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@emanuelhuber
Last active Sep 9, 2019
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What would you like to do?
From Rmarkdown to github markdown while preserving latex equations
#!/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)
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