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...ith GeneSpring} \maketitle \copyright{2003 Silicon Genetics} \section{Introduction} This package contains a number of functions to facilitate the integration of R code into the Gene Expression analysis program GeneSpring, by Silicon Genetics. Available functions include: \begin{itemize} \item \texttt{GSload.int()} - Read GeneSpring experiment interpretation from file and return a GeneSpring gene expression object (GSint) \item \texttt{GSload.intBC()} - Read GeneSpring experiment interpretation from file and return a BioConductor gene expressioon object (exprSet) \item \texttt{GSload.exp()} - Re...

...t #------------------------------------------------------------------------------# The file "QC.begin.Rnw" is as follows: \documentclass{article} \textwidth=6.2in \textheight=8.5in %\parskip=.3cm \oddsidemargin=.1in \evensidemargin=.1in \headheight=-.3in \newcommand{\Rfunction}[1]{{\texttt{#1}}} \newcommand{\Rmethod}[1]{{\texttt{#1}}} \newcommand{\Rcode}[1]{{\texttt{#1}}} \newcommand{\Robject}[1]{{\texttt{#1}}} \newcommand{\Rpackage}[1]{{\textsf{#1}}} \newcommand{\Rclass}[1]{{\textit{#1}}} \newcommand{\Cclass}[1]{{\textit{#1}}} \newcommand{\Rexten}[1]{{\textit{#1}}} \newcommand{\xps}...

...R commands into LaTeX in-line? (That is, not using Sweave.) For example, suppose I wish to place in my document this instruction: ...is done in R using the command \verb|lm( y ~ var.one + var.two )| as follows: I used \verb above, but I see three options: \verb, \url (package url), or \texttt; there are probably others. Here are my comments on these three: - Using \texttt is OK, but it disappears my tildes and can hyphenate - Using \verb is good, but it can hyphenate. - Using \url is very good, but it: * disappears my spaces; so for the above example, the spaces added for clarity ar...

Hi all, I've got a basic question regarding package documentation and rd.sty. I wrote my first own package, and now I would like to place the documentation into the appendix of another LaTex document. Seemingly I cannot simply \usepackage{Rd}, as this will modify the page-settings of my document. Is there a minimum style file which will just define the environments and commands needed for

...;>>>>>>>>>>>>>>>>>>>>>>>>>> example-windows.Rnw \documentclass[a4paper]{article} \begin{document} \noindent This is an example of what I can do on Windows. Unhappily, I seem to be able to squeeze marginally more out of \texttt{Sweave} \emph{chez\/} Bill Gates than I can under Linux. Ho, hum. <<echo=false,results=hide>>= # create a simple AR process: make.ar.1<- function(alpha=1,n=300) { Z<- rnorm(n); Y<- numeric(n); Y[1]<- Z[1]; for (i in 2:n) Y[i]<- alpha*Y[i-1]+Z[i]; return(Y...

...\documentclass[a4paper]{article} \title{R tips and tricks} \author{Murray Jorgensen} \usepackage{Sweave} \begin{document} \maketitle \section*{Entering data from a single variable} The following data are transformed tensile strength measurements on polyester fibres. They may be found on the file \texttt{TENSILE.DAT}. We may enter this data into R using the \texttt{scan} command. <<>>= strength <- scan() 0.023 0.032 0.054 0.069 0.081 0.094 0.105 0.127 0.148 0.169 0.188 0.216 @ \end{document} and now I attempt to use SWeave to convert it to minimal.tex: > Sw...

...itor at uni-bonn.de Institute for Medical Microbiology and Immunology, Bonn *** /opt/R-release/doc/manual/Rd.sty Wed Jun 17 01:17:00 1998 --- Rd.sty Sun Jul 5 18:38:43 1998 *************** *** 40,46 **** \begin{tabular}{c} \hline \rule[-0.275cm]{0cm}{0.8cm} \makebox[1in][l]{\texttt{#1}} ! \makebox[\middle]{\emph{#2}} \makebox[1in][r]{\texttt{#1}} \\ \hline \end{tabular} \end{center}} --- 40,51 ---- \begin{tabular}{c} \hline \rule[-0.275cm]{0cm}{0.8cm} \makebox[1in][l]{\texttt{#1}} ! \makebox[\middle]{ ! \begin{minipa...

...sfully run some example *.Rnw files through Sweave and generate pdf files. When I try my own example file, "test.Rnw": \documentclass[a4paper]{article} \title{Test Sweave Example} \author{Thomas Adams} \begin{document} \maketitle In this example we embed parts of the examples from the \texttt{boxplot} and \texttt{lattice} figures into a \LaTeX{} document <<>>= library(verification) library(lattice) dat<-read.table("verification_summary_20051024_table.txt",sep="\t",header=TRUE) \begin{center} <<fig=TRUE,echo=FALSE>>= boxplot(dat$MAE ~ dat$BA...

This is version 0.5 of the virtio-iommu specification, the paravirtualized IOMMU. This version addresses feedback from v0.4 and adds an event virtqueue. Please find the specification, LaTeX sources and pdf, at: git://linux-arm.org/virtio-iommu.git viommu/v0.5 http://linux-arm.org/git?p=virtio-iommu.git;a=blob;f=dist/v0.5/virtio-iommu-v0.5.pdf A detailed changelog since v0.4 follows. You can find

This is version 0.5 of the virtio-iommu specification, the paravirtualized IOMMU. This version addresses feedback from v0.4 and adds an event virtqueue. Please find the specification, LaTeX sources and pdf, at: git://linux-arm.org/virtio-iommu.git viommu/v0.5 http://linux-arm.org/git?p=virtio-iommu.git;a=blob;f=dist/v0.5/virtio-iommu-v0.5.pdf A detailed changelog since v0.4 follows. You can find

...hics/ % Sweave shell script defined as echo "Sweave(\"$1.nw\")" | R --no-save % latex or pdflatex model; bibtex model; latex or pdflatex model % To get .R file: Stangle model \documentclass{article} \usepackage{relsize,setspace} % used by latex(describe( )) \newcommand{\co}[1]{\texttt{\smaller #1}} \title{Analysis} \author{Frank E Harrell Jr} \begin{document} \SweaveOpts{prefix.string=graphics/plot} \setkeys{Gin}{width=1.0\textwidth} \maketitle <<echo=F>>= Hmisc.version <- package.description('Hmisc')['Version'] Design.version <- package.descr...

