insert\SpecialChar \menuseparator
-TeX Code
+Insert\SpecialChar menuseparator
+\SpecialChar TeX
+ Code
\family default
).
For example, we can set a global option
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).
+ R code and its output will show up in the \SpecialChar LaTeX
+ document).
\end_layout
\begin_layout Standard
-To write R code in LyX, you can first switch to the
+To write R code in \SpecialChar LyX
+, you can first insert
+\family typewriter
+Chunk
+\family default
+ insets from
+\family sans
+Insert\SpecialChar menuseparator
+Custom Insets\SpecialChar menuseparator
+Chunk
+\family default
+, or you can simply open a \SpecialChar TeX
+ code environment and write Sweave code chunks
+ in it.
+ However, \SpecialChar LyX
+ provides a summary of all 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.
+ 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.
\end_layout
\begin_layout Standard
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<setup, keep.source=TRUE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+setup, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
options(width = 70, useFancyQuotes = FALSE, digits = 4)
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## view the Sweave vignette (requires R >= 2.13.0)
+sweave-manual, eval=FALSE, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-vignette("Sweave", package = "utils")
+## view the Sweave vignette (requires R >= 2.13.0)
\end_layout
\begin_layout Plain Layout
-@
+vignette("Sweave", package = "utils")
\end_layout
\end_inset
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<print-integers, keep.source=TRUE>>=
+print-integers, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
\begin_layout Plain Layout
-1:10
+1:10
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<hide-results, results=hide>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## intentionally hide the output by setting results=hide
+hide-results, results=hide
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-print(1:20)
+## intentionally hide the output by setting results=hide
\end_layout
\begin_layout Plain Layout
-@
+print(1:20)
\end_layout
\end_inset
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<calculator>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-1 + pi
+calculator
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-sin(pi/6)
+1 + pi
\end_layout
\begin_layout Plain Layout
-@
+sin(pi/6)
\end_layout
\end_inset
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<rnorm>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+rnorm
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
t1 <- t.test(x)
\end_layout
-\begin_layout Plain Layout
-
-@
-\end_layout
-
\end_inset
\backslash
Sexpr{}
\family default
-, and the corresponding LyX menu is
+, and the corresponding \SpecialChar LyX
+ menu is
\family sans
-Insert\SpecialChar \menuseparator
-Custom Insets\SpecialChar \menuseparator
+Insert\SpecialChar menuseparator
+Custom Insets\SpecialChar menuseparator
S/R expression
\family default
-, or alternatively just use TeX code.
+, or alternatively just use \SpecialChar TeX
+ code.
For example, the third element of the vector
\family typewriter
x
\end_layout
\begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-summary>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-summary(iris[,-5])
+iris-summary
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+summary(iris[,-5])
\end_layout
\end_inset
\end_inset
-\end_layout
+\begin_inset Flex Chunk
+status open
\begin_layout Plain Layout
-\align center
-\begin_inset ERT
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
+xtable-demo,results=tex,echo=FALSE
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
)')
\end_layout
-\begin_layout Plain Layout
-
-@
-\end_layout
-
\end_inset
\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 (
+ 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_inset
-\begin_inset ERT
+\end_layout
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-pairs(iris, col = iris$Species)
+iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+pairs(iris, col = iris$Species)
\end_layout
\end_inset
\begin_layout Plain Layout
\align center
-\begin_inset ERT
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T>>=
-\end_layout
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-par(mar=c(4,5,.1,.3), las=1)
+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
-boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
+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
\end_inset
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
+File\SpecialChar menuseparator
+Export\SpecialChar menuseparator
R/S code
\family default
), which is done via
\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).
+ 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 sans
scripts
\family default
- directory of LyX.
+ directory of \SpecialChar 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.
+ 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
\family sans
sweave
\family default
- format to LaTeX is a call to R via the command line as:
+ format to \SpecialChar LaTeX
+ is a call to R via the command line as:
\end_layout
\begin_layout Standard
\end_layout
\begin_layout Standard
-The LyX library directory
+The \SpecialChar LyX
+ library directory
\family typewriter
$$s
\family default
can be found from the menu
\family sans
-Help\SpecialChar \menuseparator
-About LyX
+Help\SpecialChar menuseparator
+About \SpecialChar LyX
+
\family default
.
All the rest of options passed to R are explained in the R script, and
- the LyX Customization manual also has detailed explanations about
+ the \SpecialChar LyX
+ Customization manual also has detailed explanations about
\family typewriter
$$i
\family default
\end_layout
\begin_layout Enumerate
-the encoding string of the LyX document is passed to R as an command line
- option; possible values are
+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
\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
+ of the \SpecialChar LyX
+ document (if you are not sure, put
\family typewriter
getwd()
\family default
\end_layout
\begin_layout Enumerate
-if LaTeX cannot find
+if \SpecialChar 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.
+ the \SpecialChar LaTeX
+ compilation takes place.
\end_layout
\begin_layout Enumerate
\begin_inset CommandInset href
LatexCommand href
name "#7551"
-target "http://www.lyx.org/trac/ticket/7551"
+target "https://www.lyx.org/trac/ticket/7551"
+literal "false"
\end_inset
-) is that if the filename (without extension) contains dots, LaTeX can fail
- to deal with such files in
+) is that if the filename (without extension) contains dots, \SpecialChar LaTeX
+ can fail to
+ deal with such files in
\family typewriter
\backslash
\end_layout
\begin_layout Standard
-LyX can deal with the font encoding by default, so there is no need to ask
+\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
\end_layout
\begin_layout Standard
-Since LyX 2.0, we can see the detailed information during compilation via
-
+Since \SpecialChar LyX
+ 2.0, we can see the detailed information during compilation via
\family sans
-View\SpecialChar \menuseparator
+View\SpecialChar menuseparator
View Messages
\family default
.
- This is extremely helpful for trouble shooting -- the process of R will
+ 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
\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
+Another issue with the \SpecialChar TeX
+ code environment 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 LyX may add a macro like
+), because \SpecialChar LyX
+ may add a macro like
\family typewriter
\backslash
<<>>=
\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
-
-.
+ This does not happen when using the Chunk inset instead of the \SpecialChar TeX
+ code environmen
+t.
+
\end_layout
\begin_layout Section
\end_layout
\begin_layout Standard
-The homepage of Sweave is at
+The user manual of Sweave is at
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-http://www.stat.uni-muenchen.de/~leisch/Sweave/
+https://stat.ethz.ch/R-manual/R-devel/library/utils/doc/Sweave.pdf
\end_layout
\end_inset
\end_inset
.
- Questions about LyX and Sweave can be posted to the LyX mailing list (
+ 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
+https://www.lyx.org/MailingLists
\end_layout
\end_inset
).
- More LyX examples are provided at
+ More \SpecialChar LyX
+ examples are provided at
\begin_inset Flex URL
status collapsed
\end_layout
\begin_layout Standard
-You will end up with LaTeX errors if you use Sweave in normal beamer slides
- in LyX; the reason is the beamer frame that contains verbatim R code.
+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
\family default
to the frame title via
\family sans
-Insert\SpecialChar \menuseparator
+Insert\SpecialChar menuseparator
Frame Options
\family default
.
\emph default
(again, see
\family sans
-Help\SpecialChar \menuseparator
-About LyX
+Help\SpecialChar menuseparator
+About \SpecialChar LyX
+
\family default
).
- Note LyX will check the
+ Note \SpecialChar LyX
+ will check the
\emph on
user directory
\emph default
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).
+ 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
projects / lyx.git / blobdiff