How to have correctly rendered mathematical equations in bookdown::gitbook when self_contained = TRUE?

Question

I'm writing a GitBook style bookdown document consisting of several Rmd files, in which I use the option self_contained = TRUE to make self-contained HTML pages (so that later I could distribute them as HTML files instead of multiple files with the HTML pages separate from the pictures displayed on them). When I tried to put mathematical equations using the $ $ tags, I got something like [WARNING] Could not convert TeX math '\\frac{1}{\\sum_{i=1}^{S} p_{i}^2}', rendering as TeX and the equations were not rendered correctly.

I saw from here that MathJax may not work when self_contained = TRUE , and from here that MathJax is needed to render math in HTML. Indeed, I always get a warning like MathJax doesn't work with self_contained when not using the rmarkdown "default" template , and the equations were rendered correctly if I use self_contained = FALSE .

So, I wonder if it is possible to render math correctly in GitBook style bookdown document while self_contained = TRUE .

Answer 1

I had the same issue and found a partial solution. Right in the index.Rmd after the yaml header, I included this chunk:

<script>
(function () {
    var script = document.createElement("script");
    script.type = "text/javascript";
    var src = "true";
    if (src === "" || src === "true") src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML";
    if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, "");
    script.src = src;
    document.getElementsByTagName("head")[0].appendChild(script);
})();

</script>

<script type="text/x-mathjax-config">
MathJax.Hub.Config({
  tex2jax: {
        inlineMath: [['$', '$']],
        displayMath: [['$$', '$$']],
    }
});
</script>

Now, the html-output renders the equations but there are two caveats:

1. Display equations (with $$ . $$) do work fine, but some of the inline equations ($ . $) exhibit differing styles: In my case, some equations show up in the warnings ("Could not convert TeX math") and look normal. The remaining inline equations have a slightly different look.

2. On Firefox and Safari the equations render correctly, on Chrome unfortunately not (I did not try other browsers).

Hope that helps a bit!