vivarium-public-health 4.3.2__py3-none-any.whl → 4.3.4__py3-none-any.whl

vivarium_public_health/risks/effect.py

@@ -3,50 +3,338 @@
 Risk Effect Models
 ==================
 
-"""
+This module contains tools for modeling the relationship between risk
+exposure models and disease models.
 
-import warnings
+"""
 from collections.abc import Callable
+from importlib import import_module
 from typing import Any
 
 import numpy as np
 import pandas as pd
 import scipy
+from layered_config_tree import ConfigurationError
+from vivarium import Component
 from vivarium.framework.engine import Builder
+from vivarium.framework.values import Pipeline
 
-from vivarium_public_health.exposure import ExposureEffect
-from vivarium_public_health.exposure.distributions import MissingDataError
-from vivarium_public_health.utilities import EntityString, TargetString
+from vivarium_public_health.risks import Risk
+from vivarium_public_health.risks.data_transformations import (
+    load_exposure_data,
+    pivot_categorical,
+)
+from vivarium_public_health.risks.distributions import MissingDataError
+from vivarium_public_health.utilities import EntityString, TargetString, get_lookup_columns
 
 
-class RiskEffect(ExposureEffect):
+class RiskEffect(Component):
     """A component to model the effect of a risk factor on an affected entity's target rate.
 
     This component can source data either from builder.data or from parameters
     supplied in the configuration.
 
+    For a risk named 'risk' that affects  'affected_risk' and 'affected_cause',
+    the configuration would look like:
+
+    .. code-block:: yaml
+
+       configuration:
+            risk_effect.risk_name_on_affected_target:
+               exposure_parameters: 2
+               incidence_rate: 10
+
     """
 
+    ###############
+    # Properties #
+    ##############
+
+    @property
+    def name(self) -> str:
+        return self.get_name(self.risk, self.target)
+
+    @staticmethod
+    def get_name(risk: EntityString, target: TargetString) -> str:
+        return f"risk_effect.{risk.name}_on_{target}"
+
+    @property
+    def configuration_defaults(self) -> dict[str, Any]:
+        """Default values for any configurations managed by this component."""
+        return {
+            self.name: {
+                "data_sources": {
+                    "relative_risk": f"{self.risk}.relative_risk",
+                    "population_attributable_fraction": f"{self.risk}.population_attributable_fraction",
+                },
+                "data_source_parameters": {
+                    "relative_risk": {},
+                },
+            }
+        }
+
     @property
-    def risk(self) -> str:
-        warnings.warn(
-            "The 'risk' attribute is deprecated. Use 'entity' instead.",
-            DeprecationWarning,
-            stacklevel=2,
+    def is_exposure_categorical(self) -> bool:
+        return self._exposure_distribution_type in [
+            "dichotomous",
+            "ordered_polytomous",
+            "unordered_polytomous",
+        ]
+
+    #####################
+    # Lifecycle methods #
+    #####################
+
+    def __init__(self, risk: str, target: str):
+        """
+
+        Parameters
+        ----------
+        risk
+            Type and name of risk factor, supplied in the form
+            "risk_type.risk_name" where risk_type should be singular (e.g.,
+            risk_factor instead of risk_factors).
+        target
+            Type, name, and target rate of entity to be affected by risk factor,
+            supplied in the form "entity_type.entity_name.measure"
+            where entity_type should be singular (e.g., cause instead of causes).
+        """
+        super().__init__()
+        self.risk = EntityString(risk)
+        self.target = TargetString(target)
+
+        self._exposure_distribution_type = None
+
+        self.exposure_pipeline_name = f"{self.risk.name}.exposure"
+        self.target_pipeline_name = f"{self.target.name}.{self.target.measure}"
+        self.target_paf_pipeline_name = f"{self.target_pipeline_name}.paf"
+
+    # noinspection PyAttributeOutsideInit
+    def setup(self, builder: Builder) -> None:
+        self.exposure = self.get_risk_exposure(builder)
+
+        self._relative_risk_source = self.get_relative_risk_source(builder)
+        self.relative_risk = self.get_relative_risk_pipeline(builder)
+
+        self.register_target_modifier(builder)
+        self.register_paf_modifier(builder)
+
+    #################
+    # Setup methods #
+    #################
+
+    def build_all_lookup_tables(self, builder: Builder) -> None:
+        self._exposure_distribution_type = self.get_distribution_type(builder)
+
+        rr_data = self.load_relative_risk(builder)
+        rr_value_cols = None
+        if self.is_exposure_categorical:
+            rr_data, rr_value_cols = self.process_categorical_data(builder, rr_data)
+        self.lookup_tables["relative_risk"] = self.build_lookup_table(
+            builder, rr_data, rr_value_cols
+        )
+
+        paf_data = self.get_filtered_data(
+            builder, self.configuration.data_sources.population_attributable_fraction
         )
-        return self.entity
-
-    @risk.setter
-    def risk(self, value: str) -> None:
-        warnings.warn(
-            "The 'risk' attribute is deprecated. Use 'entity' instead.",
-            DeprecationWarning,
-            stacklevel=2,
+        self.lookup_tables["population_attributable_fraction"] = self.build_lookup_table(
+            builder, paf_data
         )
-        self.entity = value
 
