change mathjax renderer in R notebooks (with "self_contained: false") - latex

Question

I am creating R notebooks that contain equations. I am using RStudio 1.2.5033 on Windows 10, R 3.5.1, and rmarkdown 2.1. When my R notebooks are rendered as HTML, MathJax (v2.7.2) uses the "HTML-CSS" output processor to render the equations. But I think that the output from the "CommonHTML" output processor looks better. So I want to include a directive, in my R notebooks, that forces MathJax to use the CommonHTML output processor. How may I do this?
If I were rendering an ordinary R Markdown document with output format html_document, I could solve the problem via the mathjax option in my YAML header. For example, when the following file is rendered to HTML, MathJax will use the CommonHTML output processor:
---
title: "Trouble with MathJax"
output:
html_document:
mathjax: "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS_CHTML.js"
self_contained: false
---
\begin{equation}
R_3 = \alpha
\end{equation}
But this solution doesn't work well when I change the output format from html_document to html_notebook. In that case, I get output that looks like this:
The equation is rendered with CommonHTML, but there is a lot of cruft at the top of the page (note the four bullet points), and the default R Notebook CSS doesn't seem to be implemented.
The problem seems to be general to rendering R notebooks with self_contained: FALSE, as suggested in R notebooks don't render properly when "self_contained" is FALSE because the "files" directory is deleted after rendering. But I can't see a good workaround for that problem.
Dead Ends
The MathJax documentation seems to indicate that I can specify the output processor by adding the jax array in a call to MathJax.Hub.Config(). But when I've done that, my equations are still displayed via the HTML-CSS output processor. Here is a minimal example of an R Markdown document that exhibits the problem:
---
title: 'Trouble with MathJax'
output: html_notebook
---
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
jax: ["input/TeX", "output/CommonHTML"],
});
</script>
\begin{equation}
R_3 = \alpha
\end{equation}
The call to MathJax.Hub.Config() seems to do nothing here. In both Chrome and Edge, the equation is rendered via HTML-CSS, not CommonHTML. How can I change the rendering to Common HTML?
Related Posts
One year-old post, Is there a way in markdown to override default mathjax renderer?, is about Jupyter notebooks, but it's relevant. It hasn't received an answer.
Adapting the script in this post from the MathJax Google Group –– mainly by changing "HTML-CSS" to "CommonHTML" –– doesn't seem to have any effect.

Answer 1

The solution is simply to omit the self_contained line in the YAML header or, equivalently, to set self_contained to true. Here is a minimal example of an R notebook for which the user has chosen the mathjax renderer:
---
title: "Self-contained notebook with non-default Mathjax config"
output:
html_notebook:
mathjax: "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS_CHTML.js"
---
$R_3 = 2$.
When the file is rendered to HTML, the equation is displayed with CommonHTML, not with HTML-CSS. And the Mathjax script is contained within the "nb.html" file that is produced.
I was surprised that this works, because the documentation for rmarkdown::html_document() says that "even for self contained documents MathJax is still loaded externally (this is necessary because of its size)." But Section 3.1.8 of the R Markdown book indicates that the restriction applies only when Mathjax is loaded from a local file. So perhaps it shouldn't be a surprise.
Side note: the default Mathjax configuration used by the rmarkdown package is given by rmarkdown:::mathjax_config(). As of rmarkdown v2.1, the function returns "MathJax.js?config=TeX-AMS-MML_HTMLorMML".