If you want to read a FAViR paper, just go to the papers page, click on the PDF links, and read! If you see something you'd like to be able to do, you can read the associated Sweave (.Rnw) and R (.R) files to see how the author(s) did it.
Each FAViR paper is processed with Sweave and is a combination of R code and LaTeX. The Sweave file is the main source code file. When looking at it, remember that anything between the «…»= and @ markers is R code, and the rest is LaTeX.
You can also read the R code by itself, which is also on the papers page with an .R extension. You'll have less context, but you can probably figure out which code segments produce which exhibits if you follow along in the PDF file. Keep in mind that there are several functions like IncludePrelude, IncludeGraph, and FavirDF which serve only to format the results of R computations in a paper.
Modifying a Paper
If you want to try out a paper on your own data, you either need to install the necessary tools or use an Excel template. If you are making the paper locally, edit the Sweave (.Rnw) file and change the input data as desired. Then recompile the paper and look at the output. The hello world page has details on paper compilation.
If you want to significantly change a paper, the author help section of this wiki may be useful.
Other Help Pages for Readers
Also see authors and the help pages linked there.