vivarium-public-health 2.3.2__py3-none-any.whl → 3.0.0__py3-none-any.whl

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -6,24 +6,21 @@ 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
-from typing import Callable, Dict, List, Optional
+from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import numpy as np
 import pandas as pd
 from vivarium.framework.engine import Builder
 from vivarium.framework.lifecycle import LifeCycleError
-from vivarium.framework.lookup import LookupTable
 from vivarium.framework.population import SimulantData
 from vivarium.framework.values import Pipeline
 
 from vivarium_public_health.risks import Risk, RiskEffect
-from vivarium_public_health.risks.data_transformations import (
-    get_exposure_data,
-    get_exposure_post_processor,
-)
+from vivarium_public_health.risks.data_transformations import get_exposure_post_processor
 from vivarium_public_health.risks.distributions import PolytomousDistribution
-from vivarium_public_health.utilities import EntityString, to_snake_case
+from vivarium_public_health.utilities import get_lookup_columns, to_snake_case
 
 CATEGORICAL = "categorical"
 BIRTH_WEIGHT = "birth_weight"
@@ -31,63 +28,16 @@ GESTATIONAL_AGE = "gestational_age"
 
 
 class LBWSGDistribution(PolytomousDistribution):
-    CONFIGURATION_DEFAULTS = {
-        "lbwsg_distribution": {
-            "age_column": "age",
-            "sex_column": "sex",
-            "year_column": "year",
-        }
-    }
-
-    #####################
-    # Lifecycle methods #
-    #####################
 
-    def __init__(self, exposure_data: pd.DataFrame = None):
-        super().__init__(
-            EntityString("risk_factor.low_birth_weight_and_short_gestation"), exposure_data
-        )
+    #################
+    # Setup methods #
+    #################
 
     # noinspection PyAttributeOutsideInit
     def setup(self, builder: Builder) -> None:
-        self.config = builder.configuration.lbwsg_distribution
-        self._exposure_data = self.get_exposure_data(builder)
-
         super().setup(builder)
         self.category_intervals = self.get_category_intervals(builder)
 
-    #################
-    # Setup methods #
-    #################
-
-    def get_exposure_data(self, builder: Builder) -> pd.DataFrame:
-        if self._exposure_data is None:
-            self._exposure_data = get_exposure_data(builder, self.risk)
-
-        return self._exposure_data.rename(
-            columns={
-                "sex": self.config.sex_column,
-                "age_start": f"{self.config.age_column}_start",
-                "age_end": f"{self.config.age_column}_end",
-                "year_start": f"{self.config.year_column}_start",
-                "year_end": f"{self.config.year_column}_end",
-            }
-        )
-
-    def get_exposure_parameters(self, builder: Builder) -> Pipeline:
-        return builder.value.register_value_producer(
-            self.exposure_parameters_pipeline_name,
-            source=builder.lookup.build_table(
-                self._exposure_data,
-                key_columns=[self.config.sex_column],
-                parameter_columns=[self.config.age_column, self.config.year_column],
-            ),
-            requires_columns=[
-                self.config.sex_column,
-                self.config.age_column,
-            ],
-        )
-
     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
@@ -96,7 +46,7 @@ class LBWSGDistribution(PolytomousDistribution):
         :param builder:
         :return:
         """
-        categories = builder.data.load(f"{self.risk}.categories")
+        categories: Dict[str, str] = builder.data.load(f"{self.risk}.categories")
         category_intervals = {
             axis: {
                 category: self._parse_description(axis, description)
@@ -160,8 +110,8 @@ class LBWSGDistribution(PolytomousDistribution):
 
         if (categorical_propensity is None) == (categorical_exposure is None):
             raise ValueError(
-                "Either categorical propensity of categorical exposure may be provided, but not"
-                " both or neither."
+                "Exactly one of categorical propensity or categorical exposure "
+                "must be provided."
             )
 
         if categorical_exposure is None:
@@ -185,17 +135,26 @@ class LBWSGDistribution(PolytomousDistribution):
     def _parse_description(axis: str, description: str) -> pd.Interval:
         """
         Parses a string corresponding to a low birth weight and short gestation
-        category to an Interval
+        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: [
-                float(val) for val in description.split(", [")[1].split(")")[0].split(", ")
+                float(val)
+                for val in description.split(", [")[1].split(")")[0].split("]")[0].split(", ")
             ],
             GESTATIONAL_AGE: [
-                float(val) for val in description.split("- [")[1].split(")")[0].split(", ")
+                float(val)
+                for val in description.split("- [")[1].split(")")[0].split("+")[0].split(", ")
             ],
         }[axis]
         return pd.Interval(*endpoints, closed="left")  # noqa
@@ -204,6 +163,8 @@ class LBWSGDistribution(PolytomousDistribution):
 class LBWSGRisk(Risk):
     AXES = [BIRTH_WEIGHT, GESTATIONAL_AGE]
 
