auto-number equations in R markdown documents in RStudio
<p>I can auto-number mathjax equations in an R markdown document in RStudio by adding the following statement to the beginning of the Rmd document: </p>

<pre><code>&lt;script type="text/x-mathjax-config"&gt;
MathJax.Hub.Config({
  TeX: { 
      equationNumbers: { 
            autoNumber: "all",
            formatNumber: function (n) {return '9.'+n}
      } 
  }
});
&lt;/script&gt;
</code></pre>

<p>The following also works, but not with the $$..$$ equations, only equations bracketed with \begin{equation}..\end{equation}.  </p>

<pre><code>&lt;script type="text/x-mathjax-config"&gt;
MathJax.Hub.Config({
  TeX: { 
      equationNumbers: { 
            autoNumber: "AMS",
            formatNumber: function (n) {return '9.'+n}
      } 
  }
});
&lt;/script&gt;
</code></pre>

<p>I can change the numbering to a static label with <code>\tag{mylabel}</code> inside the $$..$$, and the auto-numbering will skip that equation.  </p>

<p>Unfortunately, to skip with no label add <code>\tag{}</code> results in the equation still labeled with (). </p>

<p>Does anyone know how to get rid of the empty brackets?</p>

<p>Does anybody know a <em>simple</em> statement to add to either the mathjax script statement or the $$..$$ equations within a Rmd doc that would add an auto-numbered Section number to the equation number?</p>

<p>most of the info from here: 
<a href="http://mathjax.readthedocs.org/en/latest/tex.html#automatic-equation-numbering" rel="nofollow">http://mathjax.readthedocs.org/en/latest/tex.html#automatic-equation-numbering</a></p>

<p>Thanks</p>