-    def get_name(self, risk: EntityString, target: TargetString) -> str:
-        return f"risk_effect.{risk.name}_on_{target}"
+    def get_distribution_type(self, builder: Builder) -> str:
+        """Get the distribution type for the risk from the configuration."""
+        risk_exposure_component = self._get_risk_exposure_class(builder)
+        if risk_exposure_component.distribution_type:
+            return risk_exposure_component.distribution_type
+        return risk_exposure_component.get_distribution_type(builder)
+
+    def load_relative_risk(
+        self,
+        builder: Builder,
+        configuration=None,
+    ) -> str | float | pd.DataFrame:
+        if configuration is None:
+            configuration = self.configuration
+
+        rr_source = configuration.data_sources.relative_risk
+        rr_dist_parameters = configuration.data_source_parameters.relative_risk.to_dict()
+
+        if isinstance(rr_source, str):
+            try:
+                distribution = getattr(import_module("scipy.stats"), rr_source)
+                rng = np.random.default_rng(builder.randomness.get_seed(self.name))
+                rr_data = distribution(**rr_dist_parameters).ppf(rng.random())
+            except AttributeError:
+                rr_data = self.get_filtered_data(builder, rr_source)
+            except TypeError:
+                raise ConfigurationError(
+                    f"Parameters {rr_dist_parameters} are not valid for distribution {rr_source}."
+                )
+        else:
+            rr_data = self.get_filtered_data(builder, rr_source)
+        return rr_data
+
+    def get_filtered_data(
+        self, builder: "Builder", data_source: str | float | pd.DataFrame
+    ) -> float | pd.DataFrame:
+        data = super().get_data(builder, data_source)
+
+        if isinstance(data, pd.DataFrame):
+            # filter data to only include the target entity and measure
+            correct_target_mask = True
+            columns_to_drop = []
+            if "affected_entity" in data.columns:
+                correct_target_mask &= data["affected_entity"] == self.target.name
+                columns_to_drop.append("affected_entity")
+            if "affected_measure" in data.columns:
+                correct_target_mask &= data["affected_measure"] == self.target.measure
+                columns_to_drop.append("affected_measure")
+            data = data[correct_target_mask].drop(columns=columns_to_drop)
+        return data
+
+    def process_categorical_data(
+        self, builder: Builder, rr_data: str | float | pd.DataFrame
+    ) -> tuple[str | float | pd.DataFrame, list[str]]:
+        if not isinstance(rr_data, pd.DataFrame):
+            cat1 = builder.data.load("population.demographic_dimensions")
+            cat1["parameter"] = "cat1"
+            cat1["value"] = rr_data
+            cat2 = cat1.copy()
+            cat2["parameter"] = "cat2"
+            cat2["value"] = 1
+            rr_data = pd.concat([cat1, cat2], ignore_index=True)
+        if "parameter" in rr_data.index.names:
+            rr_data = rr_data.reset_index("parameter")
+
+        rr_value_cols = list(rr_data["parameter"].unique())
+        rr_data = pivot_categorical(builder, self.risk, rr_data, "parameter")
+        return rr_data, rr_value_cols
+
+    # todo currently this isn't being called. we need to properly set rrs if
+    #  the exposure has been rebinned
+    def rebin_relative_risk_data(
+        self, builder, relative_risk_data: pd.DataFrame
+    ) -> pd.DataFrame:
+        """Rebin relative risk data.
+
+        When the polytomous risk is rebinned, matching relative risk needs to be rebinned.
+        After rebinning, rr for both exposed and unexposed categories should be the weighted sum of relative risk
+        of the component categories where weights are relative proportions of exposure of those categories.
+        For example, if cat1, cat2, cat3 are exposed categories and cat4 is unexposed with exposure [0.1,0.2,0.3,0.4],
+        for the matching rr = [rr1, rr2, rr3, 1], rebinned rr for the rebinned cat1 should be:
+        (0.1 *rr1 + 0.2 * rr2 + 0.3* rr3) / (0.1+0.2+0.3)
+        """
+        if not self.risk in builder.configuration.to_dict():
+            return relative_risk_data
+
+        rebin_exposed_categories = set(builder.configuration[self.risk]["rebinned_exposed"])
+
+        if rebin_exposed_categories:
+            # todo make sure this works
