laser.measles.biweekly

laser.measles.biweekly

laser.measles.biweekly.BaseScenario = BaseBiweeklyScenario module-attribute

Base class for scenario data wrappers.

Provides a wrapper around polars DataFrames with additional validation and convenience methods.

Example:

```python
from laser.measles.scenarios.synthetic import single_patch_scenario

scenario = single_patch_scenario(population=100_000, mcv1_coverage=0.85)
# scenario is a Polars DataFrame with columns: id, pop, lat, lon, mcv1
```

laser.measles.biweekly.BiweeklyModel(scenario, params, name='biweekly')

Bases: BaseLaserModel

Population-level measles model with 14-day (biweekly) timesteps.

Tracks SEIR compartment counts per patch without individual agents, making it significantly faster than ABMModel for large-scale parameter sweeps and multi-country analyses. Choose this model when individual-level detail is not required and computational speed is a priority. For daily timesteps with explicit SEIR compartment dynamics, see CompartmentalModel.

This is the first object created in the build model stage of the researcher workflow. After construction, attach components with add_component or by setting the components property, then call model.run().

Parameters:

Name	Type	Description	Default
scenario	DataFrame | BaseBiweeklyScenario	Metapopulation patch data. Required columns: id (str), pop (int), lat (Float64), lon (Float64), mcv1 (Float64). A plain polars.DataFrame is automatically wrapped.	required
params	BiweeklyParams	Simulation parameters including num_ticks, seed, and start_time.	required
name	str	Display name for log messages. Defaults to "biweekly".	'biweekly'

Example:

```python
from laser.measles.biweekly import BiweeklyModel, BiweeklyParams

params = BiweeklyParams(num_ticks=26, seed=42, start_time="2000-01")
model = BiweeklyModel(scenario=df, params=params)
model.components = [InfectionSeedingProcess, InfectionProcess]
model.run()
```

laser.measles.biweekly.BiweeklyModel.__call__(model, tick)

Updates the model for the next tick.

Args:

model: The model containing the patches and their populations.
tick (int): The current time step or tick.

Returns:

None

laser.measles.biweekly.BiweeklyModel.infect(indices, num_infected)

Infects the given nodes with the given number of infected individuals.

Parameters:

Name	Type	Description	Default
indices	int | ndarray	The indices of the nodes to infect.	required
num_infected	int | ndarray	The number of infected individuals to infect.	required

laser.measles.biweekly.BiweeklyModel.recover(indices, num_recovered)

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

Parameters:

Name	Type	Description	Default
indices	int | ndarray	The indices of the nodes to recover.	required
num_recovered	int | ndarray	The number of recovered individuals.	required

laser.measles.biweekly.BiweeklyParams

Bases: BaseModelParams

Parameters for the biweekly compartmental measles model (14-day timesteps).

Inherits all fields from BaseModelParams. Each tick represents 14 days, and the model tracks three SIR states (no explicit Exposed compartment).

Attributes:

Name	Type	Description
num_ticks	int	Number of biweekly simulation steps (e.g., 26 ≈ 1 year, 130 ≈ 5 years).
seed	int	Random seed for reproducibility. Default: 20250314.
start_time	str	Simulation start in "YYYY-MM" format. Default: "2000-01".
verbose	bool	Print detailed logging. Default: False.

Example:

```python
params = BiweeklyParams(num_ticks=26, seed=42, start_time="2000-01")
```

laser.measles.biweekly.BiweeklyParams.states property

SIR state names: ["S", "I", "R"].

laser.measles.biweekly.BiweeklyParams.time_step_days property

Duration of one tick in days (always 14 for the biweekly model).

laser.measles.biweekly.create_component(component_class, params=None)

Helper function to create a component instance with parameters.

This function creates a callable object that will instantiate the component with the given parameters when called by the model.

Parameters

component_class : Type[BaseComponent] The component class to instantiate params : BaseModel, optional Parameter object to pass to the component constructor as params=....

Returns

Callable[[Any], BaseComponent] A single-argument factory: when called by the model with the model instance, it returns component_class(model, params=params).

Example:

```python
from laser.measles import create_component
from laser.measles.compartmental.components import InfectionProcess, InfectionParams

model.components = [
    create_component(InfectionProcess, InfectionParams(beta=0.8)),
]
```