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Update Sweave, Knitr manual and showcase the new Navigate menu
Also mention needauth option
This commit is contained in:
Guillaume Munch
parent
d1c1a4520c
commit
d6b1dc4724
@ -1,4 +1,4 @@
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#LyX 2.2 created this file. For more info see http://www.lyx.org/
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
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\lyxformat 508
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\begin_document
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\begin_header
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@ -69,11 +69,12 @@ knitr
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\papercolumns 1
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\papersides 1
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\paperpagestyle default
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\tracking_changes false
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\tracking_changes true
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\output_changes false
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\html_math_output 0
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\html_css_as_file 0
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\html_be_strict false
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\author 2047637253 "Guillaume Munch"
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\end_header
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\begin_body
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@ -203,6 +204,31 @@ knitr
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\series default
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; many of the examples have links to the \SpecialChar LyX
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source documents.
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\change_inserted 2047637253 1483899260
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\end_layout
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\begin_layout Standard
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\change_inserted 2047637253 1483899275
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Since \SpecialChar LyX
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2.3, it is necessary to enable the use of
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\emph on
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needauth
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\emph default
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converters in
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\family sans
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Preferences\SpecialChar menuseparator
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File Handling\SpecialChar menuseparator
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Converters
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\family default
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in order to compile with
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\series bold
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knitr
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\series default
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.
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -216,6 +242,64 @@ knitr
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\end_layout
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\begin_layout Standard
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\change_inserted 2047637253 1483899195
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483899204
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483899200
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show-off
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\change_unchanged
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483899204
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rnorm(5)
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483899204
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df=data.frame(y=rnorm(100), x=1:100)
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483899204
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summary(lm(y~x, data=df))
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\change_unchanged
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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\change_deleted 2047637253 1483899208
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\begin_inset ERT
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status open
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@ -247,6 +331,8 @@ summary(lm(y~x, data=df))
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -1,4 +1,4 @@
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#LyX 2.2 created this file. For more info see http://www.lyx.org/
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
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\lyxformat 508
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\begin_document
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\begin_header
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@ -81,29 +81,45 @@ sweave
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\papercolumns 1
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\papersides 1
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\paperpagestyle default
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\tracking_changes false
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\tracking_changes true
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\output_changes false
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\html_math_output 0
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\html_css_as_file 0
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\html_be_strict false
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\author 2047637253 "Guillaume Munch"
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\end_header
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\begin_body
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897614
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\begin_inset Note Note
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status open
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\begin_layout Plain Layout
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%
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\backslash
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SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
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\change_inserted 2047637253 1483897614
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\begin_inset Flex Sweave Options
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897614
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prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
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\end_layout
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\end_inset
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -239,6 +255,27 @@ https://github.com/downloads/yihui/lyx/sweave.pdf
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\end_inset
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.
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\change_inserted 2047637253 1483898587
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\end_layout
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\begin_layout Standard
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\change_inserted 2047637253 1483899123
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Since \SpecialChar LyX
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2.3, it is necessary to enable the use of
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\emph on
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needauth
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\emph default
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converters in
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\family sans
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Preferences\SpecialChar menuseparator
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File Handling\SpecialChar menuseparator
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Converters
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\family default
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in order to compile with Sweave.
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\change_unchanged
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\end_layout
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\begin_layout Section
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@ -306,27 +343,41 @@ bin
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897627
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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<<where-is-R-bin,eval=FALSE>>=
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\end_layout
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\change_inserted 2047637253 1483897627
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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R.home('bin')
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\end_layout
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\begin_layout Plain Layout
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@
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\change_inserted 2047637253 1483897627
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where-is-R-bin,eval=FALSE
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897627
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R.home('bin')
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -361,27 +412,41 @@ Sweave.sty
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897639
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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<<sweave-sty,eval=FALSE>>=
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\end_layout
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\change_inserted 2047637253 1483897639
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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file.path(R.home('share'), 'texmf', 'tex', 'latex')
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\end_layout
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\begin_layout Plain Layout
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@
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\change_inserted 2047637253 1483897639
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sweave-sty,eval=FALSE
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897639
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file.path(R.home('share'), 'texmf', 'tex', 'latex')
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -455,15 +520,54 @@ echo=FALSE
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\begin_layout Standard
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To write R code in \SpecialChar LyX
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, you can first switch to the
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, you can first
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\change_inserted 2047637253 1483898412
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insert
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\change_deleted 2047637253 1483898419
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switch to the
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\change_unchanged
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\family typewriter
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Chunk
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\family default
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environment in the layout styles list (droplist in the top-left corner
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in the toolbar), or you can simply open a \SpecialChar TeX
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code environment and write Sweave
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code chunks in it.
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The latter approach is recommended since it is more stable.
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\change_inserted 2047637253 1483898437
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insets from
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\family sans
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Insert\SpecialChar menuseparator
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Custom Insets\SpecialChar menuseparator
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Chunk
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\change_deleted 2047637253 1483898459
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\family default
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environment in the layout styles list (droplist in the top-left corner in
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the toolbar)
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\change_unchanged
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, or you can simply open a \SpecialChar TeX
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code environment and write Sweave code chunks
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in it.
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\change_deleted 2047637253 1483898024
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The latter approach is recommended since it is more stable.
