Config writer
The model needs the configurations file to run (described in previous sections). These configs become lengthy and sometimes difficult to type manually. The config writer helps to generate configs provided the relevant files are present.
Print Functions:
These functions are used to print specific sections of the configuration files.
print_header
Used to generate the global header. For more information on global headers click HERE.
sim_name
Required
Name of the configuration file to be generated. Generally based on the type of simulation
setup_name
Optional (SMH)
Type of run - a Scenario Modeling Hub ("SMH") or Forecasting Hub ("FCH") Simulation.
disease
Optional (covid19)
Pathogen or disease being simulated
smh_round
Optional (NA)
Round number for Scenario Modeling Hub Submission
data_path
Optional (data)
Folder path which contains where population data (size, mobility, etc) and ground truth data files are stored
model_output_dir_name
Optional (model_output)
Folder path where the outputs of the simulated model is stored
sim_start_date
Required
Start date for model simulation
sim_end_date
Required
End date for model simulation
start_date_groundtruth
Optional (NA)
Start date for fitting data for inference runs
end_date_groundtruth
Optional (NA)
End date for fitting data for inference runs
nslots
Required
number of independent simulations to run
print_spatial_setup
Used to generate the spatial setup section of the configuration. For more information on spatial setup click HERE.
census_year
Optional (2019)
The year of data uses to generate the geodata files for US simulations ?? [Unsure about this]
sim_states
Required
Vector of locations that will be modeled (US Specific?)
geodata_file
Optional (geodata.csv)
Name of the geodata file which is imported
mobility_file
Optional (mobility.csv)
Name of the mobility file which is imported
popnodes
Optional (pop2019est)
Name of a column in the geodata file that specifies the population of every subpopulation column
nodenames
Optional (subpop)
Name of a column in the geodata file that specifies the name of the subpopulation
state_level
Optional (TRUE)
Specifies if the subpopulations are US states
print_compartments
Used to generate the compartment list for each way a population can be divided.
inf_stages
Optional (S,E,I1,I2,I3,R,W)
Various infection stages an individual can be in
vaccine_compartments
Optional (unvaccinated, 1dose, 2dose, waned)
Various levels of vaccinations an individual can have
variant_compartments
Optional (WILD, ALPHA, DELTA, OMICRON)
Variants of the pathogen
age_strata
Optional (age0to17, age18to64, age65to100)
Different age groups, the population has been stratified in
Parts of the configuration files that are printed but not needed for FlepiMop runs (need to be mentioned for US or COVID-19 specific runs??)
Spatial Setup:
census year: year of geodata files
modeled states (sim_states): This has US state abbreviations. Do we include the names of the sub-populations in the geodata file? Eg: small_province, large_province
state_level: Specifies if the runs are run for US states
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