+            exposure_data = load_exposure_data(builder, self.risk)
+            relative_risk_data = self._rebin_relative_risk_data(
+                relative_risk_data, exposure_data, rebin_exposed_categories
+            )
+
+        return relative_risk_data
+
+    def _rebin_relative_risk_data(
+        self,
+        relative_risk_data: pd.DataFrame,
+        exposure_data: pd.DataFrame,
+        rebin_exposed_categories: set,
+    ) -> pd.DataFrame:
+        cols = list(exposure_data.columns.difference(["value"]))
+
+        relative_risk_data = relative_risk_data.merge(exposure_data, on=cols)
+        relative_risk_data["value_x"] = relative_risk_data.value_x.multiply(
+            relative_risk_data.value_y
+        )
+        relative_risk_data.parameter = relative_risk_data["parameter"].map(
+            lambda p: "cat1" if p in rebin_exposed_categories else "cat2"
+        )
+        relative_risk_data = relative_risk_data.groupby(cols).sum().reset_index()
+        relative_risk_data["value"] = relative_risk_data.value_x.divide(
+            relative_risk_data.value_y
+        ).fillna(0)
+        return relative_risk_data.drop(columns=["value_x", "value_y"])
+
+    def get_risk_exposure(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
+        return builder.value.get_value(self.exposure_pipeline_name)
+
+    def adjust_target(self, index: pd.Index, target: pd.Series) -> pd.Series:
+        relative_risk = self.relative_risk(index)
+        return target * relative_risk
+
+    def get_relative_risk_source(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
+
+        if not self.is_exposure_categorical:
+            tmred = builder.data.load(f"{self.risk}.tmred")
+            tmrel = 0.5 * (tmred["min"] + tmred["max"])
+            scale = builder.data.load(f"{self.risk}.relative_risk_scalar")
+
+            def generate_relative_risk(index: pd.Index) -> pd.Series:
+                rr = self.lookup_tables["relative_risk"](index)
+                exposure = self.exposure(index)
+                relative_risk = np.maximum(rr.values ** ((exposure - tmrel) / scale), 1)
+                return relative_risk
+
+        else:
+            index_columns = ["index", self.risk.name]
+
+            def generate_relative_risk(index: pd.Index) -> pd.Series:
+                rr = self.lookup_tables["relative_risk"](index)
+                exposure = self.exposure(index).reset_index()
+                exposure.columns = index_columns
+                exposure = exposure.set_index(index_columns)
+
+                relative_risk = rr.stack().reset_index()
+                relative_risk.columns = index_columns + ["value"]
+                relative_risk = relative_risk.set_index(index_columns)
+
+                effect = relative_risk.loc[exposure.index, "value"].droplevel(self.risk.name)
+                return effect
+
+        return generate_relative_risk
+
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
+        return builder.value.register_value_producer(
+            f"{self.risk.name}_on_{self.target.name}.relative_risk",
+            self._relative_risk_source,
+            component=self,
+            required_resources=[self.exposure],
+        )
+
+    def register_target_modifier(self, builder: Builder) -> None:
+        builder.value.register_value_modifier(
+            self.target_pipeline_name,
+            modifier=self.adjust_target,
+            component=self,
+            required_resources=[self.relative_risk],
+        )
+
+    def register_paf_modifier(self, builder: Builder) -> None:
+        required_columns = get_lookup_columns(
+            [self.lookup_tables["population_attributable_fraction"]]
+        )
+        builder.value.register_value_modifier(
+            self.target_paf_pipeline_name,
+            modifier=self.lookup_tables["population_attributable_fraction"],
+            component=self,
+            required_resources=required_columns,
+        )
+
+    ##################
+    # Helper methods #
+    ##################
+
+    def _get_risk_exposure_class(self, builder: Builder) -> Risk:
+        risk_exposure_component = builder.components.get_component(self.risk)
+        if not isinstance(risk_exposure_component, Risk):
+            raise ValueError(
+                f"Risk effect model {self.name} requires a Risk component named {self.risk}"
+            )
+        return risk_exposure_component
 
