title: How can I left align latex equations in R Markdown?
body: <p>I'm having some difficulty left aligning equations in R Markdown (i.e. putting the equation on the far left side of page, and aligning subsequent lines). I've generally determined that I want to set the [fleqn] option in the amsmath package to left align all equations, but putting the following in my YAML header gives an error </p>
  
  <p>'Option clash for package amsmath'</p>
  
  <pre><code>---
  author: "ME"
  date: "February 26, 2015"
  header-includes:
    - \usepackage[fleqn]{amsmath}
  output: pdf_document
  ---
  </code></pre>
  
  <p>A section from my document:</p>
  
  <pre><code>$$
  \begin{aligned}
  Bias(\hat{\theta})  &amp;= E(\hat{\theta}) - \theta \\
                      &amp;= E(2 \bar{X} -1) - \theta \\
                      &amp;= \frac{2}{n}\sum_{i=1}^n E(X_i) -1 -\theta \\
                      &amp;= 2E(X) - 1 - \theta \\
                      &amp;= 2 \cdot \frac{\theta+1}{2} - 1 - \theta \\
                      &amp;= 0 \\
  \end{aligned}
  $$
  </code></pre>
  
  <p>Thanks</p>