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MetroFluSim Code Overview

Written by LP, updated 1/23/2025 (work in progress)

Overview & Assumptions

The module flu_components.py extends the base classes of base_components.py to implement MetroFluSim, a compartmental model with a specific structure. This model is given by this mathematical formulation with a few simplifying assumptions. The script flu_demo.py runs the flu model with input data given in flu_demo_input_files. Note that this input data gives "toy" values. For a realistic model, we would estimate or calibrate these values using real-world historical data.

The simplifying assumptions of flu_components.py include:

  • We model only one immunity inducing event (say, H1N1).
    • As a result, we model only one strain (and thus disregard prevalence) and we do not model vaccination.
    • Matrices that would otherwise have \(4\) indices for subpopulation, age, risk, and immunity-inducing event (e.g. \(\boldsymbol{M}_{a, r, H1}^{(\ell), H(t)}\) because they are \(\lvert \mathcal A \rvert \times \lvert \mathcal R \rvert \times \lvert \mathcal I \rvert\)) only have \(3\) indices in the code (for subpopulation and age-risk group). In other words, for a given subpopulation, these matrices are now only \(\lvert \mathcal A \rvert \times \lvert \mathcal R \rvert\) and we drop the immunity-inducing event dimension entirely.
    • Population-level immunity against infection and population-level immunity against hospitalization is modeled only for H1N1, and not for H3N2 or vaccination.

A more comprehensive model relaxing these simplifying assumptions is coming soon!

Documentation

Follow the links below for code readme's, tutorials, and other resources.

Name Explanation
Flu Model Demo Must-read. Explanation of flu_demo.py and basic simulation functionality. Helps user get started with a concrete MetroFluSim simulation right away.
Flu Input Requirements Must-read. Explanation of flu_demo_input_files and the required specifications and formats for customizing MetroFluSim model values.
Flu Components Walkthrough Advanced. Explains how flu_components.py subclasses are created to build the MetroFluSim model. Must-read for users who want to create a custom model structure. Users can use this walkthrough as reference to create custom subclasses for a customized model with a different functional form than MetroFluSim.