Contents:

CRACMMdev-2022_pye_acpd.zip 
  code: python code leading to analysis and plots in Pye et al. manuscript submitted to Atmos Chem Phys Discuss.

     main_cracmm.py: main processing routine that assembles SPECIATE representative compounds, matches with Chemicals Dashboard,
          creates figures, and performs other mapping funcations. Calls:
          cracmm_prep.py: prepares representative compound information from team members for SPECIATE and fills out species info. Calls:
               species_emissions.py: reads in, matches, and supplements species level 
                    emissions information for US anthro and biomass burning sources
               soa_yields.py: wrapper and function for estimating SOA formation potential in g/g by ROC species
               mir_estimates.py: wrapper and function for estimating ozone MIR by ROC species
          cracmm_species_mapping.py includes
               map_biogenics: wrapper for mapping MEGAN and BEIS species to CRACMM
               dfappend_cracmm: wrapper for mapping SPECIATE to CRACMM with option to output Speciation Tool input file and diagnostic species info
               calls: cracmm_mapper.py (core routine for mapping ROC species to CRACMM, schematically depicted in Supplementary Figures S1-S4)
          speciate_support.py: outputs final SPECIATE database mapped to representative compounds and CRACMM.
               Writes out Table D2.
          cracmm_util.py: version stamps CRACMM information.
          cracmm_visualize.py: makes visualizations and tabulates information by CRACMM species.
               Creates Figures 1-3, Figure 9, Figures S5-S6.

     chronic_inhalv2.py: Performs HAP analysis and creates Figure 6, Table D3, and Table D4. 
          Requires main_cracmm to be run first and generate input data frame.

     soa_sankey.py: creates Figure 5. Independent of main_cracmm.py.
          
     appendixAB_andMD.py: independent of main_cracmm.py. Call function in markdown_metadata (prep_metadata).
          Creates main text Appendix A, Figures 7-8, Table D1, Table S2.
          Calls: formula_to_elements.py function which parses elemental abundance from a chemical formula.

     hetchem.py: routine for estimating heterogeneous rate constants for organic nitrate hydrolysis.

     markdown_metadata.py
          Function used by appendixAB_andMD to assemble properties
          Creates markdown and metadata files for https://github.com/USEPA/CRACMM

  input: inputs to code

Supporting data tables. YYYYMMDD indicates the year, month, and day of last update.

     TableD1_YYYYMMDD_cracmm1.csv: CRACMM species information from Appendix A and Supplementary Table S2 (CRACMM species, description, 
          phase, lumped status, stable?, molecular weight, representative species, chemical formula, SMILES, DTXSID)
     TableD2_YYYYMMDD_speciate.csv: Mapping of SPECIATE database species to CRACMM species from Supplementary Table S1 (Species, Representative
          compound name, CRACMM species) and 2017 U.S. ROC emissions from anthropogenic and biogenic sources in Gg/yr as described by Pye et al.
     TableD3_YYYYMMDD_cracmmhaps.csv: Individual HAPs, their emissions, and risk potentials. CAS indicates
          the CAS from SPECIATE. CASRN is for the representative compound. CASfortoxmatch 
          indicates the CAS number for the species used to estimate health risk (URE in m3/microgram and RfC in milligrams/m3). SOA and ozone potentials 
          are in Giga grams. Cancer and noncancer health risk potentials have arbitrary units.
     TableD4_YYYYMMDD_haplist491.csv: 491 HAPs identified in SPECIATE