...= -0.69 \end {Sinput} \end {Schunk} \end { beamer at frameslide}\ifbeamer at twoscreenstext \beamer at dosecondscreennow {{fragile} \frametitle {Numbers} \textbf {Numbers} can be represented in a variety of dif ferent formats. For example the number $1.2345\times 10^5$ is written as 1.234e +05 in \texttt {R}. \begin {Schunk} \begin {Sinput} > a = 123450 > b = -0.69 \e nd {Sinput} \end {Schunk} }\fi \ifbeamer at anotherslide \advance \beamer at slideinf rame by 1\relax \relax \expandafter \iterate \fi \let \iterate \relax \beamer at w riteslidentry \beamer at reseteecodes ' between \begin{...

...===================== sweaveexample.tex: ============================== \documentclass[a4paper]{article} \title{Sweave Example 1} \author{Friedrich Leisch} \usepackage{C:/PROGRA~1/R/R-26~1.2/share/texmf/Sweave} \begin{document} \maketitle In this example we embed parts of the examples from the \texttt{kruskal.test} help page into a \LaTeX{} document: \begin{Schunk} \begin{Sinput} > data(airquality) > library(ctest) > kruskal.test(Ozone ~ Month, data = airquality) \end{Sinput} \begin{Soutput} Kruskal-Wallis rank sum test data: Ozone by Month Kruskal-Wallis chi-squared = 29.2666, df...

...ositioning of the caption below breaklines=true,% automatic line breaking escapeinside={(*}{*)},% escaping to LaTeX fancyvrb=true,% verbatim code is typset by listings extendedchars=false,% prohibit extended chars (chars of codes 128--255) literate={"}{{\texttt{"}}}1{<-}{{$\leftarrow$}}1{<<-}{{$\twoheadleftarrow$}}1 {~}{{$\sim$}}1{<=}{{$\le$}}1{>=}{{$\ge$}}1{!=}{{$\neq$}}1{^}{{$^\wedge$}}1,% item to replace, text, length of chars alsoletter={.<-},% becomes a letter alsoother={$},% becomes other otherk...

Hi R Gurus: I'm putting together an article about some R stuff in Latex. I refer to packages and functions. I think that I use {\em} for packages and {\tt} for functions. Is that correct, please? Thank you in advance! Sincerely, Edna Bell

...t File} \author{Friedrich Leisch} \SweaveOpts{echo=FALSE} \begin{document} \maketitle Now we look at Gaussian data: <<>>= library(stats) x <- rnorm(20) print(x) print(t1 <- t.test(x)) @ Note that we can easily integrate some numbers into standard text: The third element of vector \texttt{x} is \Sexpr{x[3]}, the $p$-value of the test is \Sexpr{format.pval(t1$p.value)}. % $ \end{document} My commands: > R.version.string [1] "R version 1.9.1, 2004-06-21" > library(R2HTML) Loading R2HTML package... > Sweave("Sweave-test-1_short.Rnw") Writing to file Swea...

...r me? Thanks, Sachin p.s. sorry about the corporate notice. example-1.Rnw: from http://www.statistik.lmu.de/~leisch/Sweave/ \documentclass[a4paper]{article} \title{Sweave Example 1} \author{Friedrich Leisch} \begin{document} \maketitle In this example we embed parts of the examples from the \texttt{kruskal.test} help page into a \LaTeX{} document: <<>>= data(airquality) library(ctest) kruskal.test(Ozone ~ Month, data = airquality) @ which shows that the location parameter of the Ozone distribution varies significantly from month to month. Finally we include a boxplot of the data:...

...r despite searching "everywhere". I couldn't find a followup to the question. I've written an instruction manual introducing R to my institute's students, which includes the suggestion to use this command, e.g. For example, to see what's in the geostatistical package \texttt{gstat}: \begin{verbatim} > package.contents("gstat") \end{verbatim} but now they see an off-putting "deprecated" message. Please advise. D G RossiterD G Rossiter Senior University Lecturer Department of Earth Systems Analysis (DESA) International Institute for Geo...

...ge Vignettes" by Friedrich Leisch. I am using a windows XP machine (other session info below). Here is what I have done. 1) I add the 'inst/doc' directory to the package source tree. 2) I have added the following information in the preamble of the .Rnw file % \VignetteIndexEntry{An \texttt{R} Package for Miscellaneous Psychometric Analyses} % \VignetteDepends{MiscPsycho, statmod} % \VignetteKeyword{misc} 3) I then copy the file "MP.Rnw" to the 'inst/doc' directory. 4) I then run Rcmd build g:\MiscPsycho The process begins as usual and it even tries to create the v...

I created a tex file following the example in the Sweave help which produced the following files in my working directory. Sweave-test-1-006.eps Sweave-test-1-006.pdf Sweave-test-1-007.eps Sweave-test-1-007.pdf Sweave-test-1.tex When I run latex on this, I get a latex error, log file below. I am running R 2.1.1 on Windows XP. I have installed "small MiKTeX" and I have added