-#LyX 2.2 created this file. For more info see http://www.lyx.org/
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 508
\begin_document
\begin_header
\papercolumns 1
\papersides 1
\paperpagestyle default
-\tracking_changes false
+\tracking_changes true
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
+\author 2047637253 "Guillaume Munch"
\end_header
\begin_body
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897614
+\begin_inset Note Note
status open
\begin_layout Plain Layout
-%
-\backslash
-SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
+\change_inserted 2047637253 1483897614
+\begin_inset Flex Sweave Options
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897614
+
+prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
\end_layout
\end_inset
+\end_layout
+
+\end_inset
+
+
+\change_unchanged
+
\end_layout
\begin_layout Standard
\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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897627
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<where-is-R-bin,eval=FALSE>>=
-\end_layout
+\change_inserted 2047637253 1483897627
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-R.home('bin')
+\change_inserted 2047637253 1483897627
+where-is-R-bin,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897627
+
+R.home('bin')
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897639
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<sweave-sty,eval=FALSE>>=
-\end_layout
+\change_inserted 2047637253 1483897639
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-file.path(R.home('share'), 'texmf', 'tex', 'latex')
+\change_inserted 2047637253 1483897639
+sweave-sty,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897639
+
+file.path(R.home('share'), 'texmf', 'tex', 'latex')
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
\begin_layout Standard
To write R code in \SpecialChar LyX
-, you can first switch to the
+, you can first
+\change_inserted 2047637253 1483898412
+insert
+\change_deleted 2047637253 1483898419
+switch to the
+\change_unchanged
+
\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.
+
+\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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897653
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897653
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<setup, keep.source=TRUE>>=
+\change_inserted 2047637253 1483897653
+setup, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897653
+
## the option 'digits' can set the (approximate) number of digits
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897653
+
options(width = 70, useFancyQuotes = FALSE, digits = 4)
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+
+\change_inserted 2047637253 1483897653
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
-\end_layout
+\change_inserted 2047637253 1483897653
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## view the Sweave vignette (requires R >= 2.13.0)
+\change_inserted 2047637253 1483897653
+sweave-manual, eval=FALSE, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-vignette("Sweave", package = "utils")
+\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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897659
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897659
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<print-integers, keep.source=TRUE>>=
+\change_inserted 2047637253 1483897659
+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
-1:10
+\change_inserted 2047637253 1483897659
+
+1:10
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+
+\change_inserted 2047637253 1483897659
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<hide-results, results=hide>>=
-\end_layout
+\change_inserted 2047637253 1483897659
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## intentionally hide the output by setting results=hide
+\change_inserted 2047637253 1483897659
+hide-results, results=hide
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-print(1:20)
+\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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897665
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<calculator>>=
-\end_layout
+\change_inserted 2047637253 1483897665
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-1 + pi
+\change_inserted 2047637253 1483897665
+calculator
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-sin(pi/6)
+\change_inserted 2047637253 1483897665
+
+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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897670
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897670
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<rnorm>>=
+\change_inserted 2047637253 1483897670
+rnorm
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
set.seed(123) # for reproducibility
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
x <- rnorm(20)
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
print(x)
\end_layout
\begin_layout Plain Layout
-t1 <- t.test(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
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897677
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-summary>>=
-\end_layout
+\change_inserted 2047637253 1483897677
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-summary(iris[,-5])
+\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
\end_inset
-\end_layout
+\change_inserted 2047637253 1483897685
+
+\begin_inset Flex Chunk
+status open
\begin_layout Plain Layout
-\align center
-\begin_inset ERT
+
+\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
-\begin_layout Plain Layout
+\end_inset
+
-<<xtable-demo,results=tex,echo=FALSE>>=
\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"
)')
-\end_layout
-
-\begin_layout Plain Layout
+\change_unchanged
-@
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\end_inset
\end_inset
-\begin_inset ERT
+\end_layout
+
+\begin_layout Plain Layout
+\align center
+
+\change_inserted 2047637253 1483897765
+\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
+\change_inserted 2047637253 1483897772
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-pairs(iris, col = iris$Species)
+\change_inserted 2047637253 1483897770
+iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
+\change_unchanged
+
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897776
+
+pairs(iris, col = iris$Species)
+\change_unchanged
+
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Plain Layout
\begin_layout Plain Layout
\align center
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897883
+\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
+\change_inserted 2047637253 1483897883
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-par(mar=c(4,5,.1,.3), las=1)
+\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
-boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
+\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
R CMD Stangle
\family default
.
+\change_inserted 2047637253 1483898877
+
\end_layout
\begin_layout Section
\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
+\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
must start in a new line with nothing before it.
- Therefore we recommend you to double check the real source code via
+
+\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
\end_inset
.
+\change_unchanged
+
\end_layout
\begin_layout Section