How can I left align latex equations in R Markdown?

Question

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

Answer 1

Try using $...$ instead of $$...$$.

In the case of $$...$$ in Rmarkdown is center aligned by default

Answer 2

This question has already been asked here: R Markdown Math Equation Allignment

The below works for me:

$\begin{aligned}
Bias(\hat{\theta})  &= E(\hat{\theta}) - \theta \\
                    &= E(2 \bar{X} -1) - \theta \\
                    &= \frac{2}{n}\sum_{i=1}^n E(X_i) -1 -\theta \\
                    &= 2E(X) - 1 - \theta \\
                    &= 2 \cdot \frac{\theta+1}{2} - 1 - \theta \\
                    &= 0 \\
\end{aligned}$