The .R3D file names are made up of the Camera (A), Magazine (001), Clip (COO2) then a unique string (0502A6). You only need to log the Camera, Magazine and Clip ie. A/3/2, and your usual Shot, Scene, Take. The magazine number will only augment with the magazines, like a new roll of film. The clip goes up by one every time the record button is pushed.
The gotcha is if someone presses record on the camera and its not logged, then there will be an extra clip on the magazine. For some reason although I hear "Hold the Roll" often enough, this still seems to be far more prevalent with digital than with film. That's pretty easy to spot.
A good DIT can be comparing logs as well. Finally of course its the assistant editor that has to struggle with any mismatches, using all the logs, camera, sound and script notes. Something has to link the script's reference of scene, shot, take - to the reference of Magazine and Clip. Hey its easier than feet and frames.