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mh-execute

Note on ithimr

This package is hosted on Github. Please install it using this command:

remotes::install_github("ithim/ithim-r")

GENERAL MH CONVENTIONS

save r: saveRds(rdsfile, version = 2)

city region names: https://github.com/metahit/mh-execute/blob/master/inputs/mh_regions_lad_lookup.csv

mh-execute: everything it calls, nothing it doesn't call

Structure

Loop through all scenarios (cyc_scen and car_scen) in global_scen:

  • Set NSAMPLES (sample size) - currently set to 4

  • Set parameters with their distributions (for instance MMET_CYCLING)

  • Set default mode speeds

  • Get DR relationships from ithimr package (NOTE: Will be replaced by drpa package)

  • Read DISEASE_INVENTORY from inputs/dose_response/disease_outcomes_lookup.csv

  • Read BACKGROUND_POLLUION_TABLE from inputs/background-air-pollution/1_apmeans.csv

  • Read age categories from inputs/scenarios/190330_sp_ind_codebook.xlsx

  • Read scenario and city specific emissions_distances and pa_distances from inputs/distances/

  • Read city_total_distances by mode, from inputs/distances/mode_road_city.csv

  • Read injury_table from inputs/injury/processed_injuries_9.Rds

  • Read city_regions_table from inputs/mh_regions_lad_lookup.csv and filter for only those regions mentioned in the injury_table

  • Read scenarios files per for the global_scen for each LAD (Local Authority District)

  • Set ithim_setup_parameters

  • Loop through all city_regions

    • Read GBD data

    • Read inh_distances

    • Filter LAD for the current city_region

    • Create per person summary (pp_summary) for all scenarios by summarizing total mode specific duration per person. Also summarize, where present, work_ltpa_marg_mmet

    • Summarise DIST for motorised modes (car, motorcycle and bus) for each LAD from emission_distances

    • Set city-specific parameters for background PM2.5 and transport_share, which are read from BACKGROUND_POLLUION_TABLE

    • For each sample, do the following:

      • Create SiN coefficients for CAS_EXPONENT and STR_EXPONENT from parameters
      • Initialize VEHICLE_INVENTORY for the modes
      • Using DIST and pp_summary to calculate scenario_pm_calculations
      • Using pm_conc_pp calcualate RR_AP_calculations using gen_ap_rr
      • Calculate total_mmet using pp_summary
      • Calculate RR_PA_calculations using ithimr::gen_pa_rr
      • Calculate combined AP and PA relative risk RR_PA_AP_calculations - by multiplying, using combined_rr_ap_pa