# Rendering Math from RMarkdown

In some of my posts, I have had trouble rendering math with MathJax. My posts that include math equations were written in R markdown. Then I used knitr to convert them into a markdown file before posting them to my webpage. However, the math written using Latex ends up converted in a way that is non-renderable.

My webpage and most others that have pages through GitHub are based on Jekyll, which cannot parse the math even after conversion. To handle this, I have come across a post by Fong Chun Chan that gives some insight. Essentially, you need to protect your latex equations with HTML tags in the R markdown file, so that when you perform the conversion, they are kept intact. Afterwards, you can remove the HTML tags and MathJax will interpret the equations and render them correctly.

## MathJax

First, we need to add the MathJax script to your website. For Jekyll,
you add it to `_includes/head.html`

. I use the Minimal
Mistakes theme so if you
have that, you can add it to `_layouts/single.html`

.

```
<script id="MathJax-script" async
src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js">
</script>
```

This enables the MathJax javascript library so it can parse the math equations and render them on your website.

## Protecting display math equations

In R markdown, a typical display equation would be:

```
$$ y = mx + b $$
```

*y* = *m**x* + *b*

As you can see, it does not render properly. It should like like the one below:

\[y = mx + b\]To solve this, we can add HTML tags prior to the knitr conversion, where knitr will not touch the equations, and then remove them later so that MathJax can parse them. I found a script that can do just that. It will look like this with tags prior to markdown conversion.

```
<pre>$$ y = mx + b $$</pre>
```

I have modified the script below. You can download it here.

```
library(rmarkdown)
library(dplyr)
library(stringr)
# 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)
read_lines <- readLines(filename)
# add pre tags around $...$
read_lines <- gsub("(\\${2}(.+?)\\${2})", "\\1<\\/pre>", read_lines)
writeLines(read_lines, tempfile)
rmarkdown::render(tempfile, output_format = "md_document"
, output_file = mdtempfile)
read_lines <- readLines(mdtempfile)
# remove pre tags
sel <- grepl("", read_lines)
read_lines[sel] <- str_replace(read_lines[sel], '', '') %>%
str_replace('</pre>', '')
# remove multiple spaces from lists
sel <- grepl("[[:space:]]{2}\\${1}(.+?)\\${1}", read_lines)
read_lines[sel] <- gsub('\\s+', ' ', read_lines[sel])
# add correct path for files
read_lines <- gsub('files/', "/files/" , read_lines) # this one is for me to add correct file path when you have output files, but you can change it to where your files are.
writeLines(read_lines, mdfile)
# delete temp files
unlink(mdtempfile)
unlink(tempfile)
```

Place the script in the same folder as your R markdown file. Then run the following in your terminal:

```
Rscript --vanilla r2jekyll.R your_RMarkdownFile.Rmd
```

Before running, if you generate output files or figures, make sure to add the following to the top of your R markdown notebook.

## Enabling inline math equations

Now, for inline math equations. MathJax does not handle this unless you properly configure it. So simply add this right before where you added the MathJax script. For instance, see below:

```
<script>
MathJax = {
tex: {
inlineMath: [['$', '$'], ['\\(', '\\)']]
}
};
</script>
<script id="MathJax-script" async
src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js">
</script>
```