Some Tweaks to the Workflow

I’ve found Jekyll to be a good mechanism for publishing these thoughts, code & analyses. However, every now and then I run into a problem which requires a bit of tweaking. For instance, getting latex to render with the Rmarkdown -> jekyll -> github pages workflow turned out to be a bit of a hassle. Here’s what I ended up doing:

1. .Rmd -> .md

I used the KnitPost function I found here. It has worked beautifully so far. We’ll see how it holds up in the long-term.

2. Latex support?

This led to output which either just displayed the latex directly, as follows:

\sigma = \sqrt{\frac{n_1 \sigma_1^2 + n_2 \sigma_2^2 + n_1(\mu_1 - \mu)^2 + n_2(\mu_2 - \mu)^2}{n_1 + n_2}

Or didn’t display at all, depending on how, exactly, I adjusted the site settings (as found in the _layouts or _includes directories; or in the _config.yml file).

The solution took a bit of digging around, but eventually after looking around Carl Boettiger’s site for long enough, I was able to figure out how this works. To the default.html file in the _layouts folder, I added:

<script type="text/javascript"
    src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>

And that seems to have taken care of the issue. What we’re doing there seems to be just linking the mathjax display library directly from the mathjax site.

Plug: Carl Boettiger’s site is really fascinating. I could (and very well might) spend quite a while digging around in there. Lots of information to digest, but it seems to be a pretty great approach to science.

Written on January 9, 2015