CODEWITHSUNDEEP
rknitr
Jeromy Anglim
Jeromy Anglim

Reputation: 34937

What command converts knitr R Markdown into Stack-Exchange-friendly Markdown?

Motivation: I often want to paste the results of a quick analysis using R Markdown into a StackExchange site. This includes the R-tag on Stack Overflow, Cross Validated, or even a domain specific analysis on sites like Cognitive Sciences Stack Exchange (e.g., this quick analysis of OECD life index data).

Problems with default conversion: The default markdown output of knitr is not suitable for inclusion on StackExchange. The main problems I can see are that

I.e., the chunks look like this:

```r
some code
```

and output looks like this

```
## some output
## ...
```

There might also be other specific issues to consider, such as

Question

What is a good command for converting R Markdown into Markdown (or HTML) suitable for simple inclusion into Stack Exchange sites?

I think an ideal command would be a one-liner that takes an R Markdown file and generates a file where the entire content can be pasted directly into Stack Exchange to yield a well-formatted question or answer.

I share this simple rmd file with a couple of code chunks, a figure, and an equation as a test example.

Initial thoughts: Hosting of images on imgur would presumably sort out the issue with images. This can be done by including the following in the R Markdown file, but it would probably be simpler if this instruction was incorporated into some one-liner command.

``` {r }
opts_knit$set(upload.fun = imgur_upload) 
````

It might be worth considering whether HTML or Markdown is the better format for pasting into StackExchange. The markdown package provides a lot of flexibility.

Upvotes: 17

Views: 776

Answers (3)

kmcital
kmcital

Reputation: 11

RStudio uses pandoc and so you can specify the markdown variant suitable for your needs. At the start of the .Rmd file:

---
output:
  md_document:
    variant: markdown_strict+autolink_bare_uris
---

You should then be able to copy/paste the resulting file contents into StackExchange.

See: http://rmarkdown.rstudio.com/markdown_document_format.html#markdown-variants

Upvotes: 1

Jeromy Anglim
Jeromy Anglim

Reputation: 34937

Although I'd still like to read other suggestions I hacked together this script using @Ramnath's answer as a starting point. It outputs a HTML fragment rather than Markdown. 

Rscript -e 'rmd_file <- dir(pattern="rmd"); md_file <- sub("rmd", "md", rmd_file); html_file <- sub("rmd", "html", rmd_file); require(methods); require(knitr); require(markdown); opts_knit$set(upload.fun = imgur_upload); knit(rmd_file); markdownToHTML(md_file, html_file, options="fragment_only") '
  • It assumes that there is a single rmd file in the working directory. I imagine that selecting the rmd file could be done in a more sophisticated way.
  • It requires that the knitr and markdown packages are installed.
  • I think because we are using 'Rscript' the methods package needs to be loaded.
  • It uploads images to imgur
  • markdownToHTML exports only the code fragment as a html file. The contents of this file can then be copied into the Stack Exchange answer.

The result looks pretty good. It overcomes the issue of excessive blank lines. However, the output is not markdown, which makes the result harder to edit.

Upvotes: 4

Ramnath
Ramnath

Reputation: 55715

Here is a utility function that should get you started. It sets auto uploads to imgur, as well as markdown rendering of source code using tabs instead of fenced blocks. You can enhance this function to add other options that would be useful.

stackify <- function(rmd_file, ...){
  require(knitr)
  opts_knit$set(upload.fun = imgur_upload) 
  render_markdown(strict = TRUE)
  out <- knit(rmd_file, ...)
  return(invisible(out))
}

UPDATE: I tested this function on your test file, and it renders well on stats.stackexchange.com which is mathjax enabled.

Upvotes: 13

Related Questions