#LyX 2.0.0svn created this file. For more info see http://www.lyx.org/ \lyxformat 410 \begin_document \begin_header \textclass article \use_default_options true \begin_modules sweave \end_modules \maintain_unincluded_children false \language english \inputencoding auto \fontencoding global \font_roman lmodern \font_sans lmss \font_typewriter lmtt \font_default_family default \use_non_tex_fonts false \font_sc false \font_osf false \font_sf_scale 100 \font_tt_scale 100 \graphics default \default_output_format default \output_sync 0 \bibtex_command default \index_command default \paperfontsize default \spacing single \use_hyperref false \papersize default \use_geometry false \use_amsmath 1 \use_esint 1 \use_mhchem 1 \use_mathdots 1 \cite_engine basic \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false \use_refstyle 0 \index Index \shortcut idx \color #008000 \end_index \secnumdepth 3 \tocdepth 3 \paragraph_separation skip \defskip medskip \quotes_language english \papercolumns 1 \papersides 1 \paperpagestyle default \tracking_changes false \output_changes false \html_math_output 0 \html_be_strict false \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 <>= \end_layout \begin_layout Chunk 1:10 \end_layout \begin_layout Chunk <>= \end_layout \begin_layout Chunk print(1:20) \end_layout \begin_layout Chunk @ % 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 <>= \end_layout \begin_layout Chunk 1 + 1 \end_layout \begin_layout Chunk 1 + pi \end_layout \begin_layout Chunk sin(pi/2) \end_layout \begin_layout Chunk @ \end_layout \begin_layout Standard Now we look at Gaussian data: \end_layout \begin_layout Chunk <<>>= \end_layout \begin_layout Chunk library(stats) \end_layout \begin_layout Chunk x <- rnorm(20) \end_layout \begin_layout Chunk print(x) \end_layout \begin_layout Chunk print(t1 <- t.test(x)) \end_layout \begin_layout Chunk @ \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 <>= \end_layout \begin_layout Chunk # A comment \end_layout \begin_layout Chunk data(iris) \end_layout \begin_layout Chunk summary(iris) \end_layout \begin_layout Chunk @ % def \end_layout \begin_layout Standard \begin_inset Float figure placement tbph wide false sideways false status open \begin_layout Plain Layout \noindent \align center \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout library(graphics) \end_layout \begin_layout Plain Layout pairs(iris) \end_layout \begin_layout Plain Layout @ \end_layout \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 open \begin_layout Plain Layout \noindent \align center \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout boxplot(Sepal.Length~Species,data=iris) \end_layout \begin_layout Plain Layout @ \end_layout \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 <>= \end_layout \begin_layout Chunk function.that.comes.only.with.Splus(x) \end_layout \begin_layout Chunk @ \end_layout \begin_layout Standard \begin_inset Float figure wide false sideways false status open \begin_layout Plain Layout \noindent \align center \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout boxplot(Sepal.Length~Species,data=iris) \end_layout \begin_layout Plain Layout @ \end_layout \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