vivarium-public-health 3.0.3__py3-none-any.whl → 3.0.5__py3-none-any.whl

vivarium_public_health/risks/effect.py

@@ -17,8 +17,6 @@ import scipy
 from layered_config_tree import ConfigurationError
 from vivarium import Component
 from vivarium.framework.engine import Builder
-from vivarium.framework.event import Event
-from vivarium.framework.population import SimulantData
 
 from vivarium_public_health.risks import Risk
 from vivarium_public_health.risks.data_transformations import (
@@ -30,10 +28,12 @@ from vivarium_public_health.utilities import EntityString, TargetString, get_loo
 
 
 class RiskEffect(Component):
-    """A component to model the impact of a risk factor on the target rate of
-    some affected entity. 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',
+    """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
@@ -59,10 +59,7 @@ class RiskEffect(Component):
 
     @property
     def configuration_defaults(self) -> Dict[str, Any]:
-        """
-        A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
+        """Default values for any configurations managed by this component."""
         return {
             self.name: {
                 "data_sources": {
@@ -89,13 +86,14 @@ class RiskEffect(Component):
 
     def __init__(self, risk: str, target: str):
         """
+
         Parameters
         ----------
-        risk :
+        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 :
+        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).
@@ -210,7 +208,9 @@ class RiskEffect(Component):
     def rebin_relative_risk_data(
         self, builder, relative_risk_data: pd.DataFrame
     ) -> pd.DataFrame:
-        """When the polytomous risk is rebinned, matching relative risk needs to be rebinned.
+        """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],
@@ -319,18 +319,22 @@ class RiskEffect(Component):
 
 
 class NonLogLinearRiskEffect(RiskEffect):
-    """A component to model the impact of an exposure-parametrized risk factor on
-    the target rate of some affected entity. This component will
-
-    1) read TMRED data from the artifact and define the TMREL
-    2) calculate the relative risk at TMREL by linearly interpolating over
-       relative risk data defined in the configuration
-    3) divide relative risk data from configuration by RR at TMREL
-       and clip to be greater than 1
-    4) build a LookupTable which returns the exposure and RR of the left and right edges
-       of the RR bin containing a simulant's exposure
-    5) use this LookupTable to modify the target pipeline by linearly interpolating
-       a simulant's RR value and multiplying it by the intended target rate
+    """A component to model the exposure-parametrized effect of a risk factor.
+
+    More specifically, this models the effect of the risk factor on the target rate of
+    some affected entity.
+
+    This component:
+    1) reads TMRED data from the artifact and define the TMREL
+    2) calculates the relative risk at TMREL by linearly interpolating over
+    relative risk data defined in the configuration
+    3) divides relative risk data from configuration by RR at TMREL
+    and clip to be greater than 1
+    4) builds a LookupTable which returns the exposure and RR of the left and right edges
+    of the RR bin containing a simulant's exposure
+    5) uses this LookupTable to modify the target pipeline by linearly interpolating
+    a simulant's RR value and multiplying it by the intended target rate
+
     """
 
     ##############
@@ -339,10 +343,7 @@ class NonLogLinearRiskEffect(RiskEffect):
 
     @property
     def configuration_defaults(self) -> Dict[str, Any]:
-        """
-        A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
+        """Default values for any configurations managed by this component."""
         return {
             self.name: {
                 "data_sources": {
@@ -485,6 +486,7 @@ class NonLogLinearRiskEffect(RiskEffect):
     ##############
 
     def validate_rr_data(self, rr_data: pd.DataFrame) -> None:
+        """Validate the relative risk data."""
         # check that rr_data has numeric parameter data
         parameter_data_is_numeric = rr_data["parameter"].dtype.kind in "biufc"
         if not parameter_data_is_numeric:

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -5,6 +5,7 @@ Low Birth Weight and Short Gestation
 
 Low birth weight and short gestation (LBWSG) is a non-standard risk
 implementation that has been used in several public health models.
+
 """
 
 import pickle
@@ -39,12 +40,16 @@ class LBWSGDistribution(PolytomousDistribution):
         self.category_intervals = self.get_category_intervals(builder)
 
     def get_category_intervals(self, builder: Builder) -> Dict[str, Dict[str, pd.Interval]]:
-        """
-        Gets the intervals for each category. It is a dictionary from the string
-        "birth_weight" or "gestational_age" to a dictionary from the category
-        name to the interval
-        :param builder:
-        :return:
+        """Gets the intervals for each category.
+
+        Parameters
+        ----------
+        builder
+            The builder object.
+
+        Returns
+        -------
+            The intervals for each category.
         """
         categories: Dict[str, str] = builder.data.load(f"{self.risk}.categories")
         category_intervals = {
@@ -61,16 +66,19 @@ class LBWSGDistribution(PolytomousDistribution):
     ##################
 
     def ppf(self, propensities: pd.DataFrame) -> pd.DataFrame:
-        """
-        Takes a DataFrame with three columns: 'categorical.propensity',
-        'birth_weight.propensity', and 'gestational_age.propensity' which
-        contain each of those propensities for each simulant.
-
-        Returns a DataFrame with two columns for birth-weight and gestational
-        age exposures.
-
-        :param propensities:
-        :return:
+        """Calculate continuous exposures from propensities.
+
+        Parameters
+        ----------
+        propensities
+            Propensities DataFrame for each simulant with three columns:
+            'categorical.propensity', 'birth_weight.propensity', and
+            'gestational_age.propensity'.
+
+        Returns
+        -------
+            A DataFrame with two columns for birth-weight and gestational age
+            exposures.
         """
 
