Knitr and pandoc-fignos

knitMe.Rmd

```{r set-options}
  my_hook <- function(x, options) {
    if (options$fig.show == 'animate') return(hook_plot_html(x, options))
    "%n%" <- knitr:::"%n%"
    base = opts_knit$get('base.url') %n% ''
    cap = knitr:::.img.cap(options)

    if (is.null(w <- options$out.width) & is.null(h <- options$out.height) &
      is.null(s <- options$out.extra) & options$fig.align == 'default') {
      return(sprintf('![%s](%s%s){#fig:%s} ', cap, base, knitr:::.upload.url(x), options$label))
    }
    # use HTML syntax <img src=...>
    kmitr:::.img.tag(
      knitr:::.upload.url(x), w, h, cap,
      c(s, sprintf('style="%s"', knitr:::css_align(options$fig.align)))
    )
  }
  knit_hooks$set(plot = my_hook)
```

```{r testFigure, fig.cap="This is the figure caption"}
plot(1,1)
```

This is a reference to Figure @fig:testFigure.

The md file can be compiled to html or pdf using pandoc:

pandoc --filter pandoc-fignos knitMe.md -o knitMe.pdf