 
 class NonLogLinearRiskEffect(RiskEffect):
@@ -78,15 +366,15 @@ class NonLogLinearRiskEffect(RiskEffect):
         return {
             self.name: {
                 "data_sources": {
-                    "relative_risk": f"{self.entity}.relative_risk",
-                    "population_attributable_fraction": f"{self.entity}.population_attributable_fraction",
+                    "relative_risk": f"{self.risk}.relative_risk",
+                    "population_attributable_fraction": f"{self.risk}.population_attributable_fraction",
                 },
             }
         }
 
     @property
     def columns_required(self) -> list[str]:
-        return [f"{self.entity.name}_exposure"]
+        return [f"{self.risk.name}_exposure"]
 
     #################
     # Setup methods #
@@ -126,8 +414,8 @@ class NonLogLinearRiskEffect(RiskEffect):
             .reset_index()
         )
         rr_data = rr_data.drop("parameter", axis=1)
-        rr_data[f"{self.entity.name}_exposure_start"] = rr_data["left_exposure"]
-        rr_data[f"{self.entity.name}_exposure_end"] = rr_data["right_exposure"]
+        rr_data[f"{self.risk.name}_exposure_start"] = rr_data["left_exposure"]
+        rr_data[f"{self.risk.name}_exposure_end"] = rr_data["right_exposure"]
         # build lookup table
         rr_value_cols = ["left_exposure", "left_rr", "right_exposure", "right_rr"]
         self.lookup_tables["relative_risk"] = self.build_lookup_table(
@@ -150,19 +438,17 @@ class NonLogLinearRiskEffect(RiskEffect):
             configuration = self.configuration
 
         # get TMREL
-        tmred = builder.data.load(f"{self.entity}.tmred")
+        tmred = builder.data.load(f"{self.risk}.tmred")
         if tmred["distribution"] == "uniform":
             draw = builder.configuration.input_data.input_draw_number
             rng = np.random.default_rng(builder.randomness.get_seed(self.name + str(draw)))
             self.tmrel = rng.uniform(tmred["min"], tmred["max"])
         elif tmred["distribution"] == "draws":  # currently only for iron deficiency
             raise MissingDataError(
-                f"This data has draw-level TMRELs. You will need to contact the research team that models {self.entity.name} to get this data."
+                f"This data has draw-level TMRELs. You will need to contact the research team that models {self.risk.name} to get this data."
             )
         else:
-            raise MissingDataError(
-                f"No TMRED found in gbd_mapping for risk {self.entity.name}"
-            )
+            raise MissingDataError(f"No TMRED found in gbd_mapping for risk {self.risk.name}")
 
