Of particular importance is the aerosol content of the atmosphere.
Aerosols are dust, water vapor, pollution, clouds, etc.
The aerosols could make a significant contribution to corrections in estimating the energy of a cosmic ray. We are currently trying to understand exactly how to model these corrections. This is a snapshot of analysis software I wrote to examine the geometry of the HiRes steerable laser system. The red line indicates the laser track across the sky. These cells collect light from the laser beam as well as comic rays.