Function reference
Main functions
Run the ITHIM model - the setting up the environments (variables and loading files), running the model and generating the outputs.
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run_ithim()
- Wrapper for running ITHIM
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run_ithim_setup()
- Run the set up scripts for ITHIM
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add_distance_columns()
- Add strike and casualty distances to injury tables
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add_ghost_trips()
- Addition of ghost trips
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add_motorcycle_trips_Chile()
- Personal motorcycle trips for Chilean cities
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add_trips()
- Additional trips for trip data set
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add_walk_trips()
- Addition of 'walk to public transport' stages to trip set
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AP_dose_response()
- Calculate relative risk given PM exposure level
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ap_dose_response_curve()
- Computes RR as a DR relationship - CURRENTLY NOT USED
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assign_age_groups()
- Assign age groups to individuals
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beta_pointiness()
- Parameterise confidence in PA data - CURRENTLY NOT IN USE
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combined_rr_ap_pa()
- Combine relative risks from air pollution and physical activity
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combine_health_and_pif()
- Combine health and potential impact fraction (PIF)
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complete_trip_distance_duration()
- Add missing trip information
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create_bogota_scenarios()
- Create scenarios for Bogota
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create_global_scenarios()
- Create global scenarios
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create_base_pop()
- Creates baseline population
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dirichlet_pointiness()
- Function for Dirichlet parameters
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distances_for_injury_function()
- Get distances and parameterise Poisson regression model for injuries
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dist_dur_tbls()
- Get distances and duration summaries by mode
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extract_data_for_voi()
- Get ITHIM-results into correct format for VoI analysis
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gen_ap_rr()
- Get relative risk for diseases given PM exposure
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gen_pa_rr()
- Get relative risk for diseases given mMETs
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get_all_distances()
- Find population distances by mode for entire population
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get_scenario_settings()
- Get values for mode share across distance categories and for max mode share scenario - CURRENTLY only used when calling summary_tables.Rmd
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get_synthetic_from_trips()
- Generate baseline population from trip data
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health_burden()
- Compute health burden
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injuries_function_2()
- Predict injuries
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injury_death_to_yll()
- Map injury death burden to YLL (years of life lost) burden
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ithim_calculation_sequence()
- Cascade of computations that form ITHIM-Global
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ithim_load_data()
- Load data for model and prepare input data for model
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ithim_setup_baseline_scenario()
- Set up baseline scenario data frame
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ithim_setup_parameters()
- Set parameters for ITHIM-Global run
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ithim_uncertainty()
- Sampling routine for running ITHIM with uncertainty
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join_hb_and_injury()
- Join disease health burden and injury data
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scale_trip_distances()
- Scale trip distances
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scenario_co2_calculations()
- Calculate total CO2 exposure per mode and scenario
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scenario_pm_calculations()
- Calculate total AP exposure per person
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set_injury_contingency()
- Injury summary statistics
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set_scenario_specific_variables()
- Set scenario specific variables - CURRENTLY NOT CALLED
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set_vehicle_inventory()
- Collate all vehicle information
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total_mmet()
- Calculate total mMETs per person
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walk_to_pt_and_combine_scen()
- Add walk to public transport stages