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.

Variable name	Required (default value if optional)	Description
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.

Variable name	Required (default value if optional)	Description
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.

Variable Name	Required (default value if optional)	Description
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