This package is hosted on Github. Please install it using this command:
remotes::install_github("ithim/ithim-r")
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
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:
SiN
coefficients for CAS_EXPONENT
and STR_EXPONENT
from parameters
VEHICLE_INVENTORY
for the modesDIST
and pp_summary
to calculate scenario_pm_calculations
pm_conc_pp
calcualate RR_AP_calculations
using gen_ap_rr
total_mmet
using pp_summary
RR_PA_calculations
using ithimr::gen_pa_rr
AP
and PA
relative risk RR_PA_AP_calculations
- by multiplying, using combined_rr_ap_pa