R Markdown Math Equation Alignment

left align the formula

$\begin{aligned}
AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{aligned}$

&...& show in the line ; $$...$$ display out;

I'm not quite sure what you're going for here, but line breaks, \\ go at the end of tthe line, not the beginning, and the aligmnent operator is &. So this:

$$
\begin{aligned}
 AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
 Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{aligned}
$$

produces this: