API reference#

This page lists laser-measles’s API.

Base Components#

Components (e.g., infection, aging, vital dynamics, etc.) setup and affect the model, its structure and dynamics. Shared base classes that provide common interfaces and functionality across all model types. Model-specific implementations inherit from these base classes.

Component Architecture#

The laser-measles framework follows a hierarchical component architecture:

Base Components (laser_measles.components) define abstract interfaces and common functionality
Model-Specific Implementations (laser_measles.{model}.components) inherit from base classes and implement model-specific behavior
Parameter Classes use Pydantic for validation and are paired with their respective component classes
Numpy/Numba Pattern - Components can provide both numpy and numba implementations for performance optimization

Inheritance Pattern Example:

# Base class in laser_measles.components
class BaseInitializeEquilibriumStatesProcess(BasePhase):
    # Common interface and default behavior
    pass

# Model-specific implementation in laser_measles.abm.components
class InitializeEquilibriumStatesProcess(BaseInitializeEquilibriumStatesProcess):
    # ABM-specific implementation
    pass

Process Base Classes#

Abstract base classes for components that modify population states and drive model dynamics:

`BaseInitializeEquilibriumStatesProcess`	Initialize S, R states of the population in each of the model states by rough equilibrium of R0.
`BaseVitalDynamicsProcess`	Phase for simulating the vital dynamics in the model with MCV1.
`BaseConstantPopProcess`	A component to handle the birth events in a model with constant population - that is, births == deaths.
`BaseInfectionProcess`	Base class for infection (transmission and disease progression).

Note that each component has a corresponding parameter class that is used to configure the component. For example, the BaseInfectionProcess has a corresponding BaseInfectionParams class. The parameter class is used to configure the component and defaults can be overridden using the create_component function.

Tracker Base Classes#

Abstract base classes for components that monitor and record model state for analysis:

`BaseStateTracker`	Component for tracking the number in each SEIR state for each time tick.
`BaseCaseSurveillanceTracker`	Component for tracking detected cases in the model.
`BasePopulationTracker`	Tracks the population size of each patch at each time tick.
`BaseFadeOutTracker`	A phase that tracks and records the number of nodes experiencing fade-outs over time.

Utilities#

Component creation and management utilities:

`component`	Decorator for creating components with default parameters.
`create_component`	Helper function to create a component instance with parameters.

ABM Model#

Core Model#

Agent based model:

`model`	A class to represent the agent-based model.
`params`	Parameters for the ABM model.
`base`	Basic classes
`utils`	This module provides utility functions for the laser-measles project.

Process Components#

Components that modify population states and drive model dynamics. Most inherit from base classes in laser_measles.components:

`components.InitializeEquilibriumStatesProcess`	Initialize S, R states of the population in each of the model states by rough equilibrium of R0.
`components.VitalDynamicsProcess`	Process for simulating vital dynamics in the ABM model with MCV1 and constant birth and mortality rates (not age-structured).
`components.ConstantPopProcess`	A component to handle the birth events in a model with constant population - that is, births == deaths.
`components.InfectionProcess`	Combined infection process that orchestrates transmission and disease progression.
`components.InfectionSeedingProcess`	Component for seeding initial infections in the compartmental model.
`components.ImportationPressureProcess`	Component for simulating the importation pressure in the model.
`components.SIACalendarProcess`	Phase for implementing Supplementary Immunization Activities (SIAs) based on a calendar schedule.

ABM-Specific Process Components#

Components unique to the ABM model:

`components.NoBirthsProcess`	Component for setting the population of the patches to not have births.
`components.TransmissionProcess`	A component to model the transmission of disease in a population.
`components.DiseaseProcess`	This component provides disease progression (E->I->R) It is used to update the infectious timers and the exposed timers.

Tracker Components#

Components that monitor and record model state for analysis. All inherit from base classes in laser_measles.components:

`components.StateTracker`	ABM state tracking component.
`components.CaseSurveillanceTracker`
`components.PopulationTracker`	Tracks the population size of each patch at each time tick.
`components.FadeOutTracker`	A component that tracks the number of nodes experiencing fade-outs over time.

Compartmental Model#

Core Model#

Compartmental model with daily timesteps:

`model`	This module defines the CompartmentalModel class for SEIR simulation with daily timesteps
`params`	Parameters for the compartmental SEIR model with daily timesteps.
`base`	Basic classes for compartmental model.

Process Components#

Components that modify population states and drive model dynamics. All inherit from base classes in laser_measles.components:

`components.InitializeEquilibriumStatesProcess`	Initialize S, R states of the population in each of the model states by rough equilibrium of R0.
`components.InfectionSeedingProcess`	Process infection seeding.
`components.InfectionProcess`	Component for simulating SEIR disease progression with daily timesteps.
`components.ImportationPressureProcess`	Component for simulating the importation pressure in the model.
`components.VitalDynamicsProcess`	Phase for simulating the vital dynamics in the model with MCV1.
`components.ConstantPopProcess`	A component to handle the birth events in a model with constant population - that is, births == deaths.
`components.SIACalendarProcess`	Phase for implementing Supplementary Immunization Activities (SIAs) based on a calendar schedule.

Tracker Components#

Components that monitor and record model state for analysis. All inherit from base classes in laser_measles.components:

`components.StateTracker`	Atate tracking component.
`components.CaseSurveillanceTracker`	Tracks detected cases in the model.
`components.PopulationTracker`	Tracks the population size of each patch.
`components.FadeOutTracker`	A component that tracks the number of nodes experiencing fade-outs over time.

Biweekly Model#

Core Model#

Compartmental model with 2-week timesteps

`model`	A class to represent the biweekly model.
`params`	Parameters for the biweekly model.
`base`	Basic classes for biweekly model.

Process Components#

Components that modify population states and drive model dynamics. All inherit from base classes in laser_measles.components:

`components.InitializeEquilibriumStatesProcess`	Initialize S, R states of the population in each of the model states by rough equilibrium of R0.
`components.InfectionSeedingProcess`	Process infection seeding.
`components.InfectionProcess`	Component for simulating the spread of infection in the model.
`components.VitalDynamicsProcess`	Phase for simulating the vital dynamics in the model with MCV1.
`components.ImportationPressureProcess`	Component for simulating the importation pressure in the model.
`components.ConstantPopProcess`	A component to handle the birth events in a model with constant population - that is, births == deaths.
`components.SIACalendarProcess`	Phase for implementing Supplementary Immunization Activities (SIAs) based on a calendar schedule.

Tracker Components#

Components that monitor and record model state for analysis. Most inherit from base classes in laser_measles.components:

`components.StateTracker`	Atate tracking component.
`components.CaseSurveillanceTracker`	Tracks detected cases in the model.
`components.PopulationTracker`	Tracks the population size of each patch.
`components.FadeOutTracker`	A component that tracks the number of nodes experiencing fade-outs over time.

Biweekly-Specific Tracker Components#

Components unique to the Biweekly model:

components.FadeOutTracker

A component that tracks the number of nodes experiencing fade-outs over time.

Utilities#

Core Framework#

Base Classes#

Foundation classes that provide the component architecture:

`base.BaseComponent`	Base class for all laser-measles components.
`base.BaseLaserModel`	Base class for laser-measles simulation models.

Utilities#

Core utilities and computation functions:

create_component

Helper function to create a component instance with parameters.

Demographics Package#

Geographic data handling for spatial epidemiological modeling:

Shapefile Utilities#

Functions for processing and visualizing geographic shapefiles:

`get_shapefile_dataframe`	Get a DataFrame containing the shapefile data with DOTNAME and shape columns.
`plot_shapefile_dataframe`
`GADMShapefile`

Raster Processing#

Tools for handling raster data and patch generation:

`RasterPatchParams`
`RasterPatchGenerator`

Mixing Models#

Spatial mixing models for population movement and disease transmission between geographic patches (see laser-core for more details):

Base Classes#

Abstract base class that defines the interface for all mixing models:

base.BaseMixing

Base class for migration models.

Mixing Implementations#

Specific mixing model implementations for different types of population movement:

`gravity.GravityMixing`	Gravity migration model.
`stouffer.StoufferMixing`	Stouffer migration model where long distance travel is impacted by intervening opportunities.
`radiation.RadiationMixing`	Radiation migration model where outbound migration flux from origin to destination is enhanced by destination population and absorbed by the density of nearer destinations.
`competing_destinations.CompetingDestinationsMixing`	Competing destinations mixing model that accounts for the effects of nearby destinations.