vivarium-public-health 3.0.5__py3-none-any.whl → 3.0.7__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "3.0.5"
+__version__ = "3.0.7"

vivarium_public_health/disease/transition.py

@@ -7,7 +7,7 @@ This module contains tools to model transitions between disease states.
 
 """
 
-from typing import TYPE_CHECKING, Any, Callable, Dict, Union
+from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Union
 
 import pandas as pd
 from vivarium.framework.engine import Builder
@@ -48,6 +48,10 @@ class RateTransition(Transition):
             },
         }
 
+    @property
+    def columns_required(self) -> Optional[List[str]]:
+        return ["alive"]
+
     @property
     def transition_rate_pipeline_name(self) -> str:
         if "incidence_rate" in self._get_data_functions:
@@ -100,8 +104,6 @@ class RateTransition(Transition):
             preferred_post_processor=union_post_processor,
         )
 
-        self.population_view = builder.population.get_view(["alive"])
-
     #################
     # Setup methods #
     #################

vivarium_public_health/risks/base_risk.py

@@ -123,7 +123,10 @@ class Risk(Component):
 
     @property
     def columns_created(self) -> List[str]:
-        return [self.propensity_column_name, self.exposure_column_name]
+        columns_to_create = [self.propensity_column_name]
+        if self.create_exposure_column:
+            columns_to_create.append(self.exposure_column_name)
+        return columns_to_create
 
     @property
     def initialization_requirements(self) -> Dict[str, List[str]]:
@@ -172,6 +175,16 @@ class Risk(Component):
         self.propensity = self.get_propensity_pipeline(builder)
         self.exposure = self.get_exposure_pipeline(builder)
 
+        # We want to set this to True iff there is a non-loglinear risk effect
+        # on this risk instance
+        self.create_exposure_column = bool(
+            [
+                component
+                for component in builder.components.list_components()
+                if component.startswith(f"non_log_linear_risk_effect.{self.risk.name}_on_")
+            ]
+        )
+
     def get_distribution_type(self, builder: Builder) -> str:
         """Get the distribution type for the risk from the configuration.
 
@@ -270,19 +283,19 @@ class Risk(Component):
     ########################
 
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
-        propensity_values = self.randomness.get_draw(pop_data.index)
-        df = pd.DataFrame(
-            {
-                self.propensity_column_name: self.randomness.get_draw(pop_data.index),
-                self.exposure_column_name: self.exposure_distribution.ppf(propensity_values),
-            }
+        propensity = pd.Series(
+            self.randomness.get_draw(pop_data.index), name=self.propensity_column_name
         )
-        self.population_view.update(df)
+        self.population_view.update(propensity)
+        self.update_exposure_column(pop_data.index)
 
     def on_time_step_prepare(self, event: Event) -> None:
-        exposure_values = self.exposure(event.index)
-        exposure_col = pd.Series(exposure_values, name=self.exposure_column_name)
-        self.population_view.update(exposure_col)
+        self.update_exposure_column(event.index)
+
+    def update_exposure_column(self, index: pd.Index) -> None:
+        if self.create_exposure_column:
+            exposure = pd.Series(self.exposure(index), name=self.exposure_column_name)
+            self.population_view.update(exposure)
 
     ##################################
     # Pipeline sources and modifiers #

vivarium_public_health/risks/effect.py

@@ -157,16 +157,19 @@ class RiskEffect(Component):
         rr_source = configuration.data_sources.relative_risk
         rr_dist_parameters = configuration.data_source_parameters.relative_risk.to_dict()
 
-        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:
+        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)
-        except TypeError:
-            raise ConfigurationError(
-                f"Parameters {rr_dist_parameters} are not valid for distribution {rr_source}."
-            )
         return rr_data
 
     def get_filtered_data(
@@ -198,6 +201,8 @@ class RiskEffect(Component):
             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")
@@ -361,6 +366,10 @@ class NonLogLinearRiskEffect(RiskEffect):
     # Setup methods #
     #################
 
+    @staticmethod
+    def get_name(risk: EntityString, target: TargetString) -> str:
+        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)
         self.validate_rr_data(rr_data)

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -191,7 +191,7 @@ class LBWSGRisk(Risk):
         return f"{axis}.birth_exposure"
 
     @staticmethod
-    def exposure_column_name(axis: str) -> str:
+    def get_exposure_column_name(axis: str) -> str:
         return f"{axis}_exposure"
 
     ##############
@@ -206,7 +206,7 @@ class LBWSGRisk(Risk):
 
     @property
     def columns_created(self) -> List[str]:
-        return [self.exposure_column_name(axis) for axis in self.AXES]
+        return [self.get_exposure_column_name(axis) for axis in self.AXES]
 
     #####################
     # Lifecycle methods #
@@ -256,7 +256,7 @@ class LBWSGRisk(Risk):
 
