-#LyX 2.2 created this file. For more info see http://www.lyx.org/
-\lyxformat 504
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
+\lyxformat 544
\begin_document
\begin_header
\save_transient_properties true
\font_osf false
\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 0
+\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 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
name "xie@yihui.name"
target "xie@yihui.name"
type "mailto:"
+literal "false"
\end_inset
.
\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
\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
-\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
\begin_layout Standard
To write R code in \SpecialChar LyX
-, you can first switch to the
+, 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 \SpecialChar 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
\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
\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
\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
\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 \SpecialChar LyX
+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
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
\begin_layout Plain Layout
-http://www.lyx.org/MailingLists
+https://www.lyx.org/MailingLists
\end_layout
\end_inset
projects / lyx.git / blobdiff