How can I left align latex equations in R Markdown? - r

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

Answer 3

$ L(x_{1}, x_{2}, ..., x_{n}| \mu) = \mu * (1-\mu) $
$log (\ L(x_{1}, x_{2}, ..., x_{n}| \mu)) = h * log(\mu) + (m-h) * log(1-\mu) $
$\frac{\partial log(\ L(x_{1}, x_{2}, ..., x_{n}| \mu)}{\partial(\mu)} = \frac{h}{\mu} + \frac{h-m}{1-\mu} $
#### We set this to zero to find the value that maximizes the likelihood
$\frac{h}{\mu} + \frac{h-m}{1-\mu} = 0 $
$h = m * \mu $
$\mu = \frac{h}{m} $