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https://git.lyx.org/repos/lyx.git
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362 lines
5.3 KiB
Plaintext
362 lines
5.3 KiB
Plaintext
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#LyX 1.6.1 created this file. For more info see http://www.lyx.org/
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\lyxformat 345
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\begin_document
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\begin_header
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\textclass article
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\use_default_options true
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\begin_modules
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sweave
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\end_modules
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\language english
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\inputencoding auto
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\font_roman default
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\font_sans default
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\font_typewriter default
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\font_default_family default
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\font_sc false
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\font_osf false
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\font_sf_scale 100
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\font_tt_scale 100
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\graphics default
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\paperfontsize default
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\spacing single
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\use_hyperref false
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\papersize default
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\use_geometry false
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\use_amsmath 1
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\use_esint 1
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\cite_engine basic
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\use_bibtopic false
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\paperorientation portrait
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\secnumdepth 3
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\tocdepth 3
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\paragraph_separation skip
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\defskip medskip
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\quotes_language english
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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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\output_changes false
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\author ""
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\author ""
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\end_header
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\begin_body
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\begin_layout Title
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A Test File
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\end_layout
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\begin_layout Author
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Friedrich Leisch
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\begin_inset Foot
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status collapsed
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\begin_layout Plain Layout
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LyX
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\begin_inset Quotes eld
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\end_inset
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port
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\begin_inset Quotes erd
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\end_inset
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by Gregor Gorjanc
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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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A simple example that will run in any S engine: The integers from 1 to 10
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are
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\end_layout
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\begin_layout Chunk
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<<print=TRUE>>=
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\begin_inset Newline newline
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\end_inset
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1:10
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\begin_inset Newline newline
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\end_inset
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<<results=hide>>=
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\begin_inset Newline newline
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\end_inset
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print(1:20)
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\begin_inset Newline newline
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\end_inset
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@ % the above is just to ensure that 2 code chunks can follow each other
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\end_layout
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\begin_layout Standard
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We can also emulate a simple calculator:
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\end_layout
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\begin_layout Chunk
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<<echo=TRUE,print=TRUE>>=
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\begin_inset Newline newline
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\end_inset
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1 + 1
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\begin_inset Newline newline
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\end_inset
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1 + pi
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\begin_inset Newline newline
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\end_inset
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sin(pi/2)
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Standard
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Now we look at Gaussian data:
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\end_layout
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\begin_layout Chunk
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<<>>=
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\begin_inset Newline newline
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\end_inset
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library(stats)
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\begin_inset Newline newline
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\end_inset
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x <- rnorm(20)
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\begin_inset Newline newline
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\end_inset
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print(x)
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\begin_inset Newline newline
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\end_inset
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print(t1 <- t.test(x))
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Standard
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Note that we can easily integrate some numbers into standard text: The third
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element of vector
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\family typewriter
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x
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\family default
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is
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\begin_inset Flex S/R expression
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status collapsed
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\begin_layout Plain Layout
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x[3]
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\end_layout
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\end_inset
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, the
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\begin_inset Formula $p$
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\end_inset
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-value of the test is
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\begin_inset Flex S/R expression
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status collapsed
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\begin_layout Plain Layout
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format.pval(t1$p.value)
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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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\family roman
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\series medium
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\shape up
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\size normal
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\emph off
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\bar no
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\noun off
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\color none
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Now we look at a summary of the famous iris dataset, and we want to see
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the commands in the code chunks:
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\end_layout
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\begin_layout Standard
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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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echo=true,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 Chunk
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<<engine=R>>=
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\begin_inset Newline newline
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\end_inset
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# A comment
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\begin_inset Newline newline
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\end_inset
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data(iris)
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\begin_inset Newline newline
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\end_inset
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summary(iris)
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\begin_inset Newline newline
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\end_inset
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@ % def
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\end_layout
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\begin_layout Standard
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\begin_inset Float figure
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placement tbph
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wide false
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sideways false
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status collapsed
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\begin_layout Chunk
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\align center
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<<fig=TRUE>>=
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\begin_inset Newline newline
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\end_inset
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library(graphics)
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\begin_inset Newline newline
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\end_inset
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pairs(iris)
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Plain Layout
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\begin_inset Caption
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\begin_layout Plain Layout
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Pairs plot of the iris data.
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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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\end_layout
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\begin_layout Standard
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\begin_inset Float figure
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placement tbph
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wide false
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sideways false
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status collapsed
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\begin_layout Chunk
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\align center
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<<fig=true>>=
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\begin_inset Newline newline
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\end_inset
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boxplot(Sepal.Length~Species,data=iris)
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Plain Layout
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\begin_inset Caption
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\begin_layout Plain Layout
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Boxplot of sepal length grouped by species.
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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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\end_layout
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\begin_layout Chunk
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<<engine=S4>>=
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\begin_inset Newline newline
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\end_inset
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function.that.comes.only.with.Splus(x)
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Standard
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\begin_inset Float figure
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wide false
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sideways false
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status open
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\begin_layout Chunk
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\align center
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<<fig=true>>=
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\begin_inset Newline newline
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\end_inset
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boxplot(Sepal.Length~Species,data=iris)
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\begin_inset Newline newline
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\end_inset
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@
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\end_layout
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\begin_layout Plain Layout
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\begin_inset Caption
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\begin_layout Plain Layout
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Boxplot of sepal length grouped by species
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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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\end_layout
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\end_body
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\end_document
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