laser.measles.abm.components.process_infection

process_infection

Component defining the InfectionProcess, which orchestrates the transmission and disease progression of measles in a population.

InfectionParams

Bases: BaseInfectionParams

Combined parameters for ABM transmission and disease processes.

Spatial mixing is controlled in one of two ways:

1. Default gravity — leave mixer as None and configure distance_exponent and mixing_scale. Internally a GravityMixing is constructed using those values.
2. Custom mixer — pass any mixing object (e.g. GravityMixing(...), RadiationMixing(...)) as mixer=. When set, this takes precedence; distance_exponent and mixing_scale are ignored.

The model sets the patch scenario on the mixer automatically at initialisation, so callers don't need to assign mixer.scenario themselves.

Examples:

# 1. Default gravity, tuned via the convenience knobs
infection_params = InfectionParams(
    beta=20.0,
    distance_exponent=2.0,
    mixing_scale=0.005,
)

# 2. Custom mixer — e.g. radiation model
from laser.measles.mixing.radiation import RadiationMixing
infection_params = InfectionParams(
    beta=20.0,
    mixer=RadiationMixing(),
)

disease_params property

Extract disease-specific parameters.

transmission_params property

Build the TransmissionParams to hand to TransmissionProcess.

If the caller supplied a mixer, pass it through. Otherwise wire distance_exponent and mixing_scale into a default GravityMixing(GravityParams(c=..., k=...)). The latter is the fix called out in #140 — passing those values to TransmissionParams directly silently dropped them because TransmissionParams doesn't declare them.

InfectionProcess(model, params=None)

Bases: BaseInfectionProcess

Combined infection process that orchestrates transmission and disease progression.

This component provides a unified interface for both disease transmission (handled by TransmissionProcess) and disease progression through states (handled by DiseaseProcess), similar to the biweekly model's InfectionProcess but for agent-based modeling.

Examples:

from laser.measles.scenarios.synthetic import single_patch_scenario
from laser.measles.abm import ABMModel, ABMParams
from laser.measles.abm import components
from laser.measles import create_component

scenario = single_patch_scenario(population=50_000, mcv1_coverage=0.85)
params = ABMParams(num_ticks=365, seed=42, start_time="2000-01")
model = ABMModel(scenario, params)
model.add_component(create_component(components.InfectionProcess, components.InfectionParams(beta=0.3)))

Initialize the combined infection process.

Parameters:

Name	Type	Description	Default
model	ABMModel	The model object that contains the patches and parameters.	required
params	InfectionParams | None	Combined parameters for both transmission and disease processes.	None

mixing_matrix property

The spatial mixing matrix the wrapped TransmissionProcess is using.

Convenience accessor that walks down to the live mixer instance: self.transmission.params.mixer.mixing_matrix. Once the model has run, mixer.scenario is set and the matrix is lazily computed on first access. Shape is (n_patches, n_patches).

Provided here so code that has a handle on the InfectionProcess (e.g. model.get_instance("InfectionProcess")[0]) can get the matrix in one hop, without knowing that TransmissionProcess is nested inside as a sub-component rather than registered separately.

__call__(model, tick)

Execute both transmission and disease progression for the given tick.

Parameters:

Name	Type	Description	Default
model	ABMModel	The model object containing the population, patches, and parameters.	required
tick	int	The current time step in the simulation.	required

infect(model, idx)

Move agents at the given indices from susceptible to exposed.

Parameters:

Name	Type	Description	Default
model	ABMModel	The ABM model instance.	required
idx	ndarray	Array of agent indices to infect.	required

plot(fig=None)

Plot cases and incidence using the transmission component's plotting functionality.

Parameters:

Name	Type	Description	Default
fig	Figure | None	A Matplotlib Figure object to plot on. If None, a new figure is created.	None