$$
r = \frac{1}{n-1} \sum_{i=1}^{n} \frac{(X_i - \bar{X})(Y_i - \bar{Y})}{S_xS_y}
$$
The rendered equation is not numbered. Using \begin{aligned} and \end{aligned} generates an error.
I am also using knitr in RStudio, knitting to PDF using pandoc and xelatex engine.
Thank you.
As pointed out amsmath is already in the default template, so you can invoke the equation environment
\begin{equation}
y = mx+b
\end{equation}
This will automatically number equations in order of use. To use another character, say *,
\begin{equation}
\tag{*}
y = ax^2 + bx + c
\end{equation}
To leave equation unmarked simply leave tag{} blank.
For differences between align and equation see this answer
Try align not aligned
\begin{align}
r = \frac{1}{n-1} \sum_{i=1}^{n} \frac{(X_i - \bar{X})(Y_i - \bar{Y})}{S_xS_y}
\end{align}