vivarium-public-health 3.1.2__py3-none-any.whl → 3.1.3__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "3.1.2"
+__version__ = "3.1.3"

vivarium_public_health/risks/effect.py

@@ -17,6 +17,7 @@ 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.risks import Risk
 from vivarium_public_health.risks.data_transformations import (
@@ -112,7 +113,8 @@ class RiskEffect(Component):
     def setup(self, builder: Builder) -> None:
         self.exposure = self.get_risk_exposure(builder)
 
-        self.target_modifier = self.get_target_modifier(builder)
+        self._relative_risk_source = self.get_relative_risk_source(builder)
+        self.relative_risk = self.get_relative_risk(builder)
 
         self.register_target_modifier(builder)
         self.register_paf_modifier(builder)
@@ -124,7 +126,7 @@ class RiskEffect(Component):
     def build_all_lookup_tables(self, builder: Builder) -> None:
         self._exposure_distribution_type = self.get_distribution_type(builder)
 
-        rr_data = self.get_relative_risk_data(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)
@@ -146,7 +148,7 @@ class RiskEffect(Component):
             return risk_exposure_component.distribution_type
         return risk_exposure_component.get_distribution_type(builder)
 
-    def get_relative_risk_data(
+    def load_relative_risk(
         self,
         builder: Builder,
         configuration=None,
@@ -260,24 +262,27 @@ class RiskEffect(Component):
     def get_risk_exposure(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
         return builder.value.get_value(self.exposure_pipeline_name)
 
-    def get_target_modifier(
-        self, builder: Builder
-    ) -> Callable[[pd.Index, pd.Series], pd.Series]:
+    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 adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
+            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 target * relative_risk
+                return relative_risk
 
         else:
             index_columns = ["index", self.risk.name]
 
-            def adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
+            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
@@ -288,16 +293,24 @@ class RiskEffect(Component):
                 relative_risk = relative_risk.set_index(index_columns)
 
                 effect = relative_risk.loc[exposure.index, "value"].droplevel(self.risk.name)
-                affected_rates = target * effect
-                return affected_rates
+                return effect
 
-        return adjust_target
+        return generate_relative_risk
+
+    def get_relative_risk(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.target_modifier,
-            requires_values=[f"{self.risk.name}.exposure"],
+            modifier=self.adjust_target,
+            component=self,
+            required_resources=[self.relative_risk],
         )
 
     def register_paf_modifier(self, builder: Builder) -> None:
@@ -307,7 +320,8 @@ class RiskEffect(Component):
         builder.value.register_value_modifier(
             self.target_paf_pipeline_name,
             modifier=self.lookup_tables["population_attributable_fraction"],
-            requires_columns=required_columns,
+            component=self,
+            required_resources=required_columns,
         )
 
     ##################
@@ -371,7 +385,7 @@ class NonLogLinearRiskEffect(RiskEffect):
         return f"non_log_linear_risk_effect.{risk.name}_on_{target}"
 
     def build_all_lookup_tables(self, builder: Builder) -> None:
-        rr_data = self.get_relative_risk_data(builder)
+        rr_data = self.load_relative_risk(builder)
         self.validate_rr_data(rr_data)
 
         def define_rr_intervals(df: pd.DataFrame) -> pd.DataFrame:
@@ -415,7 +429,7 @@ class NonLogLinearRiskEffect(RiskEffect):
             builder, paf_data
         )
 
-    def get_relative_risk_data(
+    def load_relative_risk(
         self,
         builder: Builder,
         configuration=None,
@@ -472,10 +486,8 @@ class NonLogLinearRiskEffect(RiskEffect):
 
         return rr_data
 
-    def get_target_modifier(
-        self, builder: Builder
-    ) -> Callable[[pd.Index, pd.Series], pd.Series]:
-        def adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
+    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.risk.name}_exposure"]
             x1, x2 = (
@@ -486,9 +498,9 @@ class NonLogLinearRiskEffect(RiskEffect):
             m = (y2 - y1) / (x2 - x1)
             b = y1 - m * x1
             relative_risk = b + m * exposure
-            return target * relative_risk
+            return relative_risk
 
-        return adjust_target
+        return generate_relative_risk
 
     ##############
     # Validators #

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -336,7 +336,6 @@ class LBWSGRiskEffect(RiskEffect):
 
         super().setup(builder)
         self.interpolator = self.get_interpolator(builder)
-        self.relative_risk = self.get_relative_risk_pipeline(builder)
 