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         birth_exposures = {
-            self.exposure_column_name(axis): self.birth_exposures[
+            self.get_exposure_column_name(axis): self.birth_exposures[
                 self.birth_exposure_pipeline_name(axis)
             ](pop_data.index)
             for axis in self.AXES
@@ -318,7 +318,7 @@ class LBWSGRiskEffect(RiskEffect):
         super().__init__("risk_factor.low_birth_weight_and_short_gestation", target)
 
         self.lbwsg_exposure_column_names = [
-            LBWSGRisk.exposure_column_name(axis) for axis in LBWSGRisk.AXES
+            LBWSGRisk.get_exposure_column_name(axis) for axis in LBWSGRisk.AXES
         ]
         self.relative_risk_pipeline_name = (
             f"effect_of_{self.risk.name}_on_{self.target.name}.relative_risk"
@@ -433,8 +433,8 @@ class LBWSGRiskEffect(RiskEffect):
         pop = self.population_view.subview(["sex"] + self.lbwsg_exposure_column_names).get(
             pop_data.index
         )
-        birth_weight = pop[LBWSGRisk.exposure_column_name(BIRTH_WEIGHT)]
-        gestational_age = pop[LBWSGRisk.exposure_column_name(GESTATIONAL_AGE)]
+        birth_weight = pop[LBWSGRisk.get_exposure_column_name(BIRTH_WEIGHT)]
+        gestational_age = pop[LBWSGRisk.get_exposure_column_name(GESTATIONAL_AGE)]
 
         is_male = pop["sex"] == "Male"
         is_tmrel = (self.TMREL_GESTATIONAL_AGE_INTERVAL.left <= gestational_age) & (

{vivarium_public_health-3.0.5.dist-info → vivarium_public_health-3.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.5
+Version: 3.0.7
 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 → vivarium_public_health-3.0.7.dist-info}/RECORD

@@ -1,13 +1,13 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=3kxZhPRWwAKER8BleEtUBQTUGwcBGPmrbjLu-HEi-hI,22
+vivarium_public_health/_version.py,sha256=tP42eveLWP9Mgm4I435dKZC463zDP4G3Rq_XJ9XMJAg,22
 vivarium_public_health/utilities.py,sha256=5cl9jjVkOQ1UeXT4DjDMAhaBNNjAsDo-SVJwpv6FDw0,3071
 vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
 vivarium_public_health/disease/model.py,sha256=0WIYDEx-hwlUJp6Zl8m8bUMoWxuVkOWsJvh_YlZiOPs,8234
 vivarium_public_health/disease/models.py,sha256=01UK7yB2zGPFzmlIpvhd-XnGe6vSCMDza3QTidgY7Nc,3479
 vivarium_public_health/disease/special_disease.py,sha256=3vS1WsO__IwOK0Oe_CUmh3aaKrXIf2CANtmiqlS3pjc,14614
 vivarium_public_health/disease/state.py,sha256=PUSDE1UlvoCPT6jPEyCTQO1bXjjYxqzdIa6-Bxpd-7I,22370
-vivarium_public_health/disease/transition.py,sha256=ZxYXZBo2EEXzuQCbaj2pHTyj61hYkdqBH1ce2Htdnb4,6412
+vivarium_public_health/disease/transition.py,sha256=fgeVMy86GLrNpZ3J9E4AC0iA5z3aVdP0ZQ0AWa_odTY,6452
 vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 vivarium_public_health/mslt/delay.py,sha256=aOYjMpMSHEVlJs0FuC2gdq3uj6_vKmkhDjoBtC4i9G0,22812
 vivarium_public_health/mslt/disease.py,sha256=TBqa7yj6k1oUbgkAe0rIgLpbdMLMFs4DiZ1Igi2BQBg,16663
@@ -32,18 +32,18 @@ vivarium_public_health/results/risk.py,sha256=GS4qJVjW3MqsDeRDDac2etFQlqIluxOxIZ
 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=WhvB0RRYIsGsPQvJEWckcBlOVSh4Rx-B-VGZDSWWb7s,10416
+vivarium_public_health/risks/base_risk.py,sha256=fNQZIgGHYnWFWdLA9qmtTA66ujCGq2jgA5S1-MadWT8,10900
 vivarium_public_health/risks/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
 vivarium_public_health/risks/distributions.py,sha256=7xCI2zSpnKUEWow4ywRirVbvbpeJaxo6g9us0-Lh0kE,18197
-vivarium_public_health/risks/effect.py,sha256=Oc_3A0fbMDUBAJAMJ9aeDRDqdgW_aF75B3SbGv9QELw,20351
+vivarium_public_health/risks/effect.py,sha256=fc_MrhmJLQcpaiZk12klric2c5-BY1gZaWMbsEjBUlY,20766
 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=o3Uo6_AQoUHJeGo4HpB0PlouNqKst9NFmm3PRiTr5bg,17924
+vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=kxuJwkpJzGF8CqwNEemEA7CrohcxKQJtvUXLJtD1xm0,17948
 vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=i9N57-MEuQv5B6dQ5iVMTAdOPghYcgiRRz-dTzigf1s,1980
 vivarium_public_health/treatment/scale_up.py,sha256=aKJmZ2G6N80n7oPkJM8IpqZOhftUBkAMBn4hR4EZzhE,7015
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
-vivarium_public_health-3.0.5.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-3.0.5.dist-info/METADATA,sha256=FX6CeaoApBMGJFO3USOMhAIsMpl7srL1gQIkUV8Ay54,4061
-vivarium_public_health-3.0.5.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
-vivarium_public_health-3.0.5.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-3.0.5.dist-info/RECORD,,
+vivarium_public_health-3.0.7.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.0.7.dist-info/METADATA,sha256=yrIrajFSQQDZMMSZMwVgi8dW3iHFLhEDnmKnyspCDiY,4061
+vivarium_public_health-3.0.7.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+vivarium_public_health-3.0.7.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.0.7.dist-info/RECORD,,

{vivarium_public_health-3.0.5.dist-info → vivarium_public_health-3.0.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.0.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any