+    exposure_distributions = {"lbwsg": LBWSGDistribution}
+
     @staticmethod
     def birth_exposure_pipeline_name(axis: str) -> str:
         return f"{axis}.birth_exposure"
@@ -216,6 +177,12 @@ class LBWSGRisk(Risk):
     # Properties #
     ##############
 
+    @property
+    def configuration_defaults(self) -> Dict[str, Any]:
+        configuration_defaults = super().configuration_defaults
+        configuration_defaults[self.name]["distribution_type"] = "lbwsg"
+        return configuration_defaults
+
     @property
     def columns_created(self) -> List[str]:
         return [self.exposure_column_name(axis) for axis in self.AXES]
@@ -232,13 +199,6 @@ class LBWSGRisk(Risk):
         super().setup(builder)
         self.birth_exposures = self.get_birth_exposure_pipelines(builder)
 
-    ##########################
-    # Initialization methods #
-    ##########################
-
-    def get_exposure_distribution(self) -> LBWSGDistribution:
-        return LBWSGDistribution()
-
     #################
     # Setup methods #
     #################
@@ -252,13 +212,17 @@ class LBWSGRisk(Risk):
         return None
 
     def get_birth_exposure_pipelines(self, builder: Builder) -> Dict[str, Pipeline]:
+        required_columns = get_lookup_columns(
+            self.exposure_distribution.lookup_tables.values()
+        )
+
         def get_pipeline(axis_: str):
             return builder.value.register_value_producer(
                 self.birth_exposure_pipeline_name(axis_),
                 source=lambda index: self.get_birth_exposure(axis_, index),
-                requires_columns=["age", "sex"],
+                requires_columns=required_columns,
                 requires_streams=[self.randomness_stream_name],
-                preferred_post_processor=get_exposure_post_processor(builder, self.risk),
+                preferred_post_processor=get_exposure_post_processor(builder, self.name),
             )
 
         return {
@@ -307,7 +271,7 @@ class LBWSGRiskEffect(RiskEffect):
 
     @property
     def columns_created(self) -> List[str]:
-        return self._rr_column_names
+        return self.rr_column_names
 
     @property
     def columns_required(self) -> Optional[List[str]]:
@@ -321,6 +285,10 @@ class LBWSGRiskEffect(RiskEffect):
             "requires_streams": [],
         }
 
+    @property
+    def rr_column_names(self) -> List[str]:
+        return [self.relative_risk_column_name(age_group) for age_group in self.age_intervals]
+
     #####################
     # Lifecycle methods #
     #####################
@@ -335,7 +303,7 @@ class LBWSGRiskEffect(RiskEffect):
             f"effect_of_{self.risk.name}_on_{self.target.name}.relative_risk"
         )
 
-    def relative_risk_column_name(self, age_group_id) -> str:
+    def relative_risk_column_name(self, age_group_id: str) -> str:
         return (
             f"effect_of_{self.risk.name}_on_{age_group_id}_{self.target.name}_relative_risk"
         )
@@ -343,21 +311,35 @@ class LBWSGRiskEffect(RiskEffect):
     # noinspection PyAttributeOutsideInit
     def setup(self, builder: Builder) -> None:
         self.age_intervals = self.get_age_intervals(builder)
-        self._rr_column_names = self.get_rr_column_names()
 
         super().setup(builder)
         self.interpolator = self.get_interpolator(builder)
+        self.relative_risk = self.get_relative_risk_pipeline(builder)
 
     #################
     # Setup methods #
     #################
 
+    # noinspection PyAttributeOutsideInit
+    def build_all_lookup_tables(self, builder: Builder) -> None:
+        paf_data, paf_value_cols = self.get_population_attributable_fraction_source(builder)
+        self.lookup_tables["population_attributable_fraction"] = self.build_lookup_table(
+            builder, paf_data, paf_value_cols
+        )
+
     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)
 
         return exposure
 
+    def get_population_attributable_fraction_source(
+        self, builder: Builder
+    ) -> Tuple[pd.DataFrame, List[str]]:
+        paf_key = f"{self.risk}.population_attributable_fraction"
+        paf_data = builder.data.load(paf_key)
+        return paf_data, builder.data.value_columns()(paf_key)
+
     def get_target_modifier(
         self, builder: Builder
     ) -> Callable[[pd.Index, pd.Series], pd.Series]:
@@ -370,7 +352,7 @@ class LBWSGRiskEffect(RiskEffect):
         builder.value.register_value_modifier(
             self.target_pipeline_name,
             modifier=self.target_modifier,
-            requires_columns=["age", "sex"],
+            requires_values=[self.relative_risk_pipeline_name],
         )
 
     def get_age_intervals(self, builder: Builder) -> Dict[str, pd.Interval]:
@@ -389,21 +371,11 @@ class LBWSGRiskEffect(RiskEffect):
             for age_start in exposed_age_group_starts
         }
 
