When using markdown for reproducible research , it is better to know how your writing will be rendered. That determines not only supported markdown syntax but also math typesetting.

Rendering Math

It depends on the output (pdf or html), the following engines (all open sources) can be used to render math.

Here is a webpage for a KaTeX and MathJax Comparison Demo.

Markdown Parsers

Markdown itself is just a lightweight markup language. To preview the files with styles, we need Markdown parsers. There are a lot of Markdown parsers. Here are a few widely used parsers.

One can also find an incomplete list of Markdown parsers in the post Choosing the Right Markdown Parser.

Implementations

There are specific designed editors and code editors with extensions to preview and/or convert Markdown files. For better math rendering, here are some Markdown implementations that I would like to recommend.

Code Editors with Extensions

Note: VS Code can also be used as an alternative to Rstudio for R.

Markdown Editors

Many good markdown editors don’t support math well. If you don’t want to use VS Code, you may try Typora.

Online Markdown Editors

Overall, my recommendation for Markdown implements is VS Code plus extensions using MathJax.