Example of producing Tufte latex from knitr Rmd. Use knit('tufteknitr.Rmd') in R, then mmd2pdf tufteknitr.md at command prompt.

tufteknitr.Rmd

latex input:            mmd-tufte-handout-header  
Title:                  Tufte latex from Rmd example
Base Header Level:      2
latex mode:             memoir  
author:                 Jaime Ashander
copyright:              2011 Jaime Ashander
                        This work is licensed under a Creative Commons License.  
                        http://creativecommons.org/licenses/by-nc-sa/3.0/  
latex input:            mmd-natbib-plain
latex input:            mmd-tufte-handout-begin-doc  
latex footer:           mmd-tufte-footer

`r opts_chunk$set(message=FALSE, warning=FALSE, cache=FALSE)`


```{r startup, echo=TRUE, fig.cap="Figure caption"}
plot(0,0)
```

This statement is footnoted[^fn].

[^fn]: Pointlessly.

The "Newest Synthesis" is part of the title of a recent article[#ref1].

[#ref1]: Schoener 2011 _Science_

Note I had to charge through an error (below) to get a pdf from commands listed above in description.

! LaTeX Error: Cannot determine size of graphic in figure/startup.png (no Bound
ingBox).