Retain code highlighting when converting .Rmd to .md - github

Question

I have an .rmd file that I want to put on GitHub. In order for the results to be visible along with the code I converted my .rmd file to .md via RStudio.
After conversion, however, the (r-)code is not highlighted anymore, when I view the .md file on GitHub. I noticed that a code block in the .md file is identified by indending 4 times instead of three backticks + language definition. So obviously the language definition from the .rmd file gets lost.
How can I fix this?
Note: To reproduce you can just open a new .rmd file in RStudio and change the YAML header to:
---
title: "TestRun"
output:
md_document:
variant: markdown_github
---
Help is much appreciated!

Answer 1

Indentation is important in YAML.
Here's an example from the R Markdown documentation:
---
output:
md_document:
variant: markdown_github
---
This YAML document has a mapping with the key output, whose value is a mapping with one key, md_document, whose value is a mapping with one key, variant, whose value is the scalar markdown_github.
The equivalent in JSON (for example) would be:
{ "output": {
"md_document": {
"variant": "markdown_github"
}
}
}
Here's your document (disregarding the title key for clarity):
---
output:
md_document:
variant: markdown_github
---
Your document has a mapping with the key output, whose value is a mapping with two keys, md_document (with an empty or null value) and variant (with the scalar value markdown_github). The JSON equivalent would be:
{ "output": {
"md_document": null,
"variant": "markdown_github"
}
}
See the difference?

Answer 2

Fenced code blocks (backticks + language definition) is a non-standard (although increasingly common) way of marking up code blocks. Therefore, it is not understood by all Markdown implementations. In fact, standard Markdown offers no way to identify the language of a code block. That being the case, when converting to standard Markdown, that info is appropriately lost. If you would like to retain that info, then I would suggest converting to something other that standard Markdown. Although, according to another answer, if you fix your YAML config, then you would be using the non-standard GitHub Flavored Markdown, which does support fenced code blocks.
If you really need standard Markdown, then you may find that a JavaScript highlighting engine will serve you fine. Some of the better JavaScript highlighting engines have pretty good language detection, so you usually don't need to label the language of the code blocks.