Daniel Patterson has written a really great post/tutorial on how to use R to identify what routes are most frequently used by cyclists in the bike sharing program of the Twin Cities area of Minnesota. It's a good and quick read, you should check it out.
Daniel's analysis was conducted using stplanr, an R package for sustainable transport planning. This package was developed by Robin Lovelace, who is a great enthusiast for active transport and one of the most important developers for spatial and transport analysis in R.