CompartmentalModel#

class CompartmentalModel(scenario, params, name='compartmental')[source]#

Bases: BaseLaserModel

A class to represent the compartmental model with daily timesteps.

Parameters:

  • scenario (BaseCompartmentalScenario | DataFrame) – A scenario containing the scenario data, including population, latitude, and longitude.

  • params (CompartmentalParams) – A set of parameters for the model.

  • name (str) – The name of the model. Defaults to “compartmental”.

Notes

This class initializes the model with the given scenario and parameters. The scenario must include the following columns:

  • id (string): The name of the patch or location.

  • pop (integer): The population count for the patch.

  • lat (float degrees): The latitude of the patches (e.g., from geographic or population centroid).

  • lon (float degrees): The longitude of the patches (e.g., from geographic or population centroid).

  • mcv1 (float): The MCV1 coverage for the patches.

The default model uses SEIR compartments:

  • S: Susceptible individuals

  • E: Exposed individuals (infected but not yet infectious)

  • I: Infectious individuals

  • R: Recovered/immune individuals

Initialize the disease model with the given scenario and parameters.

Parameters:

  • scenario (BaseCompartmentalScenario | DataFrame) – A scenario containing the scenario data, including population, latitude, and longitude.

  • params (CompartmentalParams) – A set of parameters for the model, including seed, num_ticks, beta, sigma, gamma, and other SEIR parameters.

  • name (str) – The name of the model. Defaults to “compartmental”.

Returns:

None

Attributes

ParamsType

ScenarioType

components

Retrieve the list of model components.

Methods

scenario_wrapper_class#

alias of BaseCompartmentalScenario

__call__(model, tick)[source]#

Hook for subclasses to update the model for a given tick.

Parameters:

  • model (BaseLaserModel) – The model instance.

  • tick (int) – The current time step or tick.

Return type:

None

expose(indices, num_exposed)[source]#

Exposes the given nodes with the given number of exposed individuals. Moves individuals from Susceptible to Exposed compartment.

Parameters:

  • indices (int | ndarray) – The indices of the nodes to expose.

  • num_exposed (int | ndarray) – The number of exposed individuals.

Return type:

None

infect(indices, num_infected)[source]#

Infects the given nodes with the given number of infected individuals. Moves individuals from Exposed to Infected compartment.

Parameters:

  • indices (int | ndarray) – The indices of the nodes to infect.

  • num_infected (int | ndarray) – The number of infected individuals.

Return type:

None

recover(indices, num_recovered)[source]#

Recovers the given nodes with the given number of recovered individuals. Moves individuals from Infected to Recovered compartment.

Parameters:

  • indices (int | ndarray) – The indices of the nodes to recover.

  • num_recovered (int | ndarray) – The number of recovered individuals.

Return type:

None