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Modify configuration parameters

Configuration parameters are simulation-wide parameters that affect how EMOD runs at a fundamental level. These include parameters related, but not limited to:

  • Model duration, timestep length, and simulation start time
  • How a disease progresses and transmits
  • Whether agents can be born, age, and/or die

Overview

Configuration parameters are assigned values in functions initialize_config and get_config_parameterized_calls in a frame, however, it is common practice to set default/initial values in the country model versions of these methods.

Example

In this example, we update the value of configuration parameter named Base_Infectivity, which alters how infectious a disease is at a fundamental level (before any other modifiers apply).

Prerequisites

This tutorial requires you to have done the following:

Extend the baseline frame for alteration

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python -m emodpy_workflow.scripts.extend_frame --source baseline --dest more_infectious

Edit the frame config.py

Here we edit the initialize_config function, opting to not make a hyperparameter for setting Base_Infectivity for simplicity. An alternative example that makes a hyperparameter is located at how to use elements in a frame.

Edit file frames/more_infectious/config.py to have 10 times greater infectivity. It should contain the following:

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from typing import List

from emod_api.schema_to_class import ReadOnlyDict
from emodpy_hiv.parameterized_call import ParameterizedCall
from emodpy_hiv.reporters.reporters import Reporters

from .. import baseline as source_frame


def initialize_config(manifest):
    config = source_frame.model.config_initializer(manifest=manifest)
    config.parameters.x_Base_Population = config.parameters.x_Base_Population
    config.parameters.Base_Infectivity = config.parameters.Base_Infectivity * 10  # Increasing infectivity here.
    return config


def get_config_parameterized_calls(config: ReadOnlyDict) -> List[ParameterizedCall]:
    parameterized_calls = source_frame.model.config_parameterizer(config=config)
    return parameterized_calls


def build_reports(reporters: Reporters):
    reporters = source_frame.model.build_reports(reporters)
    return reporters

Run EMOD

We will run the baseline frame and more_infectious frames:

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python -m emodpy_workflow.scripts.run -f baseline -N ConfigUpdate -o config_baseline_output -p ContainerPlatform -d output/InsetChart.json

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python -m emodpy_workflow.scripts.run -f more_infectious -N ConfigUpdate -o config_more_infectious_output -p ContainerPlatform -d output/InsetChart.json

Compare InsetChart.json

Run:

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python -m emodpy_hiv.plotting.plot_inset_chart config_baseline_output/ConfigUpdate--0/InsetChart/InsetChart_sample00000_run00001.json config_more_infectious_output/ConfigUpdate--0/InsetChart/InsetChart_sample00000_run00001.json

Blue below represents the more_infectious frame and red represents the frame baseline. As can be seen, highly infectious HIV results in higher infection rates and mortality.

image