How to compile RMarkdown in Atom

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How to compile RMarkdown in Atom

I love Atom editor and I really wish I could do everything in Atom.

Currently, I mainly work with Python, R, LaTeX and sometime RMarkdown and I haven’t found ANY editor that could EVERYTHING in the best way. You might want to argue that different editors have their specific audiences and targeted languages in mind, and we shouldn’t expect One Editor to Rule Them ALL. Alas, this is true. But since I have (finally) settled down to use Atom for my daily LaTeX writing (because of the snippets support and sync-settings package to synchronize Atom settings across machines), and I would like to use Atom for RMD writing as well.

Now, can we knit RMD files within Atom editor, just like what we can achieve in RStudio, where you click the knitr button?

This question has been puzzling me since I first knew RMD, and it seems that there hasn’t been a mature solution to this problem. After some frustration, I could finally come up with my solution and it would worth putting it down so that it may help someone in the future.

There are several packages to be used for this purpose:

  1. language-markdown
  2. markdown-preview-enhanced
  3. language-r
  4. atom-shell-commands

Here the first package will enable language support for Markdown families, which includes RMarkdown. (Click: control-shift-l and choose Markdown from the dropdown list).

The second package will generate a preview for your current markdown file.

The third package will enable syntax hightlighting for R. Note that this package will throw an error whenever you opened up Atom, saying that there is duplicate keys. Since this package is no longer maintained, we cannot expect it to be updated so that this issue will go away automatically. Instead we need to manually modify the file ~/.atom/packages/language-r/snippets/language-r.cson and change the following lines as shown:

At line 14-19:

'Cummulative min':
  'prefix': 'cumi'
  'body': 'cummin(${1:x})'
'Cummulative max':
  'prefix': 'cuma'
  'body': 'cummax(${1:x})'

At line 47-52:

  'prefix': 'grep'
  'body': 'grep(${1:pattern}, ${2:x}, ${ = ${4:FALSE}}, ${5:perl = ${6:FALSE}})'
'Grep 2':
  'prefix': 'grep2'
  'body': 'grep(${1:pattern}, ${2:x}, ${ = ${4:FALSE}}, ${5:perl = ${6:FALSE}}, ${7:value = ${8:FALSE}}, ${9:fixed = ${10:TRUE}})'

This way, there is no duplicate keys error anymore.

The fourth package is the crucial part. The first three packages are there because of aesthetic reasons, and you can live without them. But this fourth package is really the one that will allow us to compile the RMD file. Once you have installed this package, click Atom-Config (on macOS) or Edit-Config (on Ubuntu) and copy paste the following commands into the config.cson file.

  commands: [
      arguments: [
      command: "R"
      name: "knitRmd"
        cwd: "{FileDir}"
        keymap: "ctrl-2"
        save: true

Note that if you have R installed properly and rmarkdown package installed, this should work fine. The command field you should put the path for the R executables, and if you open up a terminal, type “R” and return and observe you are inside R environment, then you should be fine. Otherwise, change this path to the one that actually works for you. In options, you can also change the “keymap.” The default is “ctrl-2,” but you can change to whatever you like. Just to make sure that there is not conflict with other keymaps.

Voila! Now you are done!

You can try to click ctrl-2 at your RMD file, and the output should be compiled in the same folder as your RMD file.

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