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.

These functions are used to print specific sections of the configuration files.

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

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

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

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