-    def get_rr_column_names(self) -> List[str]:
-        return [self.relative_risk_column_name(age_group) for age_group in self.age_intervals]
-
-    def get_relative_risk_source(self, builder: Builder) -> Pipeline:
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             self.relative_risk_pipeline_name,
             source=self.get_relative_risk,
-            requires_columns=["age"] + self._rr_column_names,
-        )
-
-    def get_population_attributable_fraction_source(self, builder: Builder) -> LookupTable:
-        return builder.lookup.build_table(
-            builder.data.load(f"{self.risk}.population_attributable_fraction"),
-            key_columns=["sex"],
-            parameter_columns=["age", "year"],
+            requires_columns=["age"] + self.rr_column_names,
         )
 
     def get_interpolator(self, builder: Builder) -> pd.Series:
@@ -448,7 +420,7 @@ class LBWSGRiskEffect(RiskEffect):
             self.TMREL_BIRTH_WEIGHT_INTERVAL.left <= birth_weight
         )
 
-        def get_relative_risk_for_age_group(age_group: int) -> pd.Series:
+        def get_relative_risk_for_age_group(age_group: str) -> pd.Series:
             column_name = self.relative_risk_column_name(age_group)
             log_relative_risk = pd.Series(0.0, index=pop_data.index, name=column_name)
 

vivarium_public_health/treatment/magic_wand.py

@@ -7,6 +7,7 @@ This module contains simple intervention models that work at the population
 level by providing direct shifts to epidemiological measures.
 
 """
+
 from typing import Any, Dict, List, Optional
 
 from vivarium import Component

vivarium_public_health/treatment/scale_up.py

@@ -6,6 +6,7 @@ Linear Scale-Up Model
 This module contains tools for applying a linear scale-up to an intervention
 
 """
+
 from typing import Any, Callable, Dict, Tuple
 
 import pandas as pd

vivarium_public_health/treatment/therapeutic_inertia.py

@@ -7,6 +7,7 @@ This module contains a model for therapeutic inertia which represents the
 variety of reasons why a treatment algorithm might deviate from guidelines.
 
 """
+
 import pandas as pd
 import scipy.stats
 from vivarium import Component

vivarium_public_health/utilities.py

@@ -7,10 +7,12 @@ This module contains utility classes and functions for use across
 vivarium_public_health components.
 
 """
-from typing import Iterable, Union
+
+from pathlib import Path
+from typing import Any, Dict, Iterable, List, Optional, Union
 
 import pandas as pd
-from vivarium.framework.lookup import ScalarValue
+from vivarium.framework.lookup import LookupTable, ScalarValue
 
 
 class EntityString(str):
@@ -97,3 +99,16 @@ def is_non_zero(data: Union[Iterable[ScalarValue], ScalarValue, pd.DataFrame]) -
         attribute_sum = data
 
     return attribute_sum != 0.0
+
+
+def get_lookup_columns(
+    lookup_tables: Iterable[LookupTable], necessary_columns: Iterable = ()
+) -> List[str]:
+    necessary_columns = set(necessary_columns)
+    for lookup_table in lookup_tables:
+        necessary_columns.update(set(lookup_table.key_columns))
+        necessary_columns.update(set(lookup_table.parameter_columns))
+    if "year" in necessary_columns:
+        necessary_columns.remove("year")
+
+    return list(necessary_columns)

{vivarium_public_health-2.3.2.dist-info → vivarium_public_health-3.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.3.2
+Version: 3.0.0
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,31 +26,41 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium >=2.0.0
+Requires-Dist: vivarium >=3.0.0
+Requires-Dist: layered-config-tree >=1.0.1
 Requires-Dist: loguru
-Requires-Dist: numpy
+Requires-Dist: numpy <2.0.0
 Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk-distributions >=2.0.11
+Requires-Dist: pyarrow
 Provides-Extra: dev
 Requires-Dist: sphinx <7.0 ; extra == 'dev'
 Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
 Requires-Dist: sphinx-click ; extra == 'dev'
+Requires-Dist: sphinx-autodoc-typehints ; extra == 'dev'
 Requires-Dist: IPython ; extra == 'dev'
 Requires-Dist: matplotlib ; extra == 'dev'
+Requires-Dist: vivarium-testing-utils ; extra == 'dev'
 Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: pytest-cov ; extra == 'dev'
 Requires-Dist: pytest-mock ; extra == 'dev'
 Requires-Dist: hypothesis ; extra == 'dev'
 Requires-Dist: pyyaml ; extra == 'dev'
+Requires-Dist: black ==22.3.0 ; extra == 'dev'
+Requires-Dist: isort ; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: sphinx <7.0 ; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
 Requires-Dist: sphinx-click ; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints ; extra == 'docs'
 Requires-Dist: IPython ; extra == 'docs'
 Requires-Dist: matplotlib ; extra == 'docs'
 Provides-Extra: test
+Requires-Dist: vivarium-testing-utils ; extra == 'test'
 Requires-Dist: pytest ; extra == 'test'
+Requires-Dist: pytest-cov ; extra == 'test'
 Requires-Dist: pytest-mock ; extra == 'test'
 Requires-Dist: hypothesis ; extra == 'test'
 Requires-Dist: pyyaml ; extra == 'test'

