knitr - set chunk options *outside* document?

knitr, r

Solution

It is possible to set global options outside a document, and the `dev` option is the only exception. When the output is HTML, the `dev` is (re)set to `'png'` internally by `render_markdown()`. If you want to change this option, you have to call this function before it:

knit2 <- function (input, out=c('pdf', 'html')) {
  if (out == 'html') {
    render_markdown()
    # use SVG for HTML output
    opts_chunk$set(dev='svg')
  }

  # knit to md
  o <- knit(input)

  # knit md to html or pdf
  pandoc(input=o, format=ifelse(out == 'pdf', 'latex', 'html'))
}

Actually I have had a very similar problem, and illustrated this in the example 084 (see `084-pandoc.R` there; I changed `dev` to `'pdf'` for Markdown).

Problem

I'm trying to set a global chunk option outside my call to `knit` like so: ``` opts_chunks$set(dev='pdf') knit(input) ``` However, it isn't working, as `knit` seems to use a fresh set of `opts_chunks` within `knit`. Is it possible to set a global chunk option outside a call to `knit`, and have it apply for the call to `knit`? Reason I'm doing this: I'm writing `Rmd` (R markdown) documents, and I want to be able to knit these to pdf or HTML, my choice, like so: ``` knit2 <- function (input, out=c('pdf', 'html')) { # set the appropriate output image format opts_chunk$set(dev=ifelse(out == 'pdf', 'pdf', 'svg')) # <-- # knit to md o <- knit(input) # knit md to html or pdf pandoc(input=o, format=ifelse(out == 'pdf', 'latex', 'html')) } ``` So the idea is that I can `knit2('mydoc.Rmd', 'pdf')` OR `knit2('mydoc.Rmd', 'html')` and I don't have to change the Rmd depending on the output. The problem I encountered was that I want my images to be SVG for HTML output, and PDF for PDF output (I wanted vector graphics but SVG doesn't work in Latex, and pdf doesn't work in HTML, so I need to modify this based on the output format), i.e. ``` opts_chunk$set(dev=ifelse(out == 'pdf', 'pdf', 'svg')) ``` I know that if I put this in a chunk in my Rmd file along with a definition of `out`, it will work. However, I don't want to embed this within `mydoc.Rmd`, as I can't assign `output` until `knit2` is called an I know what output I actually want. Hence, I want knit2 to somehow set the `dev` option for me before calling `knit` and have that option apply for th duration of the `knit`. (I would also accept embedding my `opts_chunk$set(dev=ifelse(out=='pdf', 'pdf', 'svg'))` into my Rmd file, provided that I could define `out` outside the Rmd file, i.e. in `knit2`, although if I can handle it all from `knit2` I'd prefer that)

Original source