Minimal example of a Rmd file that can be processed to produce both pdf and html output through pandoc, using two different file formats for the figures.

knit

#!/usr/bin/Rscript

require(knitr)
lf <- commandArgs(trailingOnly = TRUE)
if(!length(lf))
 lf = list.files(pattern="\\.rmd")
for (f in lf)
 try(knit(f))

md = paste0(sub("\\.[[:alnum:]]*$", "", lf), ".md")

for (f in md){
try({
  knitr::pandoc(f, c("html", "latex"))
  })

}

template.rmd

%knitr template
%baptiste Auguié
%`r format(Sys.time(), "%d %B, %Y")`

<!--pandoc
s: 
S:
toc:
number-sections: 

format: html
mathjax: 
default-image-extension: png

format: latex
latex-engine: xelatex
default-image-extension: pdf
-->

```{r setup, echo=FALSE,results='hide',cache=FALSE}
library(knitr)
opts_chunk$set(cache=TRUE, fig.width=c(10, 8),
               dev=c('png','pdf'), echo=FALSE,
               warning=FALSE, error=TRUE, message=FALSE, tidy=FALSE)
opts_knit$set('upload.fun' = function(x) sub("\\.[[:alnum:]]*$", "", x) ) 
```

# First section

_Lorem ipsum dolor sit amet, mea enim exerci deserunt in. Zril legimus at vel. His ut nusquam fabellas, vero suscipit eos in, per an quem apeirian explicari. Sea ex prompta fastidii consetetur. Ut eos nostrud definiebas, ut probatus singulis vel, sed an errem ponderum elaboraret._

## Markdown features

- first item

- second item

$$
\frac{\alpha}{\infty} = \int_0^\beta f(x) dx
$$

# Plots

```{r}
plot(1:10, cumsum(runif(10)))
```