vivarium_public_health-3.0.0.dist-info/RECORD

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+vivarium_public_health-3.0.0.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+vivarium_public_health-3.0.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.0.0.dist-info/RECORD,,

{vivarium_public_health-2.3.2.dist-info → vivarium_public_health-3.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (72.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

vivarium_public_health/metrics/disability.py

@@ -1,118 +0,0 @@
-"""
-===================
-Disability Observer
-===================
-
-This module contains tools for observing years lived with disability (YLDs)
-in the simulation.
-
-"""
-from typing import List
-
-import pandas as pd
-from vivarium import Component
-from vivarium.framework.engine import Builder
-from vivarium.framework.values import Pipeline, list_combiner, union_post_processor
-
-from vivarium_public_health.disease import DiseaseState, RiskAttributableDisease
-from vivarium_public_health.utilities import to_years
-
-
-class DisabilityObserver(Component):
-    """Counts years lived with disability.
-
-    By default, this counts both aggregate and cause-specific years lived
-    with disability over the full course of the simulation.
-
-    In the model specification, your configuration for this component should
-    be specified as, e.g.:
-
-    .. code-block:: yaml
-
-        configuration:
-            observers:
-                disability:
-                    exclude:
-                        - "sex"
-                    include:
-                        - "sample_stratification"
-    """
-
-    CONFIGURATION_DEFAULTS = {
-        "stratification": {
-            "disability": {
-                "exclude": [],
-                "include": [],
-            }
-        }
-    }
-
-    ##############
-    # Properties #
-    ##############
-
-    @property
-    def disease_classes(self) -> List:
-        return [DiseaseState, RiskAttributableDisease]
-
-    #####################
-    # Lifecycle methods #
-    #####################
-
-    def __init__(self):
-        super().__init__()
-        self.disability_weight_pipeline_name = "disability_weight"
-
-    # noinspection PyAttributeOutsideInit
-    def setup(self, builder: Builder) -> None:
-        self.config = builder.configuration.stratification.disability
-        self.step_size = pd.Timedelta(days=builder.configuration.time.step_size)
-        self.disability_weight = self.get_disability_weight_pipeline(builder)
-        cause_states = builder.components.get_components_by_type(tuple(self.disease_classes))
-
-        builder.results.register_observation(
-            name="ylds_due_to_all_causes",
-            pop_filter='tracked == True and alive == "alive"',
-            aggregator_sources=[self.disability_weight_pipeline_name],
-            aggregator=self.disability_weight_aggregator,
-            requires_columns=["alive"],
-            requires_values=["disability_weight"],
-            additional_stratifications=self.config.include,
-            excluded_stratifications=self.config.exclude,
-            when="time_step__prepare",
-        )
-
-        for cause_state in cause_states:
-            cause_disability_weight_pipeline_name = (
-                f"{cause_state.state_id}.disability_weight"
-            )
-            builder.results.register_observation(
-                name=f"ylds_due_to_{cause_state.state_id}",
-                pop_filter='tracked == True and alive == "alive"',
-                aggregator_sources=[cause_disability_weight_pipeline_name],
-                aggregator=self.disability_weight_aggregator,
-                requires_columns=["alive"],
-                requires_values=[cause_disability_weight_pipeline_name],
-                additional_stratifications=self.config.include,
-                excluded_stratifications=self.config.exclude,
-                when="time_step__prepare",
-            )
-
-    #################
-    # Setup methods #
-    #################
-
-    def get_disability_weight_pipeline(self, builder: Builder) -> Pipeline:
-        return builder.value.register_value_producer(
-            self.disability_weight_pipeline_name,
-            source=lambda index: [pd.Series(0.0, index=index)],
-            preferred_combiner=list_combiner,
-            preferred_post_processor=union_post_processor,
-        )
-
-    ###############
-    # Aggregators #
-    ###############
-
-    def disability_weight_aggregator(self, dw: pd.DataFrame) -> float:
-        return (dw * to_years(self.step_size)).sum().squeeze()