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---+ =Sweave= and =LaTeX= The following file are to help you start to learn and use both =Sweave= and =LaTeX=: * =Sweave= Manual: [[%ATTACHURL%/Sweave-manual-20050606.pdf][Sweave-manual-20050606.pdf]] * Example =.nw= =Sweave= files used in the =Sweave= manual: * [[%ATTACHURL%/example-1.nw][example-1.nw]]: Example =Sweave .nw= file 1 * [[%ATTACHURL%/example-2.nw][example-2.nw]]: Example =Sweave .nw= file 2 * [[%ATTACHURL%/example-3.nw][example-3.nw]]: Example =Sweave .nw= file 3 * Not So Short Intro to =LaTeX=: [[%ATTACHURL%/lshort.pdf][lshort.pdf]] * Some =Sweave= and =LaTeX= basics: [[%ATTACHURL%/ex.sweave.latex.nw][ex.sweave.latex.nw]] * Results of the =Sweave= and =LaTeX= basics: [[%ATTACHURL%/ex.sweave.latex.pdf][ex.sweave.latex.pdf]] * Useful =\usepackage= statements, modified title, and modified page numbering: [[%ATTACHURL%/Latex.template.nw][Latex.template.nw]] ---++ Some Helpful Tips: 1 You need to add a blank line (with no extra spaces) after the =\end{document}= expression if you get the following error from =Sweave=:<br> =Warning message:= <br> =incomplete final line found by readLines on `blah.nw'= 1 _Commenting_ in your =.nw= file: * Use =%= (percent) signs (the =LaTeX= comment symbol) to comment out lines of text and whole R code chunks (i.e., from the =<<>>== to the =@= headers). * Use =#= (number) signs (the R comment symbol) to comment out lines of R code _within_ an R code chunk (i.e., between the =<<>>== to the =@= headers). 1 To setup =Sweave= to run outside of R (i.e., from a konsole command prompt): * Open a Konsole window. * Change to the =~/bin= (i.e., =/home/scottt/bin=) directory: =cd ~\bin= * List the =~/bin= directory to see if a =Sweave= shell script is already present: =ls= * If =Sweave= is listed in the contents of the directory, open =Sweave= in a text editor (here I use =pico=): =pico Sweave= 1 If =Sweave= is not present, open a new file to be named =Sweave= in a text editor (again using =pico=): =pico Sweave= * If =Sweave= was already present, make sure the opened file contains the following two lines (make sure it matches exactly). If =Sweave= was not present, type the following lines in the text editor: <br> =#!/bin/sh= <br> =echo "library(tools) ; Sweave(\"$1.nw\")" | R --no-save --no-restore= * Exit =pico= by typing =Ctrl+X= to save the =Sweave= file (answer =Yes= to saving changes, and keep the name of the file as =Sweave=). * At the command prompt type the following to initiate =Sweave= as a shell script: =chmod +x= * Change your 'path' to include the =~/bin= directory. * Change to your 'home' directory: =cd ~= * Open your =.bashrc= (a hidden file) in a text editor: =pico .bashrc= * In the text editor, type a new line at the end of the file: =export PATH=$PATH:~/bin= * Exit =pico= by typing =Ctrl+X= to save your =.bashrc= file (answer =Yes= to saving changes, and keep the name of the file as =.bashrc=). 1 Converting Sweave files (Frank's 7/26/06 email): * Some of you have needed to give reports created using Sweave to collaborators so they can extract tables and other components into a manuscript. The best approach I've found is to use tth to convert from <nop>LaTeX to html. The resulting file can be opened in Word or viewed with a web browser, as long as all the graphics files are available. The following twiki page shows how to do this in linux ([[http://biostat.mc.vanderbilt.edu/SweaveConvert][click here]]). You can also view the output in a browser such as konqueror and copy and paste it into an <nop>OpenOffice document and save in a variety of formats including Word. 1 See the following [[%ATTACHURL%/RCitation.pdf][pdf file]] to learn how to incorporate the proper R citation into your =Sweave= documents. * The raw =.nw= file used to create the linked pdf file: [[%ATTACHURL%/RCitation.nw][RCitation.nw]]: * The needed =.bib= file to create and reference: [[%ATTACHURL%/Rbiblioref.bib][Rbiblioref.bib]]
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Topic revision: r6 - 08 Nov 2006,
TheresaScott
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