Heres how youd write your example equation. If an equation is longer than one line or several formulas must be grouped together the eqnarray environment could be used. There are several ways to format multiple equations and the amsmath package adds several more.
With R v302 64-bit Windows 7 RStudio 098490 knitr v15 when the code you provided above was copied and pasted into RStudio with no changes it produced two lines of equations.
The next lines contain only the equations and annotations I would like them aligned with the equation and annotation of the second line. It only takes a minute to sign up. With R v302 64-bit Windows 7 RStudio 098490 knitr v15 when the code you provided above was copied and pasted into RStudio with no changes it produced two lines of equations. That can be achieve in plain LaTeX without any specific package.