The LPhyBEAST tutorials are written on a Kramdown format, and rendered automatically by Jekyll. Its Step by Step Tutorial will help beginners to get started quickly. It is supporting Liquid and MathJax.

Reusing templates

When you start to write your own tutorial for new models in LPhy or LPhyBEAST, please consider to reuse the existing templates first, if necessary, you are welcome to create new templates.

To reuse these templates in your main markdown file, you can simply copy the example below using a template lphy-beast.md:

{% include_relative templates/lphy-beast.md lphy="hcv_coal" %}

As you can see, lphy-beast.md has 1 variable lphy, which is declared as {{include.lphy}} in the template. The prefix include is always required for any variables.

Then, given lphy="hcv_coal", this variable will be replaced to hcv_coal when the corresponding HTML page is created.

Auto-numbering figures

Liquid is so powerful, if you embed the following code into your markdown, Jekyll will automatically create the correct numbers for figures, even though you would change their ordering later.

Assign 1 to the variable current_fig_num:

{% assign current_fig_num = 1 %}

Then append “Figure “ before 1:

{% assign bs1_fig_num = "Figure " | append: current_fig_num  %}

So you will have “Figure 1” in your first figure caption:

<figure class="image" id="bs1_fig">
  <img src="BS1.png" alt="Bayesian Skyline">
  <figcaption>{{ bs1_fig_num }}: ... </figcaption>
</figure>

For the rest of numbers, just add 1 each time before you use it:

{% assign current_fig_num = current_fig_num | plus: 1 %}

If you want to refer to this figure in the context, you can define another variable to keep its value, such as

{% assign pop_fig_num = "Figure " | append: current_fig_num  %}

In practice, whatever you move, add, or delete your figures, as long as plus: 1 is correctly distributed, you do not have to manually check and correct these numbers anymore.
😁

Writing math in Latex

You can directly write math symbols and equations in your markdown file, wrapped by dollar signs like $$…$$ or $…$ for inline.

For example,

$$ P(t) = e^{\Lambda t} $$

will look like this in the website:

\[P(t) = e^{\Lambda t}\]

More details are described in MathJax doc.

Auto-generated narrative

NarrativeCreator inside LPhy project can automatically create a narrative for data and graphical models defined in a lphy script.

NarrativeCreator tutorials/h5n1.lphy

The program will create lphy.md, narrative.md, and references.md. You can include them into your tutorial, to save some efforts for common introductions and references.