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