Demonstration of creating automatically-numbered equations in RMarkdown documents.

rmarkdown_num_equations.rmd

At the top of your R markdown, beneath the yaml title block, add the following `<script>` section

    ---

    <script type="text/x-mathjax-config">
    MathJax.Hub.Config({
      TeX: { 
        equationNumbers: { 
          autoNumber: "all",
          formatNumber: function (n) {return n}
        } 
      }
    });
    </script>
    
Then insert your displaymath equations normally:

    $$g(x) = \int f(x) \mathrm{d}x$$

To prevent numbering, use the `\nonumber` switch

    $$g(x) = \int f(x) \mathrm{d}x\nonumber$$