         # calculate RR at TMREL
         rr_source = configuration.data_sources.relative_risk
@@ -203,7 +489,7 @@ class NonLogLinearRiskEffect(RiskEffect):
     def get_relative_risk_source(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
         def generate_relative_risk(index: pd.Index) -> pd.Series:
             rr_intervals = self.lookup_tables["relative_risk"](index)
-            exposure = self.population_view.get(index)[f"{self.entity.name}_exposure"]
+            exposure = self.population_view.get(index)[f"{self.risk.name}_exposure"]
             x1, x2 = (
                 rr_intervals["left_exposure"].values,
                 rr_intervals["right_exposure"].values,
@@ -226,7 +512,7 @@ class NonLogLinearRiskEffect(RiskEffect):
         parameter_data_is_numeric = rr_data["parameter"].dtype.kind in "biufc"
         if not parameter_data_is_numeric:
             raise ValueError(
-                f"The parameter column in your {self.entity.name} relative risk data must contain numeric data. Its dtype is {rr_data['parameter'].dtype} instead."
+                f"The parameter column in your {self.risk.name} relative risk data must contain numeric data. Its dtype is {rr_data['parameter'].dtype} instead."
             )
 
         # and that these RR values are monotonically increasing within each demographic group

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -22,12 +22,12 @@ from vivarium.framework.population import SimulantData
 from vivarium.framework.resource import Resource
 from vivarium.framework.values import Pipeline
 
-from vivarium_public_health.exposure.distributions import PolytomousDistribution
 from vivarium_public_health.risks import Risk, RiskEffect
 from vivarium_public_health.risks.data_transformations import (
     get_exposure_post_processor,
     pivot_categorical,
 )
+from vivarium_public_health.risks.distributions import PolytomousDistribution
 from vivarium_public_health.utilities import EntityString, get_lookup_columns, to_snake_case
 
 CATEGORICAL = "categorical"
@@ -71,10 +71,7 @@ class LBWSGDistribution(PolytomousDistribution):
 
             if isinstance(birth_exposure_data, pd.DataFrame):
                 birth_exposure_data = pivot_categorical(
-                    builder,
-                    self.exposure_component.entity,
-                    birth_exposure_data,
-                    "parameter",
+                    builder, self.risk, birth_exposure_data, "parameter"
                 )
 
             self.lookup_tables["birth_exposure"] = self.build_lookup_table(
@@ -121,9 +118,7 @@ class LBWSGDistribution(PolytomousDistribution):
         -------
             The intervals for each category.
         """
-        categories: dict[str, str] = builder.data.load(
-            f"{self.exposure_component.entity}.categories"
-        )
+        categories: dict[str, str] = builder.data.load(f"{self.risk}.categories")
         category_intervals = {
             axis: {
                 category: self._parse_description(axis, description)
@@ -276,7 +271,7 @@ class LBWSGRisk(Risk):
         # Add birth exposure data source
         configuration_defaults[self.name]["data_sources"][
             "birth_exposure"
-        ] = f"{self.entity}.birth_exposure"
+        ] = f"{self.risk}.birth_exposure"
         configuration_defaults[self.name]["distribution_type"] = "lbwsg"
         return configuration_defaults
 
@@ -305,7 +300,7 @@ class LBWSGRisk(Risk):
         # Propensity only used on initialization; not being saved to avoid a cycle
         return None
 
-    def get_exposure_callable(self, builder: Builder) -> Pipeline | None:
+    def get_exposure_pipeline(self, builder: Builder) -> Pipeline | None:
         # Exposure only used on initialization; not being saved to avoid a cycle
         return None
 
@@ -364,7 +359,7 @@ class LBWSGRisk(Risk):
 
     def get_current_exposure(self, index: pd.Index) -> pd.DataFrame:
         raise LifeCycleError(
-            f"The {self.entity.name} exposure pipeline should not be called. You probably want to"
+            f"The {self.risk.name} exposure pipeline should not be called. You probably want to"
             f" refer directly one of the exposure columns. During simulant initialization the birth"
             f" exposure pipelines should be used instead."
         )
@@ -405,12 +400,12 @@ class LBWSGRiskEffect(RiskEffect):
             LBWSGRisk.get_exposure_column_name(axis) for axis in LBWSGRisk.AXES
         ]
         self.relative_risk_pipeline_name = (
-            f"effect_of_{self.entity.name}_on_{self.target.name}.relative_risk"
+            f"effect_of_{self.risk.name}_on_{self.target.name}.relative_risk"
         )
 
     def relative_risk_column_name(self, age_group_id: str) -> str:
         return (
-            f"effect_of_{self.entity.name}_on_{age_group_id}_{self.target.name}_relative_risk"
+            f"effect_of_{self.risk.name}_on_{age_group_id}_{self.target.name}_relative_risk"
         )
 
