RNotebooks - The Powerful Polyglot

Markdown was first released in 2004 by John Gruber and Aaron Swartz

It was designed firstly to be human-readable, and secondly to be machine readable. Like YAML in the world of configuration files, Markdown was a response to the failed aspirations of XML to be a human-readable language.

It has become a de-facto standard in many environments, including GitHub, and is available either out-of-the box or as a plug in for many wikis and issue tracking systems.

Quick Markdown Example

- the Polyglot Appears

Simply works.

I've had success with with Anaconda and babun and cygwin should work too.

But, as for the much talked-about feather package that promises efficient file-inter-op between R and python; I totally failed to get that python module to install on Windows 10 Home. It requires a recent C++ compiler to build.

Works, as seen above, but I used the Strawberry Perl as the babun version was getting linker errors.

(The truth is, I probably have too many cygwin-based tools all on my path, and the poor things are getting confused and intertwined in an unpleasant way!)

I use the bash in a babun distribution and it worked well. It's even tolerant of windows-style file names being passed to it. However, it's not tolerant of the full-stop that the RNotebook environment adds to the end of its file names ☹

So, getting bash to work on Windows take a little bit of trickery, especially since the style of invocation is different between the RNotebook environment and the knitr processor.

The following batch file proved to be the key for me:

@rem bash.bat - a Windows batch file for invoking bash from RNotebooks
@echo off
SET BASH_PATH=C:\Users\Derek Slone-Zhen\.babun\cygwin\bin
PATH=%BASH_PATH%;%PATH%
"%BASH_PATH%\bash.exe" < "%~1"

Together with an explicit engine.path for bash blocks to be used by knitr.
(RNotebook processing engine appears to ignore theses.)

knitr::opts_chunk$set(engine.path = list(
  bash = 'C:/Users/Derek Slone-Zhen/.babun/cygwin/bin/bash.exe'
))

A code engine for Windows users!

# Based on knitr::knit_engines$get('bash')
win_cmd <- function (options) 
{
  cmd = 'C:/WINDOWS/system32/cmd.exe'
  out = if (options$eval) {
    message("running: ", cmd, " ", options$code)
    tmp_file <- tempfile(fileext = ".bat")
    writeLines(options$code, tmp_file)
    opts <- paste(options$engine.opts, "/c", tmp_file) 
    tryCatch(system2(cmd, opts, stdout = TRUE, stderr = TRUE, env = options$engine.env),
             error = function(e) { if (!options$error) stop(e)
               paste("Error in running command", cmd, code)
             },
             finally = { file.remove(tmp_file) })
  } else ""
  if (!options$error && !is.null(attr(out, "status"))) 
    stop(paste(out, collapse = "\n"))
  knitr::engine_output(options, options$code, out)
}
knitr::knit_engines$set(cmd=win_cmd)

https://support.rstudio.com/hc/en-us/articles/200486468-Authoring-R-Presentations

A system for authoring complete books, too large for a single document

• https://bookdown.org/yihui/bookdown/
• https://bookdown.org/

Go on, take a guess!

After much searching around, I found blogdown by Yihui Xie, the man who created Knitr. Blogdown uses Hugo, a blogging framework for static pages built using the Go language. One word of warning, blogdown is still under development, but I’ve tested it out and there have been minor issues, but most of it is because there is no documentation right now if you’re stuck.

[http://kevinfw.com/post/blogging-with-r-markdown/]

• https://github.com/rstudio/blogdown

• Interactive workbench for rapid prototyping
• Reproducible research
• Amenable to source control (git is the integrated into RSudio)
• Languange “neutrality”
  • pick the right / best / easiest / one-you-know langauge for the job
• Alows for embedded sql too
• Can also be knitted to HTML, PDF or Word
  • (PDF requires a LaTeX installation, typically MikTeX on windows.)

Demo RNotebook available at
https://github.com/dereksz/RMarkdown-SURF-2017