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\change_inserted 2047637253 1483961753
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However, \SpecialChar LyX
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provides a summary of all the
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\family typewriter
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Chunk
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\family default
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insets in the document in the
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\family sans
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Navigate\SpecialChar menuseparator
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Literate Programming
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\family default
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and
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\family sans
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View\SpecialChar menuseparator
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Outline Pane
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\family default
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menus.
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -483,52 +587,91 @@ useFancyQuotes
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897653
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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<<setup, keep.source=TRUE>>=
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\change_inserted 2047637253 1483897653
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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setup, keep.source=TRUE
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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## the option 'digits' can set the (approximate) number of digits
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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options(width = 70, useFancyQuotes = FALSE, digits = 4)
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Standard
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\change_inserted 2047637253 1483897653
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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@
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\change_inserted 2047637253 1483897653
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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sweave-manual, eval=FALSE, keep.source=TRUE
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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## view the Sweave vignette (requires R >= 2.13.0)
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897653
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vignette("Sweave", package = "utils")
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\end_layout
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\begin_layout Plain Layout
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@
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -536,52 +679,91 @@ A simple example that will run in any S engine:
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897659
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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<<print-integers, keep.source=TRUE>>=
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\change_inserted 2047637253 1483897659
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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print-integers, keep.source=TRUE
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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## the integers from 1 to 10 are
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\end_layout
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\begin_layout Plain Layout
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1:10
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\change_inserted 2047637253 1483897659
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1:10
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Standard
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\change_inserted 2047637253 1483897659
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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hide-results, results=hide
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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@
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\end_layout
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\begin_layout Plain Layout
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<<hide-results, results=hide>>=
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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## intentionally hide the output by setting results=hide
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897659
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print(1:20)
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\end_layout
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\begin_layout Plain Layout
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@
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\end_layout
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\end_inset
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\change_unchanged
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\end_layout
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\begin_layout Standard
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@ -589,32 +771,48 @@ We can also emulate a simple calculator:
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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\change_inserted 2047637253 1483897665
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\begin_inset Flex Chunk
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status open
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\begin_layout Plain Layout
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<<calculator>>=
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\change_inserted 2047637253 1483897665
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\begin_inset Argument 1
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status open
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897665
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calculator
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Plain Layout
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\change_inserted 2047637253 1483897665
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1 + pi
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\end_layout
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\begin_layout Plain Layout
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|
||||
\change_inserted 2047637253 1483897665
|
||||
|
||||
sin(pi/6)
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Standard
|
||||
@ -622,42 +820,62 @@ Now we look at some Gaussian data:
|
||||
\end_layout
|
||||
|
||||
\begin_layout Standard
|
||||
\begin_inset ERT
|
||||
|
||||
\change_inserted 2047637253 1483897670
|
||||
\begin_inset Flex Chunk
|
||||
status open
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
<<rnorm>>=
|
||||
\change_inserted 2047637253 1483897670
|
||||
|
||||
\begin_inset Argument 1
|
||||
status open
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
\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
|
||||
|
||||
\change_inserted 2047637253 1483897670
|
||||
|
||||
t1 <- t.test(x)
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Standard
|
||||
@ -753,27 +971,41 @@ iris
|
||||
\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])
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\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
|
||||
@ -803,46 +1035,60 @@ name "tab:xtable-demo"
|
||||
\end_inset
|
||||
|
||||
|
||||
\end_layout
|
||||
\change_inserted 2047637253 1483897685
|
||||
|
||||
\begin_layout Plain Layout
|
||||
\align center
|
||||
\begin_inset ERT
|
||||
\begin_inset Flex Chunk
|
||||
status open
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
\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
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
<<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
|
||||
\change_unchanged
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
@ -925,27 +1171,49 @@ Both eps and pdf are set to true so that both latex and pdflatex work.
|
||||
\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$Species)
|
||||
\end_layout
|
||||
\change_inserted 2047637253 1483897770
|
||||
iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
|
||||
\change_unchanged
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
\change_inserted 2047637253 1483897776
|
||||
|
||||
pairs(iris, col = iris$Species)
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
@ -984,32 +1252,48 @@ status open
|
||||
|
||||
\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>>=
|
||||
\change_inserted 2047637253 1483897883
|
||||
|
||||
\begin_inset Argument 1
|
||||
status open
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
\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
|
||||
|
||||
\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
|
||||
|
||||
\begin_layout Plain Layout
|
||||
|
||||
@
|
||||
\end_layout
|
||||
|
||||
\end_inset
|
||||
|
||||
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Plain Layout
|
||||
@ -1049,6 +1333,8 @@ R/S code
|
||||
R CMD Stangle
|
||||
\family default
|
||||
.
|
||||
\change_inserted 2047637253 1483898877
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Section
|
||||
@ -1408,8 +1694,17 @@ label=
|
||||
\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
|
||||
@ -1461,7 +1756,16 @@ This is not a legitimate Sweave code chunk, since
|
||||
<<>>=
|
||||
\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
|
||||
@ -1480,6 +1784,8 @@ reference "tab:xtable-demo"
|
||||
\end_inset
|
||||
|
||||
.
|
||||
\change_unchanged
|
||||
|
||||
\end_layout
|
||||
|
||||
\begin_layout Section
|
||||
|
||||
Loading…
Reference in New Issue
Block a user