SweaveLatex < Main < Vanderbilt Biostatistics Wiki

---+ =Sweave= =knitr= and !LaTeX

---++ Introduction and Helpful Templates:
The following will help you start to learn and use =knitr= =Sweave= and =LaTeX=:
   * =[[KnitrHowto][knitr]]= howto and template
   * An introductory lecture to 'Reproducible Research with R, <nop>LaTeX, & Sweave' can be found [[TheresaScott][here]]
   * An extended example of a Sweave source file ([[%ATTACHURL%/extended.example.nw][extended.example.nw]]) and its output ([[%ATTACHURL%/extended.example.pdf][extended.example.pdf]])
   * An extended example of the =LaTeX= "preamble" to use in your .nw file: [[%ATTACHURL%/Sweave.Template.nw][Sweave.Template.nw]]
   * The =Sweave= Manual and _example_ .nw =Sweave= files used in the =Sweave= manual can be found [[http://www.ci.tuwien.ac.at/~leisch/Sweave/][here]].
   * Not So Short Intro to =LaTeX= can be found [[http://www.ctan.org/tex-archive/info/lshort/english/lshort.pdf][here]].
   * A [[SweaveTemplate][template]] in which everyone can edit their latest ideas
   * Frank Harrell's handout [[%ATTACHURL%/fhsweave.pdf Sweave for Reproducible Research and Beautiful Statistical Reports]]
   * [[%ATTACHURL%/fhsweaveEx.pdf LaTeX and R code exemplifying the above]]
   * [[BeamerTemplate][Template for Presentations and Handouts using LaTeX, Beamer, and a PDF Viewer]]
   * How to [[http://andreas.kiermeier.googlepages.com/essmaterials run =Sweave= from within Emacs]] 
   * [[http://www.stat.auckland.ac.nz/~stat782/downloads/Sweave-customisation.pdf Customizing Sweave]]
   * Charles Geyer's excellent [[http://www.stat.umn.edu/~charlie/Sweave page on Sweave]]
   * Excellent material from [[http://bioinformatics.mdanderson.org/tutorial.html Keith Baggerly]]
   * [[http://book-by-sweave.wikidot.com Useful material]] on using Sweave to create a book
   * [[http://blog.revolutionanalytics.com/2010/12/how-to-create-pdf-reports-with-r.html Excellent Sweave tutorials]] including how to use =makefiles=

---++ 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 run =Sweave= as a batch process outside of R (i.e., from a =konsole= command prompt), run this command: =R CMD Sweave foo.Rnw= , replacing =.Rnw= with =.nw= or whatever you use for the file suffix.   You may want to run this command after R finishes if you have set up to use a directory =graphics= and forgot to tell =Sweave= not to create =.eps= files when you are using =pdflatex= : =rm -f Rplots.ps graphics/*.eps=
   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]]
   1 The following code in an example of how to use an =upData()= function invocation to generate a long variable label that will automatically _wrap_ in the =LaTeX= version of a =summary.formula()= (with =reverse = TRUE=) table.  The =strwrap()= function =width== argument will dictate how wide the label is.
<highlight>
x <- data.frame(var1 = sample(1:100, size = 250, replace = TRUE), 
   group = sample(c("A", "B"), size = 250, replace = TRUE))
x <- upData(x,
  labels = c(var1 = paste(strwrap(paste("This is an extremely long and descriptive",
     "variable label that would normally run off the page.",        
      "Our goal is to break this variable label over multiple lines so we won't have to",
      "truncate the variable label in any way."), width = 60), collapse = "\\\\")))
latex(summary(group ~ var1, method = "reverse", data = x, overall = TRUE, 
   file = "", landscape = TRUE)) 
</highlight>

---++ pgfSweave
=pgfSweave= allows you to use the excellent =tikz= graphics driver that produces !LaTeX code to render R graphics.  To install it do the following:
<verbatim>
install.packages(c('getopt', 'cacheSweave', 'stashR'))
install.packages('pgfSweave', repos='http://R-Forge.R-project.org')
</verbatim>
Soon we will had a template for its use.  For details see http://cran.at.r-project.org/web/packages/pgfSweave.

Topic attachments
I	Attachment	Action	Size	Date	Who	Comment
pdf	fhsweave.pdf	manage	237.1 K	11 May 2010 - 12:01	FrankHarrell	Sweave for Reproducible Research and Beautiful Statistical Reports
Rnw	fhsweaveEx.Rnw	manage	7.5 K	12 Sep 2010 - 12:17	FrankHarrell	Sweave source file for enhanced report
pdf	fhsweaveEx.pdf	manage	199.0 K	11 May 2010 - 12:04	FrankHarrell	Example enhanced report

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