# Sweave and LaTeX

The following file are to help you start to learn and use both Sweave and LaTeX:
• Sweave Manual: Sweave-manual-20050606.pdf
• Example .nw Sweave files used in the Sweave manual:
• Not So Short Intro to LaTeX: lshort.pdf
• Some Sweave and LaTeX basics: ex.sweave.latex.nw
• Useful \usepackage statements, modified title, and modified page numbering: Latex.template.nw

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:
Warning message:
incomplete final line found by readLines on blah.nw'
2. 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).
3. 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:
#!/bin/sh
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).
4. 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 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 (click here). You can also view the output in a browser such as konqueror and copy and paste it into an OpenOffice document and save in a variety of formats including Word.
5. See the following 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: RCitation.nw:
• The needed .bib` file to create and reference: Rbiblioref.bib
Edit | Attach | Print version |  | Backlinks | View wiki text | Edit WikiText | More topic actions...
Topic revision: r6 - 08 Nov 2006, TheresaScott

• Biostatistics Webs

Copyright © 2013-2022 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Vanderbilt Biostatistics Wiki? Send feedback