vivarium-public-health 4.3.2__py3-none-any.whl → 4.3.3__py3-none-any.whl

vivarium_public_health/results/intervention.py

@@ -1,139 +0,0 @@
-"""
-======================
-Intervention Observers
-======================
-
-This module contains tools for observing risk exposure during the simulation.
-
-"""
-
-import pandas as pd
-from vivarium.framework.engine import Builder
-
-from vivarium_public_health.results.columns import COLUMNS
-from vivarium_public_health.results.observer import PublicHealthObserver
-from vivarium_public_health.utilities import to_years
-
-
-class CategoricalInterventionObserver(PublicHealthObserver):
-    """
-    A class for observering interventions. This class has the same implementation as
-    the 'CategoricalRiskObserver' class.
-
-    """
-
-    @property
-    def columns_required(self) -> list[str] | None:
-        """The columns required by this observer."""
-        return ["alive"]
-
-    #####################
-    # Lifecycle methods #
-    #####################
-
-    def __init__(self, intervention: str) -> None:
-        """Constructor for this observer.
-
-        Parameters
-        ----------
-        intervention
-            The name of the intervention being observed
-        """
-        super().__init__()
-        self.intervention = intervention
-        self.coverage_pipeline_name = f"{self.intervention}.coverage"
-
-    #################
-    # Setup methods #
-    #################
-
-    def setup(self, builder: Builder) -> None:
-        """Set up the observer."""
-        self.step_size = builder.time.step_size()
-        self.categories = builder.data.load(f"intervention.{self.intervention}.categories")
-
-    def get_configuration_name(self) -> str:
-        return self.intervention
-
-    def register_observations(self, builder: Builder) -> None:
-        """Register a stratification and observation.
-
-        Notes
-        -----
-        While it's typical for all stratification registrations to be encapsulated
-        in a single class (i.e. the
-        :class:ResultsStratifier <vivarium_public_health.results.stratification.ResultsStratifier),
-        this observer registers an additional one. While it could be registered
-        in the ``ResultsStratifier`` as well, it is specific to this observer and
-        so it is registered here while we have easy access to the required categories
-        and value names.
-        """
-        builder.results.register_stratification(
-            f"{self.intervention}",
-            list(self.categories.keys()),
-            requires_values=[self.coverage_pipeline_name],
-        )
-        self.register_adding_observation(
-            builder=builder,
-            name=f"person_time_{self.intervention}",
-            pop_filter=f'alive == "alive" and tracked==True',
-            when="time_step__prepare",
-            requires_columns=["alive"],
-            requires_values=[self.coverage_pipeline_name],
-            additional_stratifications=self.configuration.include + [self.intervention],
-            excluded_stratifications=self.configuration.exclude,
-            aggregator=self.aggregate_intervention_category_person_time,
-        )
-
-    ###############
-    # Aggregators #
-    ###############
-
-    def aggregate_intervention_category_person_time(self, x: pd.DataFrame) -> float:
-        """Aggregate the person time for this time step."""
-        return len(x) * to_years(self.step_size())
-
-    ##############################
-    # Results formatting methods #
-    ##############################
-
-    def format(self, measure: str, results: pd.DataFrame) -> pd.DataFrame:
-        """Rename the appropriate column to 'sub_entity'.
-
-        The primary thing this method does is rename the risk column
-        to 'sub_entity'. We do this here instead of the 'get_sub_entity_column'
-        method simply because we do not want the risk column at all. If we keep
-        it here and then return it as the sub-entity column later, the final
-        results would have both.
-
-        Parameters
-        ----------
-        measure
-            The measure.
-        results
-            The results to format.
-
-        Returns
-        -------
-            The formatted results.
-        """
-        results = results.reset_index()
-        results.rename(columns={self.intervention: COLUMNS.SUB_ENTITY}, inplace=True)
-        return results
-
-    def get_measure_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
-        """Get the 'measure' column values."""
-        return pd.Series("person_time", index=results.index)
-
-    def get_entity_type_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
-        """Get the 'entity_type' column values."""
-        return pd.Series("rei", index=results.index)
-
-    def get_entity_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
-        """Get the 'entity' column values."""
-        return pd.Series(self.intervention, index=results.index)
-
-    def get_sub_entity_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
-        """Get the 'sub_entity' column values."""
-        # The sub-entity col was created in the 'format' method
-        return results[COLUMNS.SUB_ENTITY]

vivarium_public_health/treatment/intervention.py

@@ -1,85 +0,0 @@
-from typing import NamedTuple
-
-from vivarium_public_health.exposure import Exposure
-from vivarium_public_health.exposure.effect import ExposureEffect
-from vivarium_public_health.utilities import EntityString, TargetString
-
-
-class Intervention(Exposure):
-    """A model for an intervention defined by coverage (access to intervention).
-
-    This component models access to an intervention as a dichotomous exposure where
-    simulants are either covered or uncovered by the intervention.
-
-    For example,
-
-    #. vaccination coverage where simulants are either vaccinated (covered) or
-       unvaccinated (uncovered).
-    #. treatment access where simulants either have access to treatment (covered)
-       or do not have access (uncovered).
-
-    This component can source data either from a key in an Artifact
-    ("intervention.intervention_name.coverage") or from parameters
-    supplied in the configuration. If data is derived from the configuration, it
-    must be an integer or float expressing the desired coverage level or a
-    covariate name that is intended to be used as a proxy. For example, for an
-    intervention named "intervention", the configuration could look like this:
-
-    .. code-block:: yaml
-
-       configuration:
-           intervention.intervention_name:
-               coverage: 0.8
-
-    Interventions should be configured with names in the format of
-    "intervention.intervention_name".
-
-    """
-
-    @property
-    def exposure_type(self) -> str:
-        """The measure of the intervention access."""
-        return "coverage"
-
-    @property
-    def dichotomous_exposure_category_names(self) -> NamedTuple:
-        """The name of the covered and uncovered categories for this intervention."""
-
-        class __Categories(NamedTuple):
-            exposed: str = "covered"
-            unexposed: str = "uncovered"
-
-        categories = __Categories()
-        return categories
-
-
-class InterventionEffect(ExposureEffect):
-    """A component to model the effect of an intervention on an affected entity's target rate.
-
-    This component models how intervention coverage affects the rate of some target
-    entity (e.g., disease incidence, mortality, disability). The effect is typically
-    protective, reducing the target rate for covered simulants compared to uncovered
-    simulants.
-
-    This component can source data either from builder.data or from parameters
-    supplied in the configuration. The data should specify the relative risk or
-    rate ratio associated with intervention coverage.
-
-    For example, an intervention effect might model how vaccination coverage affects
-    disease incidence, where vaccinated individuals have a lower risk of disease
-    compared to unvaccinated individuals.
-
-    For an exposure named 'exposure_name' that affects  'affected_entity' and 'affected_cause',
-    the configuration would look like:
-
-    .. code-block:: yaml
-
-       configuration:
-            intervention_effect.exposure_name_on_affected_target:
-               exposure_parameters: 2
-               incidence_rate: 10
-
-    """
-
-    def get_name(self, intervention: EntityString, target: TargetString) -> str:
-        return f"intervention_effect.{intervention.name}_on_{target}"