     # noinspection PyAttributeOutsideInit
@@ -431,7 +426,7 @@ class LBWSGRiskEffect(RiskEffect):
             builder, paf_data, paf_value_cols
         )
 
-    def get_exposure_callable(self, builder: Builder) -> Callable[[pd.Index], pd.DataFrame]:
+    def get_risk_exposure(self, builder: Builder) -> Callable[[pd.Index], pd.DataFrame]:
         def exposure(index: pd.Index) -> pd.DataFrame:
             return self.population_view.subview(self.lbwsg_exposure_column_names).get(index)
 
@@ -440,7 +435,7 @@ class LBWSGRiskEffect(RiskEffect):
     def get_population_attributable_fraction_source(
         self, builder: Builder
     ) -> tuple[pd.DataFrame, list[str]]:
-        paf_key = f"{self.entity}.population_attributable_fraction"
+        paf_key = f"{self.risk}.population_attributable_fraction"
         paf_data = builder.data.load(paf_key)
         return paf_data, builder.data.value_columns()(paf_key)
 
@@ -454,7 +449,7 @@ class LBWSGRiskEffect(RiskEffect):
 
     def get_age_intervals(self, builder: Builder) -> dict[str, pd.Interval]:
         age_bins = builder.data.load("population.age_bins").set_index("age_start")
-        relative_risks = builder.data.load(f"{self.entity}.relative_risk")
+        relative_risks = builder.data.load(f"{self.risk}.relative_risk")
         exposed_age_group_starts = (
             relative_risks.groupby("age_start")["value"].any().reset_index()["age_start"]
         )
@@ -481,7 +476,7 @@ class LBWSGRiskEffect(RiskEffect):
         }
 
         # get relative risk data for target
-        interpolators = builder.data.load(f"{self.entity}.relative_risk_interpolator")
+        interpolators = builder.data.load(f"{self.risk}.relative_risk_interpolator")
         interpolators = (
             # isolate RRs for target and drop non-neonatal age groups since they have RR == 1.0
             interpolators[

vivarium_public_health/treatment/__init__.py

@@ -1,4 +1,3 @@
-from vivarium_public_health.treatment.intervention import Intervention, InterventionEffect
 from vivarium_public_health.treatment.magic_wand import AbsoluteShift
 from vivarium_public_health.treatment.scale_up import LinearScaleUp
 from vivarium_public_health.treatment.therapeutic_inertia import TherapeuticInertia

{vivarium_public_health-4.3.2.dist-info → vivarium_public_health-4.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.2
+Version: 4.3.4
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -31,7 +31,7 @@ Requires-Dist: vivarium>=3.4.3
 Requires-Dist: layered_config_tree>=3.2.0
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0
-Requires-Dist: pandas>=2.2.0
+Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk_distributions>=2.0.11

