├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── pkgdown.yaml ├── .gitignore ├── Bogota_InputParameters_v4.0.xlsx ├── Create_output_summaries.R ├── DESCRIPTION ├── ITHIM-R.Rproj ├── InputParameters_v42.0.xlsx ├── LICENSE.md ├── NAMESPACE ├── OutputVersionControl.txt ├── R ├── AP_dose_response.R ├── add_distance_columns.R ├── add_ghost_trips.R ├── add_motorcycle_trips_Chile.R ├── add_trips.R ├── add_walk_trips.R ├── assign_age_groups.R ├── call_evppi.R ├── call_evppi_age_sex.R ├── call_evppi_sex.R ├── combine_health_and_pif.R ├── combined_rr_ap_pa.R ├── complete_trip_distance_duration.R ├── compute_evppi.R ├── create_africa-india_scenarios.R ├── create_bogota_scenarios.R ├── create_global_scenarios.R ├── create_latam_scenarios.R ├── create_synth_pop.R ├── dist_dur_tbls.R ├── distances_for_injury_function.R ├── extract_data_for_voi.R ├── gen_ap_rr.R ├── gen_pa_rr.R ├── get_all_distances.R ├── get_scenario_settings.R ├── get_synthetic_from_trips.R ├── health_burden.R ├── injuries_function_2.R ├── injury_death_to_yll.R ├── ithim_load_data.R ├── ithim_setup_baseline_scenario.R ├── ithim_setup_parameters.R ├── ithim_uncertainty.R ├── run_ithim.R ├── run_ithim_setup.R ├── scenario_co2_calculations.R ├── scenario_pm_calculations.R ├── set_injury_contingency.R ├── set_scenario_specific_variables.R ├── set_vehicle_inventory.R ├── total_mmet.R └── walk_to_pt_and_combine_scen.R ├── README.md ├── _config.yml ├── _pkgdown.yml ├── diagnostic └── README.md ├── figures ├── ap_pm2.5_dist.svg ├── pa_deciles.svg ├── pa_distr.svg ├── pa_vol_base_bus.svg ├── pa_vol_base_cyc.svg └── scen_defn_mode.svg ├── injury_tables.Rmd ├── injury_tables.html ├── inst ├── CITATION └── extdata │ ├── global │ ├── dose_response │ │ ├── disease_outcomes_lookup.csv │ │ └── drap │ │ │ └── extdata │ │ │ ├── all_cause_ap.csv │ │ │ ├── cvd.csv │ │ │ ├── cvd_ihd_25.csv │ │ │ ├── cvd_ihd_30.csv │ │ │ ├── cvd_ihd_35.csv │ │ │ ├── cvd_ihd_40.csv │ │ │ ├── cvd_ihd_45.csv │ │ │ ├── cvd_ihd_50.csv │ │ │ ├── cvd_ihd_55.csv │ │ │ ├── cvd_ihd_60.csv │ │ │ ├── cvd_ihd_65.csv │ │ │ ├── cvd_ihd_70.csv │ │ │ ├── cvd_ihd_75.csv │ │ │ ├── cvd_ihd_80.csv │ │ │ ├── cvd_ihd_85.csv │ │ │ ├── cvd_ihd_90.csv │ │ │ ├── cvd_ihd_95.csv │ │ │ ├── cvd_stroke_25.csv │ │ │ ├── cvd_stroke_30.csv │ │ │ ├── cvd_stroke_35.csv │ │ │ ├── cvd_stroke_40.csv │ │ │ ├── cvd_stroke_45.csv │ │ │ ├── cvd_stroke_50.csv │ │ │ ├── cvd_stroke_55.csv │ │ │ ├── cvd_stroke_60.csv │ │ │ ├── cvd_stroke_65.csv │ │ │ ├── cvd_stroke_70.csv │ │ │ ├── cvd_stroke_75.csv │ │ │ ├── cvd_stroke_80.csv │ │ │ ├── cvd_stroke_85.csv │ │ │ ├── cvd_stroke_90.csv │ │ │ ├── cvd_stroke_95.csv │ │ │ ├── lri.csv │ │ │ ├── neo_lung.csv │ │ │ ├── resp_copd.csv │ │ │ ├── respiratory.csv │ │ │ └── t2_dm.csv │ ├── ventilation_rate │ │ ├── BodyMass.csv │ │ ├── ECF.csv │ │ ├── NVO2max.csv │ │ ├── RMR.csv │ │ ├── VentilationFromOxygenUptake.csv │ │ └── readme.txt │ └── voi │ │ └── parameter_explanations.csv │ └── local │ ├── .DS_Store │ ├── accra │ ├── gbd_accra.csv │ ├── injuries_accra.csv │ ├── pa_accra.csv │ ├── population_accra.csv │ └── trips_accra.csv │ ├── antofagasta │ ├── gbd_antofagasta.csv │ ├── injuries_antofagasta.csv │ ├── pa_antofagasta.csv │ ├── population_antofagasta.csv │ └── trips_antofagasta.csv │ ├── arica │ ├── gbd_arica.csv │ ├── injuries_arica.csv │ ├── pa_arica.csv │ ├── population_arica.csv │ └── trips_arica.csv │ ├── bangalore │ ├── gbd_bangalore.csv │ ├── injuries_bangalore.csv │ ├── pa_bangalore.csv │ ├── population_bangalore.csv │ └── trips_bangalore.csv │ ├── belo_horizonte │ ├── Data sources.txt │ ├── concentration and transport share in pollution.txt │ ├── emissions_belo_horizonte.csv │ ├── gbd_belo_horizonte.csv │ ├── injuries_belo_horizonte.csv │ ├── pa_belo_horizonte.csv │ ├── population_belo_horizonte.csv │ └── trips_belo_horizonte.csv │ ├── bogota │ ├── gbd_bogota.csv │ ├── injuries_bogota.csv │ ├── pa_bogota.csv │ ├── population_bogota.csv │ └── trips_bogota.csv │ ├── bogota_wb │ ├── gbd_bogota_wb.csv │ ├── injuries_bogota_wb.csv │ ├── pa_bogota_wb.csv │ ├── population_bogota_wb.csv │ └── trips_bogota_wb.csv │ ├── buenos_aires │ ├── gbd_buenos_aires.csv │ ├── injuries_buenos_aires.csv │ ├── pa_buenos_aires.csv │ ├── population_buenos_aires.csv │ └── trips_buenos_aires.csv │ ├── cali │ ├── gbd_cali.csv │ ├── injuries_cali.csv │ ├── pa_cali.csv │ ├── population_cali.csv │ └── trips_cali.csv │ ├── cape_town │ ├── gbd_cape_town.csv │ ├── injuries_cape_town.csv │ ├── injuries_cape_town_NAs.csv │ ├── injuries_cape_town_original.csv │ ├── pa_cape_town.csv │ ├── population_cape_town.csv │ └── trips_cape_town.csv │ ├── copiapo │ ├── gbd_copiapo.csv │ ├── injuries_copiapo.csv │ ├── pa_copiapo.csv │ ├── population_copiapo.csv │ └── trips_copiapo.csv │ ├── coquimbo_laserena │ ├── gbd_coquimbo_laserena.csv │ ├── injuries_coquimbo_laserena.csv │ ├── pa_coquimbo_laserena.csv │ ├── population_coquimbo_laserena.csv │ └── trips_coquimbo_laserena.csv │ ├── delhi │ ├── gbd_delhi.csv │ ├── injuries_delhi.csv │ ├── pa_delhi.csv │ ├── population_delhi.csv │ └── trips_delhi.csv │ ├── gran_valparaiso │ ├── gbd_gran_valparaiso.csv │ ├── injuries_gran_valparaiso.csv │ ├── pa_gran_valparaiso.csv │ ├── population_gran_valparaiso.csv │ └── trips_gran_valparaiso.csv │ ├── iquique_altohospicio │ ├── gbd_iquique_altohospicio.csv │ ├── injuries_iquique_altohospicio.csv │ ├── pa_iquique_altohospicio.csv │ ├── population_iquique_altohospicio.csv │ └── trips_iquique_altohospicio.csv │ ├── kisumu │ ├── gbd_kisumu.csv │ ├── injuries_kisumu.csv │ ├── injuries_kisumu_1.csv │ ├── pa_kisumu.csv │ ├── population_kisumu.csv │ └── trips_kisumu.csv │ ├── medellin │ ├── gbd_medellin.csv │ ├── injuries_medellin.csv │ ├── pa_medellin.csv │ ├── population_medellin.csv │ └── trips_medellin.csv │ ├── mexico_city │ ├── gbd_mexico_city.csv │ ├── injuries_mexico_city.csv │ ├── pa_mexico_city.csv │ ├── population_mexico_city.csv │ ├── trips_mexico_city.csv │ └── trips_mexico_city_WeekAndSaturday.csv │ ├── montevideo │ ├── gbd_montevideo.csv │ ├── injuries_montevideo.csv │ ├── pa_montevideo.csv │ ├── population_montevideo.csv │ └── trips_montevideo.csv │ ├── nairobi │ ├── gbd_nairobi.csv │ ├── injuries_nairobi.csv │ ├── injuries_nairobi_1.csv │ ├── pa_nairobi.csv │ ├── population_nairobi.csv │ └── trips_nairobi.csv │ ├── osorno │ ├── gbd_osorno.csv │ ├── injuries_osorno.csv │ ├── pa_osorno.csv │ ├── population_osorno.csv │ └── trips_osorno.csv │ ├── port_louis │ ├── gbd_port_louis.csv │ ├── injuries_port_louis.csv │ ├── pa_port_louis.csv │ ├── population_port_louis.csv │ └── trips_port_louis.csv │ ├── puerto_montt │ ├── gbd_puerto_montt.csv │ ├── injuries_puerto_montt.csv │ ├── pa_puerto_montt.csv │ ├── population_puerto_montt.csv │ └── trips_puerto_montt.csv │ ├── san_antonio │ ├── gbd_san_antonio.csv │ ├── injuries_san_antonio.csv │ ├── pa_san_antonio.csv │ ├── population_san_antonio.csv │ └── trips_san_antonio.csv │ ├── santiago │ ├── gbd_santiago.csv │ ├── injuries_santiago.csv │ ├── pa_santiago.csv │ ├── population_santiago.csv │ ├── trips_santiago.csv │ └── trips_santiago_regular_summer_season.csv │ ├── sao_paulo │ ├── gbd_sao_paulo.csv │ ├── injuries_sao_paulo.csv │ ├── pa_sao_paulo.csv │ ├── population_sao_paulo.csv │ ├── trips_sao_paulo.csv │ └── trips_sao_paulo_2012.csv │ ├── temuco_padrelascasas │ ├── gbd_temuco_padrelascasas.csv │ ├── injuries_temuco_padrelascasas.csv │ ├── pa_temuco_padrelascasas.csv │ ├── population_temuco_padrelascasas.csv │ └── trips_temuco_padrelascasas.csv │ ├── valdivia │ ├── gbd_valdivia.csv │ ├── injuries_valdivia.csv │ ├── pa_valdivia.csv │ ├── population_valdivia.csv │ └── trips_valdivia.csv │ └── vizag │ ├── gbd_vizag.csv │ ├── injuries_vizag.csv │ ├── pa_vizag.csv │ ├── population_vizag.csv │ └── trips_vizag.csv ├── man ├── AP_dose_response.Rd ├── add_distance_columns.Rd ├── add_ghost_trips.Rd ├── add_motorcycle_trips_Chile.Rd ├── add_trips.Rd ├── add_walk_trips.Rd ├── ap_dose_response_curve.Rd ├── assign_age_groups.Rd ├── beta_pointiness.Rd ├── call_evppi.Rd ├── call_evppi_age_sex.Rd ├── call_evppi_sex.Rd ├── combine_health_and_pif.Rd ├── combined_rr_ap_pa.Rd ├── complete_trip_distance_duration.Rd ├── compute_evppi.Rd ├── create_africa_india_scenarios.Rd ├── create_base_pop.Rd ├── create_bogota_scenarios.Rd ├── create_global_scenarios.Rd ├── create_latam_scenarios.Rd ├── dirichlet_pointiness.Rd ├── dist_dur_tbls.Rd ├── distances_for_injury_function.Rd ├── extract_data_for_voi.Rd ├── figures │ ├── BigPicture_v3-7.svg │ ├── Build_package.png │ ├── Clone_package.png │ ├── Git_pull.png │ ├── Install_packages.png │ ├── Model_output.png │ ├── Run_model.png │ ├── Update_branch.png │ ├── build_tab.png │ ├── build_tabwa.png │ ├── disease_interaction_table.png │ ├── install_drpa.png │ ├── ithim_objects_bogota.png │ ├── ithim_objects_bogotawa.png │ ├── multi_city_script.png │ ├── multi_city_script_specifcy_cities.png │ ├── multi_city_script_specifcy_cities_gh.png │ ├── multi_city_script_specifcy_cities_gh1.png │ ├── multi_city_scriptwa.png │ ├── new_terminal.png │ ├── renv_restore.png │ ├── renv_status.png │ ├── screenshot-RS.png │ ├── terminal.png │ ├── view_ithim_objects.png │ └── view_ithim_objectswa.png ├── gen_ap_rr.Rd ├── gen_pa_rr.Rd ├── get_all_distances.Rd ├── get_scenario_settings.Rd ├── get_synthetic_from_trips.Rd ├── health_burden.Rd ├── injuries_function_2.Rd ├── injury_death_to_yll.Rd ├── ithim_calculation_sequence.Rd ├── ithim_load_data.Rd ├── ithim_setup_baseline_scenario.Rd ├── ithim_setup_parameters.Rd ├── ithim_uncertainty.Rd ├── join_hb_and_injury.Rd ├── run_ithim.Rd ├── run_ithim_setup.Rd ├── scale_trip_distances.Rd ├── scenario_co2_calculations.Rd ├── scenario_pm_calculations.Rd ├── set_injury_contingency.Rd ├── set_scenario_specific_variables.Rd ├── set_vehicle_inventory.Rd ├── total_mmet.Rd └── walk_to_pt_and_combine_scen.Rd ├── multi_city_script.R ├── multi_city_voi.R ├── renv.lock ├── renv └── activate.R ├── results └── multi_city │ ├── .gitignore │ ├── health_impacts │ ├── deaths.csv │ ├── deaths_pathway.csv │ ├── ylls.csv │ └── ylls_pathway.csv │ ├── inj │ ├── distances.csv │ ├── inj_counts.csv │ ├── inj_data.xlsx │ ├── injury_risks_per_100k_pop.csv │ ├── injury_risks_per_100million_h.csv │ └── injury_risks_per_billion_kms.csv │ ├── io_ac8aa8a0_test_run.rds │ ├── mode_order.csv │ ├── standardized_modes.csv │ └── yll_per_hundred_thousand │ └── Summary_ylls_all_cities_v0.3.csv ├── results_app ├── app.R ├── data │ └── PIF.csv ├── function.R ├── images │ ├── bus-transport-scenario.png │ ├── car-scenario.png │ ├── cycle-scenario.png │ ├── distance-table-bus-scenario.png │ ├── distance-table-car-scenario.png │ ├── distance-table-cycle-scenario.png │ ├── distance-table.png │ ├── duration-table-bus-scenario.png │ ├── duration-table-car-scenario.png │ ├── duration-table-cycle-scenario.png │ ├── duration-table.png │ ├── ithim-accra.png │ └── trip-prop.png ├── quartomonothemer.scss ├── results_presentation.qmd ├── rsconnect │ └── shinyapps.io │ │ └── 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