Sublime knitr

• Version: 1.2.2
• Date: January 30, 2015

This package provides knitr Markdown and LaTeX support in Sublime Text 2 and 3. It comes with:

• Language definitions for knitr LaTeX and Markdown files
• A build system for R Markdown files.
• The following commands (available via the command palette and with keyboard shortcuts):
  • Insert knitr chunk snippet: super+alt+c
  • Move between chunks: super+alt+, and super+alt+.
  • Send chunk to R GUI: super+b (requires R-Box)

By default, ctrl is used in place of super on Windows and Linux.

Dependencies

In order to use all the features of this package, you'll need to install two other packages. Both are easily installable via Package Control:

• R-Box
• SendTextPlus
• LaTeXing or LaTeXTools (see patch below for LaTeXTools)

The easiest way to use this plugin is to use LaTeXing, especially since development on LaTeXTools has slowed significantly. Simply enable the knitr setting and adjust the command in knitr_command if required.

Alternatively, you can use this plugin with LaTeXTools, with three manual patches, listed below.

Building R Markdown files

Building an .Rmd file creates an .md file in the same directory. It's up to you to use that file elsewhere (i.e. use Pandoc to convert it .html, .docx, .rtf, or even .tex if you feel like being extra circuitous).

There is also a build variant that will create an HTML file from the knitted Markdown file. Use this with super + shift + b.

I typically build the .Rmd file once, open the resulting .md file in Marked, and then leave it open in Marked as I make further changes and newer builds.

Alternatively, you can force the build system to open the resulting .md file in the default program for Markdown files by changing the "cmd": line in knitr-Markdown.sublime-build to:

"cmd": [ "Rscript -e \"library(knitr); knit('$file_name')\"; open $file_base_name.md" ],

Unicode and other encoding issues

Working with non-ASCII characters in plots is a little tricky because of how LaTeX and R differently support Unicode. Here's are some general guidelines for fixing character encoding issues:

1. Add LANG=en_US.UTF-8 to ~/.Renviron (create this file if needed). This will ensure that R runs with Unicode support whenver it opens.
2. Add a separate chunk near the beginning of your document with this: pdf.options(encoding = '<encoding>'), where encoding is any of those listed in the output of this command: list.files(system.file('enc', package = 'grDevices')). Choose an encoding that encompasses all the characters you're using in your plots.
3. If using .Rnw and LaTeX, ensure that \usepackage[utf8]{inputenc} is in your preamble.

Roadmap and wish list

• Better Markdown syntax highlighting, including Multimarkdown and Pandoc extras like footnotes, tables, and citations.
• Create commands for Pandoc conversion from R Markdown to other formats? (or maybe just use actual Pandoc packages for that).

Manual patch for LaTeXTools

If you want to use the LaTeXTools plugin, you need to patch three files to make the standard LaTeXTools build system knit and typest the .Rnw file. Make these three changes (huge thanks to Heberto del Rio for this!):

Important: Copying and pasting code from GitHub can do unexpected things to indentation (replacing tabs with spaces) and can temporarily break LaTeXTools. Make sure the indentation is correct after pasting.

File 1: Packages/LaTeX/LaTeX.tmLanguage

Add Rnw to the list of accepted LaTeX file types, like so:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>fileTypes</key>
    <array>
        <string>tex</string>
        <string>Rnw</string>
    </array>

Instructions for Sublime Text 3: In ST3, default packages are hidden deep within ST itself and are difficult to access, let alone edit. However, you can still get to LaTeX.tmLanguage relatively easily if you install the PackageResourceViewer plugin. After installing it, run the “PackageResourceViewer: Open Resource:” command through the command pallete (command/ctrl + shift + p) and navigate to LaTeX.tmLanguage. After making changes, ST will save a copy of the file in a more accessible location (Packages/LaTeX/LaTeX.tmLanguage), overriding the default built-in file.

File 2: Packages/LaTeXTools/makePDF.py

Find this:

if self.tex_ext.upper() != ".TEX":
    sublime.error_message("%s is not a TeX source file: cannot compile." % (os.path.basename(view.file_name()),))
    return

And replace with this:

if (self.tex_ext.upper() != ".TEX") and (self.tex_ext.upper() != ".RNW"):
    sublime.error_message("%s is not a TeX or Rnw source file: cannot compile." % (os.path.basename(view.file_name()),))
    return

Then find this:

# We should now be able to construct the builder object
self.builder = builder_class(self.file_name, self.output, builder_settings, platform_settings)

And replace with this:

if self.tex_ext.upper() == ".RNW":
    # Run Rscript -e "library(knitr); knit('" + self.file_name + "')"
    os.system("Rscript -e \"library(knitr); knit('"+ self.file_name +"')\"")
    self.file_name = self.tex_base + ".tex"
    self.tex_ext = ".tex"

# We should now be able to construct the builder object
self.builder = builder_class(self.file_name, self.output, builder_settings, platform_settings)

(If you want to use Sweave instead of knitr, change the Rscript command accordingly.)

File 3: Packages/LaTeXTools/jumpToPDF.py

Find this:

if texExt.upper() != ".TEX":
    sublime.error_message("%s is not a TeX source file: cannot jump." % (os.path.basename(view.fileName()),))
    return

And replace with this:

if (texExt.upper() != ".TEX") and (texExt.upper() != ".RNW"):
    sublime.error_message("%s is not a TeX or Rnw source file: cannot jump." % (os.path.basename(view.fileName()),))
    return

File 4: Packages/LaTeXTools/viewPDF.py

Find this:

if texExt.upper() != ".TEX":
    sublime.error_message("%s is not a TeX source file: cannot view." % (os.path.basename(view.fileName()),))
    return

And replace with this:

if (texExt.upper() != ".TEX") and (texExt.upper() != ".RNW"):
    sublime.error_message("%s is not a TeX or Rnw source file: cannot view." % (os.path.basename(view.fileName()),))
    return

If you want to be able to use multiple files and to find your bib file, you'll also need to change the following files:

File 5: Packages/LaTeXTools/getTeXRoot.py

Find this:

mroot = re.match(r"%\s*!TEX\s+root *= *(.*(tex|TEX))\s*$",line)

And replace with this:

mroot = re.match(r"%\s*!TEX\s+root *= *(.*(tex|rnw))\s*$",line, flags=re.IGNORECASE)

File 6: Packages/LaTeXTools/latex_cite_completions.py

Find this:

if src[-4:].lower() != ".tex":

And replace with this:

if src[-4:].lower() not in [".tex",".rnw"]: