There is a specific way that the .R3D file contains the frames captured at a high frame rate, such as 96fps or 120fps. Clips captured at these speeds playback at a slightly slower rate and are contained inside of a 60fps time base. That way all of the captured frames are included in the playback.

More specific information, as well as a few interactive examples of how this works can be found inside of this "Intro to Slow Motion" article from RED.