From Rmarkdown to github markdown while preserving latex equations

r2jekyll.R

#!/usr/bin/env Rscript

#-----------------------------------------------------------------------------
# How to run? 
# In terminal enter: Rscript --vanilla r2jekyll.R my_RMarkdownFile.Rmd

#-----------------------------------------------------------------------------
# Problem while rendering Rmarkdown files with latex equation into markdown file
# -> Rmarkdown try to convert the equation into markdown instead of leaving them
#    as latex equation. In consequences, the equations within the mardown file
#    are not correctly rendered in a website powered by jekyll and using
#    MathJax.js (a JavaScript display engine for mathematics)

#-----------------------------------------------------------------------------
# What does r2jekyll.R do?
# 1) it reads the Rmarkdown file
# 2) wrap the latex equation with the HTML tags <pre> and </pre> 
#    This "trick" to protect the latex equation from being knitted
#    into markdown
# 3) knit the Rmarkdown file into markdown
# 4) remove the <pre> and </pre> tags

#-----------------------------------------------------------------------------
# How to write latex equation
# - Inline equation -> on one line! MUST be a space or a punctuation character
#     in front of the first dollar sign. Examples
#       This is an equation, $f(x) = \alpha + \frac{\beta}{x}$, that it is nice.
#       This will no work$f(x) = \alpha + \frac{\beta}{x}$.
#       This will work ($f(x) = \alpha + \frac{\beta}{x}$)
# - Block equation -> new line after the first '$$' and new line
#     before the last '$$', example:
#       A nice equation:
#
#       $$
#       f(x) = \alpha + \frac{\beta}{x}$
#       $$
#
#       How did you find the equation above?



#-----------------------------------------------------------------------------
# inspired by:
# - Nicole White
#    https://nicolewhite.github.io/2015/02/07/r-blogging-with-rmarkdown-knitr-jekyll.html
# - Fong Chun Chan
#    http://tinyheero.github.io/2015/12/06/rmd-to-jekyll-protect-eqn.html

library(rmarkdown)

# Get the filename given as an argument in the shell.
args <- commandArgs(TRUE)
filename <- args[1]

# Check that it's a .Rmd file.
if(!grepl(".Rmd", filename)) {
  stop("You must specify a .Rmd file.")
}

tempfile <- sub('.Rmd', '_deleteme.Rmd', filename)
mdtempfile <- sub('.Rmd', '_deleteme.md', filename)
mdfile <- sub('.Rmd', '.md', filename)

x0 <- readLines(filename)

sel <- grepl("([[:blank:]]|[[:punct:]]){1}\\${1}(.+?)\\$", x0)

x1 <- x0
x1[sel] <- gsub("(\\${1}(.+?)\\$)", "<pre>\\1<\\/pre>", x0[sel])

x2 <- paste(x1, collapse = "!@#:")

x3 <- gsub("(\\${2}(.+?)\\${2})", "<pre>\\1<\\/pre>", x2)

x4 <- strsplit(x3, split="!@#:", fixed = TRUE)

writeLines(x4[[1]], tempfile)


rmarkdown::render(tempfile, output_format = 'all', output_file = mdtempfile)



x0 <- readLines(mdtempfile)

x <- paste(x0, collapse = "!@#:")

x1 <- gsub("<pre>\\${2}", "$$", x)
x2 <- gsub("\\${2}</pre>", "$$!@#:", x1)

x3 <- gsub("(!@#:[[:space:]]*)<pre>\\${1}", " $", x2)
x4 <- gsub("\\${1}</pre>(!@#:)", "$ ", x3)
# remove space before punctuation!
x5 <- gsub("\\s+([,;:)!\\.\\?])", "\\1", x4)
x6 <- strsplit(x5, split="!@#:", fixed = TRUE)

writeLines(x6[[1]], mdfile)


unlink(mdtempfile)
unlink(tempfile)