How can I left align latex equations in R Markdown?

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 'Option clash for package amsmath' ``` --- author: "ME" date: "February 26, 2015" header-includes: - \usepackage[fleqn]{amsmath} output: pdf_document --- ``` A section from my document: ``` $$ \begin{aligned} Bias(\hat{\theta}) &= E(\hat{\theta}) - \theta \\ &= E(2 \bar{X} -1) - \theta \\ &= \frac{2}{n}\sum_{i=1}^n E(X_i) -1 -\theta \\ &= 2E(X) - 1 - \theta \\ &= 2 \cdot \frac{\theta+1}{2} - 1 - \theta \\ &= 0 \\ \end{aligned} $$ ``` Thanks