     #################
     # Setup methods #
@@ -393,10 +392,10 @@ class LBWSGRiskEffect(RiskEffect):
             for age_start in exposed_age_group_starts
         }
 
-    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
+    def get_relative_risk(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             self.relative_risk_pipeline_name,
-            source=self.get_relative_risk,
+            source=self.get_relative_risk_source,
             requires_columns=["age"] + self.rr_column_names,
         )
 
@@ -470,7 +469,7 @@ class LBWSGRiskEffect(RiskEffect):
     # Pipeline sources and modifiers #
     ##################################
 
-    def get_relative_risk(self, index: pd.Index) -> pd.Series:
+    def get_relative_risk_source(self, index: pd.Index) -> pd.Series:
         pop = self.population_view.get(index)
         relative_risk = pd.Series(1.0, index=index, name=self.relative_risk_pipeline_name)
 

{vivarium_public_health-3.1.2.dist-info → vivarium_public_health-3.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.1.2
+Version: 3.1.3
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,44 +26,44 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium >=3.2.0
-Requires-Dist: layered-config-tree >=1.0.1
+Requires-Dist: vivarium>=3.2.0
+Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
-Requires-Dist: numpy <2.0.0
+Requires-Dist: numpy<2.0.0
 Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
-Requires-Dist: risk-distributions >=2.0.11
+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'
+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'
+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"
+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"
 
 Vivarium Public Health
 ======================

{vivarium_public_health-3.1.2.dist-info → vivarium_public_health-3.1.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=GDeeP-7OlCBwPuv_xQoB1wNmvCaFsqfTB7qnnYApm0w,1343
-vivarium_public_health/_version.py,sha256=EkxTxShULe9D7KtZB_iICEO13IyzloAxfYgXHGwpMhQ,22
+vivarium_public_health/_version.py,sha256=xoSqNkNOCK0xzFXnsO80epHc1vbiRC8Nbn4Cy-2wBX4,22
 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/model.py,sha256=ZwhhQCc8jj_QeJZO2zLtp_yWzqRxvLjuzW7iDUmmBGA,8852
@@ -35,15 +35,15 @@ vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4iz
 vivarium_public_health/risks/base_risk.py,sha256=XQ_7rYJS5gh0coEKDqcc_zYdjPDBZlj6-THsIQxL3zs,10888
 vivarium_public_health/risks/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
 vivarium_public_health/risks/distributions.py,sha256=a63-ihg2itxqgowDZbUix8soErxs_y8TRwsdtTCIUU4,18121
-vivarium_public_health/risks/effect.py,sha256=BN7XzmCutG5yCIcw9uxl_yKBTtqrL_Y4trrj5wND62w,20735
+vivarium_public_health/risks/effect.py,sha256=2DaBKxncS94cm8Ih-TQtbV1mGsEZhx6fEnB5V_ocIZM,21241
 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=8L-19voqV0URpkbJlgIfdGSJAwEu-y-J9_KGJUJUYgY,17931
+vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=Iw5e7sCrWplEu6dic1Wu6q9e0rdeem_6gQ_-N52G54E,17866
 vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=zGIhrNgB9q6JD7fHlvbDQb3H5e_N_QsROO4Y0kl_JQM,1955
 vivarium_public_health/treatment/scale_up.py,sha256=hVz0ELXDqlpcExI31rKdepxqcW_hy2hZSa6qCzv6udU,7020
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
-vivarium_public_health-3.1.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-3.1.2.dist-info/METADATA,sha256=m30cn1jwJksbLgxSqetpor3zYnZZdHQ6BqDBQ3l2hnA,4061
-vivarium_public_health-3.1.2.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-vivarium_public_health-3.1.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-3.1.2.dist-info/RECORD,,
+vivarium_public_health-3.1.3.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.1.3.dist-info/METADATA,sha256=csuhuXUl84A5QlA7S10sjMvafQXonRvAlwm2XSj-ck4,4028
+vivarium_public_health-3.1.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+vivarium_public_health-3.1.3.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.1.3.dist-info/RECORD,,

{vivarium_public_health-3.1.2.dist-info → vivarium_public_health-3.1.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.5.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any