{vivarium_public_health-4.3.2.dist-info → vivarium_public_health-4.3.4.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
-vivarium_public_health/__init__.py,sha256=OMVtFq_K6QhpSxj1Y-pLsDeYooGI06zWR8ahqoUMcOw,1402
-vivarium_public_health/_version.py,sha256=yLGM4izTFYAco_KyNHOnLCDPCtERPpxlH_qI5n-sU7E,22
+vivarium_public_health/__init__.py,sha256=GDeeP-7OlCBwPuv_xQoB1wNmvCaFsqfTB7qnnYApm0w,1343
+vivarium_public_health/_version.py,sha256=215K0AQu12pX2_elDj3eHwDGWbBrLpNequvlrMryST8,22
 vivarium_public_health/utilities.py,sha256=QNXQ6fhAr1HcV-GwKw7wQLz6QyuNxqNvMA-XujKjTgs,3035
 vivarium_public_health/disease/__init__.py,sha256=VUJHDLlE6ngo2qHNQUtZ8OWH5H_T7_ao-xsYKDkRmHw,443
 vivarium_public_health/disease/exceptions.py,sha256=vb30IIV82OiDf2cNZCs_E2rF6mdDDHbnZSND60no5CU,97
@@ -9,11 +9,6 @@ vivarium_public_health/disease/models.py,sha256=01UK7yB2zGPFzmlIpvhd-XnGe6vSCMDz
 vivarium_public_health/disease/special_disease.py,sha256=4tGfnXSVuNYsA7izX9y81ByJe46c4h293szVt7AyPMA,14605
 vivarium_public_health/disease/state.py,sha256=ptcNETOo8a0NRXOdUhZMgCJa2h3Pt5ZElhMOKonkD4c,28560
 vivarium_public_health/disease/transition.py,sha256=HPvv1l322XiQcNXIgDTt3WvytxSbuz_2jyPj-spQE3Y,9209
-vivarium_public_health/exposure/__init__.py,sha256=CgpEy1CCkfVEyKwKh3nknyWAv4wUuvqpHzbit7DOvzA,66
-vivarium_public_health/exposure/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
-vivarium_public_health/exposure/distributions.py,sha256=XSGDT1TR0HVr4Gqi_Mc7m9nz5aMiDrrfr0WTU572Vsk,20827
-vivarium_public_health/exposure/effect.py,sha256=cb-as4133uUXntyV-vZ3hv1drE_ylCLd8upR978yOXk,14416
-vivarium_public_health/exposure/exposure.py,sha256=woAPnhDSILhZ2D3cQkGQvSwniPhXKmaHcwH1XrsNmUc,9261
 vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 vivarium_public_health/mslt/delay.py,sha256=_neQ8oL2IhCqH0hiM4Od4Eb8NfYjyjSoniq02PFieTw,22872
 vivarium_public_health/mslt/disease.py,sha256=Kwy7cDqiE9yYCsLV_7pAP7ZOe7GWVHUBe39a-GOInVU,16867
@@ -26,32 +21,30 @@ vivarium_public_health/plugins/parser.py,sha256=WoUisq0d-PfJtSzKYZ6C-s-fYdQpNiRB
 vivarium_public_health/population/__init__.py,sha256=x_9rB93q64Krw-kbBDI1-_U_JsPO1_QrL03AwiFlwXI,243
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=x6A60GE_F3I8AgLABNJ-2ziiUj52lAd66uX5yc2vIDI,9038
 vivarium_public_health/population/base_population.py,sha256=Wu797AL13KRLhXkYni_XocJBLfhfvCVgGeas08U3tCM,18898
-vivarium_public_health/population/data_transformations.py,sha256=59wQvv-Uvr8qEhqJK2DoUKZJ8TYvBR5TBNAs2vdQnng,22498
+vivarium_public_health/population/data_transformations.py,sha256=YHbwfb40EPbXsPW-Rk1s5d61rP8fqgDtMELB7OJG3mo,22662
 vivarium_public_health/population/mortality.py,sha256=Mtv45FENNY0GlPIoVd3d3pRq01aEh4cjzNXIgEe6hMo,10364
-vivarium_public_health/results/__init__.py,sha256=l9oB36il1nUl2cd2FSd9r65VVdBHSCZvxA2VkuqHkdQ,377
+vivarium_public_health/results/__init__.py,sha256=rKUZGlRXJgEyFY4a_WJeg3XnC0l34S5guYZ0N9JJS4E,319
 vivarium_public_health/results/columns.py,sha256=V-L3JgTcsk51Zx9PcUwSgaE1iZjuGyfZ8aShPjynadU,495
 vivarium_public_health/results/disability.py,sha256=OijmWbPkaxmMT4xJ44rWgPz67lVfcLtEloaNwnOiK_g,9459
