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