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Some states and locales are in attainment of the national ambient air quality standards (NAAQS) from the Clean Air Act, so there is little need for air quality analysis for highway projects.
Otherwise, for guidance on estimating GHG emissions from HPMS data or from travel models, see FHWA’s, “Handbook for Estimating Transportation Greenhouse Gas Emissions for Integration into the Planning Process”. The methods presented in this Handbook are largely based on obtaining good VMT and speed estimates for a whole region. Emission factors may be improved by introducing a customized vehicle mix in MOVES. Although written for GHG gases, the advice in this Handbook applies equally well to the process of estimating energy consumption from highway vehicles.
As of this writing, there is an ongoing NCHRP project NCHRP 25-25/Task 96, "Quick Reference Guide for Traffic Modelers for Generating Traffic and Activity Data for Project-Level Air Quality Analyses", which should provide additional advice on this subject.
FHWA, “Handbook for Estimating Transportation Greenhouse Gas Emissions for Integration into the Planning Process”