 vivarium_public_health/results/disease.py,sha256=ni599TKhV3YKQb8_rlnTVt9tIFq_SiM-z8qaoBEdO6s,11764
-vivarium_public_health/results/intervention.py,sha256=M9cGZOamxaXUXy6dOchHE7RXKh43bXyk9SNeMDur6Nc,5004
 vivarium_public_health/results/mortality.py,sha256=9L8tphHn2BEt5sSDkvSfcAyyhsGA_xylEjTed-fv0YI,9206
 vivarium_public_health/results/observer.py,sha256=ADikaV6TvHVaysWoeux_DcvmzAFT7kpD6KtRSl16SaY,7277
 vivarium_public_health/results/risk.py,sha256=bPZq2El00MZ5A6ttqA-wvbHLm4E3OZcEZOkqV_GENk4,5838
 vivarium_public_health/results/simple_cause.py,sha256=ibdE6KwhDfQWntCVkOEooBcmUydEoupmd3_poHSHyu8,1007
 vivarium_public_health/results/stratification.py,sha256=4I3YGHVabNAZENE7YboOtWsWU4X-8LUBJ9iwYMbpl6E,5387
 vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4izju_0DNe2Ghw,212
-vivarium_public_health/risks/base_risk.py,sha256=CKZM1cGYRInxiM738bMxmaNIKkPg6yX5VaWglzBzLsM,3930
-vivarium_public_health/risks/data_transformations.py,sha256=JiTBBY8xyZx_idoYk-UALRdAnLE20nywcTqi0_PKaB4,1123
-vivarium_public_health/risks/distributions.py,sha256=XFbGhtCT7cQRS859RIQO0XPyEK0BsK8czv2CxI8BWO4,771
-vivarium_public_health/risks/effect.py,sha256=RhBNsKinVRIYwX0PnrpkbaI2U9HDmBPCEEQDGVh41r0,9365
+vivarium_public_health/risks/base_risk.py,sha256=XrZ5iytFabPS2_9-jI0dZQKK206yy_ZvCbReUoAVrAQ,10851
+vivarium_public_health/risks/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
+vivarium_public_health/risks/distributions.py,sha256=5gkurGTPqZczIKum5NgJ-DbJ2bxA1tRbLe7jKgCqkQg,18203
+vivarium_public_health/risks/effect.py,sha256=Cw-V1rMPaAPZsirbUElPzksvNuXLQc8TIIk0hgaFzvA,21259
 vivarium_public_health/risks/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=32nvILduve34PQF1kNGlx-qAuJAL69irQm92FKwJFEQ,21305
-vivarium_public_health/treatment/__init__.py,sha256=lTZhcgR0yjzlmfravIrkbwJ7zdR9aGqKVaJAn2AYyBY,313
-vivarium_public_health/treatment/intervention.py,sha256=A7vqrIUgmMggZnSoaOIf0xYHHwSzyG5huXYPk7j21R0,3223
+vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=wKVGHhdIas9WOrgA5wpwkSSDrZwBtaCqkZXfQH6jrkY,21159
+vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=zg4I48G-l9fC6-qjvApbM1zNACJimZlX9ZZ9fdHKwvc,1985
 vivarium_public_health/treatment/scale_up.py,sha256=_bsf9c_yVc7-q_-yBcXimISTUfYzPps1auH0uEf7sfQ,7048
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=ZIHnpuszZwA_BkS53JbSLvpcnX_bqG2knwCUyUgkA9M,2362
-vivarium_public_health-4.3.2.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-4.3.2.dist-info/METADATA,sha256=oyZCIq5r1mV53SjyuCtHIMN5TO8IEaBlnfo-lr8UGC8,4294
-vivarium_public_health-4.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-vivarium_public_health-4.3.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-4.3.2.dist-info/RECORD,,
+vivarium_public_health-4.3.4.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-4.3.4.dist-info/METADATA,sha256=nNlKCkVxNAu6ftFCGJ_-6o_4TRXBCeQ7nbGfEWgUd1E,4287
+vivarium_public_health-4.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+vivarium_public_health-4.3.4.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-4.3.4.dist-info/RECORD,,

vivarium_public_health/exposure/__init__.py

@@ -1,2 +0,0 @@
-from .effect import ExposureEffect
-from .exposure import Exposure