         categorical_exposure = super().ppf(propensities[f"{CATEGORICAL}_propensity"])
@@ -88,10 +96,11 @@ class LBWSGDistribution(PolytomousDistribution):
         self,
         axis: str,
         propensity: pd.Series,
-        categorical_propensity: pd.Series = None,
-        categorical_exposure: pd.Series = None,
+        categorical_propensity: Optional[pd.Series] = None,
+        categorical_exposure: Optional[pd.Series] = None,
     ) -> pd.Series:
-        """
+        """Calculate continuous exposures from propensities for a single axis.
+
         Takes an axis (either 'birth_weight' or 'gestational_age'), a propensity
         and either a categorical propensity or a categorical exposure and
         returns continuous exposures for that axis.
@@ -101,11 +110,27 @@ class LBWSGDistribution(PolytomousDistribution):
         categorical exposure parameters pipeline
         ("risk_factor.low_birth_weight_and_short_gestation.exposure_parameters").
 
-        :param axis:
-        :param propensity:
-        :param categorical_propensity:
-        :param categorical_exposure:
-        :return:
+        Parameters
+        ----------
+        axis
+            The axis for which to calculate continuous exposures ('birth_weight'
+            or 'gestational_age').
+        propensity
+            The propensity for the axis.
+        categorical_propensity
+            The categorical propensity for the axis.
+        categorical_exposure
+            The categorical exposure for the axis.
+
+        Returns
+        -------
+            The continuous exposures for the axis.
+
+        Raises
+        ------
+        ValueError
+            If neither categorical propensity nor categorical exposure is provided
+            or both are provided.
         """
 
         if (categorical_propensity is None) == (categorical_exposure is None):
@@ -133,19 +158,15 @@ class LBWSGDistribution(PolytomousDistribution):
 
     @staticmethod
     def _parse_description(axis: str, description: str) -> pd.Interval:
-        """
-        Parses a string corresponding to a low birth weight and short gestation
+        """Parses a string corresponding to a low birth weight and short gestation
         category to an Interval.
+
         An example of a standard description:
         'Neonatal preterm and LBWSG (estimation years) - [0, 24) wks, [0, 500) g'
         An example of an edge case for gestational age:
         'Neonatal preterm and LBWSG (estimation years) - [40, 42+] wks, [2000, 2500) g'
         An example of an edge case of birth weight:
         'Neonatal preterm and LBWSG (estimation years) - [36, 37) wks, [4000, 9999] g'
-
-        :param axis:
-        :param description:
-        :return:
         """
         endpoints = {
             BIRTH_WEIGHT: [

vivarium_public_health/treatment/scale_up.py

@@ -20,8 +20,7 @@ from vivarium_public_health.utilities import EntityString
 
 
 class LinearScaleUp(Component):
-    """
-    A model for applying a linear scale-up to an intervention.
+    """A model for applying a linear scale-up to an intervention.
 
     This component requires input data for beginning and end dates, as well as
     beginning and end values. Scale-up start and end dates are by default the
@@ -75,10 +74,11 @@ class LinearScaleUp(Component):
 
     def __init__(self, treatment: str):
         """
+
         Parameters
         ----------
-        treatment :
-            the type and name of a treatment, specified as "type.name". Type is singular.
+        treatment
+            The type and name of a treatment, specified as "type.name". Type is singular.
         """
         super().__init__()
         self.treatment = EntityString(treatment)
@@ -113,8 +113,7 @@ class LinearScaleUp(Component):
         return pd.Timestamp(scale_up_config["start"]), pd.Timestamp(scale_up_config["end"])
 
     def get_scale_up_values(self, builder: Builder) -> Tuple[LookupTable, LookupTable]:
-        """
-        Get the values at the start and end of the scale-up period.
+        """Get the values at the start and end of the scale-up period.
 
         Parameters
         ----------
@@ -123,7 +122,6 @@ class LinearScaleUp(Component):
 
         Returns
         -------
-        LookupTable
             A tuple of lookup tables returning the values at the start and end
             of the scale-up period.
         """
@@ -172,8 +170,7 @@ class LinearScaleUp(Component):
     def get_endpoint_value_from_data(
         self, builder: Builder, endpoint_type: str
     ) -> LookupTable:
-        """
-        Get the value at the start or end of the scale-up period from data.
+        """Get the value at the start or end of the scale-up period from data.
 
         Parameters
         ----------
@@ -185,7 +182,6 @@ class LinearScaleUp(Component):
 
         Returns
         -------
-        LookupTable
             A lookup table returning the value at the start or end of the
             scale-up period.
         """

vivarium_public_health/treatment/therapeutic_inertia.py

@@ -17,7 +17,9 @@ from vivarium.framework.engine import Builder
 class TherapeuticInertia(Component):
     """Expose a therapeutic inertia pipeline that defines
     a population-level therapeutic inertia.
-    This is the probability of treatment during a healthcare visit."""
+
+    This is the probability of treatment during a healthcare visit.
+    """
 
     CONFIGURATION_DEFAULTS = {
         "therapeutic_inertia": {

{vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.3
+Version: 3.0.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers

vivarium_public_health-3.0.5.dist-info/RECORD

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{vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (73.0.1)
+Generator: setuptools (74.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

vivarium_public_health-3.0.3.dist-info/RECORD

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