Including R data and plots in a Latex document with knitr

knitr default typesetting:

"The chunk option out.width is set to '\\maxwidth' by default if the output format is LaTeX."

Add a table of content to HTML files generated from R Markdown

Update November 2014

With the new version of knitr and Rmarkdown, the custom function is not necessary anymore. One can add a yaml at the beginning of a Rmd file:

---
title: "Development scrap concerning the input data"
output:
  html_document:
    toc: true
---

Old content from January 2014

Knitr creator Yihui explained in a comment on this forum how to add a table of content to a Rmd file using the knit2html() function:

library(knitr)
knit2html('docs/clean.example.Rmd', options = c('toc', markdown::markdownHTMLOptions(TRUE)))

I followed the RSTUDIO advice on how to customize markdown rendering.
A .Rprofile  at the root of my project directory with the following content does the tric:

options(rstudio.markdownToHTML =
  function(inputFile, outputFile) {     
    require(markdown)
    htmlOptions <- defaults="TRUE)<br" markdownhtmloptions="">    htmlOptions <- br="" c="" htmloptions="" toc="">    markdownToHTML(inputFile, outputFile, options = htmlOptions)
  }
)

I works, I can now use the RStudio button "knit html" or the shortcut CTRL+SHIFT+H and get an html file that includes a table of content!