vivarium-public-health 3.0.4__py3-none-any.whl → 3.0.6__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "3.0.4"
+__version__ = "3.0.6"

vivarium_public_health/results/disability.py

@@ -1,7 +1,7 @@
 """
-===================
-Disability Observer
-===================
+====================
+Disability Observers
+====================
 
 This module contains tools for observing years lived with disability (YLDs)
 in the simulation.
@@ -102,7 +102,7 @@ class DisabilityObserver(PublicHealthObserver):
         )
         # Convert to SimpleCause instances and add on all_causes
         causes_of_disability = [
-            SimpleCause.create_from_disease_state(cause) for cause in causes_of_disability
+            SimpleCause.create_from_specific_cause(cause) for cause in causes_of_disability
         ] + [SimpleCause("all_causes", "all_causes", "cause")]
 
         excluded_causes = (

vivarium_public_health/results/disease.py

@@ -1,7 +1,7 @@
 """
-================
-Disease Observer
-================
+=================
+Disease Observers
+=================
 
 This module contains tools for observing disease incidence and prevalence
 in the simulation.

vivarium_public_health/results/mortality.py

@@ -1,7 +1,7 @@
 """
-==================
-Mortality Observer
-==================
+===================
+Mortality Observers
+===================
 
 This module contains tools for observing cause-specific and
 excess mortality in the simulation, including "other causes".
@@ -130,7 +130,7 @@ class MortalityObserver(PublicHealthObserver):
 
         # Convert to SimpleCauses and add on other_causes and not_dead
         self.causes_of_death = [
-            SimpleCause.create_from_disease_state(cause) for cause in causes_of_death
+            SimpleCause.create_from_specific_cause(cause) for cause in causes_of_death
         ] + [
             SimpleCause("not_dead", "not_dead", "cause"),
             SimpleCause("other_causes", "other_causes", "cause"),

vivarium_public_health/results/observer.py

@@ -1,3 +1,13 @@
+"""
+===============
+Basic Observers
+===============
+
+This module contains convenience classes for building concrete observers in
+public health models.
+
+"""
+
 from typing import Callable, List, Optional, Union
 
 import pandas as pd

vivarium_public_health/results/simple_cause.py

@@ -1,12 +1,21 @@
+"""
+============
+Simple Cause
+============
+
+This module contains tools for creating a minimal representation of a cause
+as required by observers.
+
+"""
+
 from dataclasses import dataclass
 
 
 @dataclass
 class SimpleCause:
-    """A simple dataclass to represent the bare minimum information needed
-    for observers, e.g. 'all_causes' as a cause of disability.
+    """A simple dataclass to represent the bare minimum information needed by observers.
 
-    It also includes a class method to convert a provided disease state into a
+    It also includes a class method to convert a provided cause into a
     ``SimpleCause`` instance.
 
     """
@@ -19,6 +28,16 @@ class SimpleCause:
     """The cause type of the cause."""
 
     @classmethod
-    def create_from_disease_state(cls, disease_state: type) -> "SimpleCause":
-        """Create a SimpleCause instance from a"""
-        return cls(disease_state.state_id, disease_state.model, disease_state.cause_type)
+    def create_from_specific_cause(cls, cause: type) -> "SimpleCause":
+        """Create a SimpleCause instance from a more specific cause.
+
+        Parameters
+        ----------
+        cause
+            The cause to be converted into a SimpleCause instance.
+
+        Returns
+        -------
+            A SimpleCause instance.
+        """
+        return cls(cause.state_id, cause.model, cause.cause_type)

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-3.0.4.dist-info → vivarium_public_health-3.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.4
+Version: 3.0.6
 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-3.0.4.dist-info → vivarium_public_health-3.0.6.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=gNoy6uoSQO4ZzowTZAJz3hphzq1F_Y-3X9YrQdb7ppc,22
+vivarium_public_health/_version.py,sha256=uC8HeJcsNKDMSm12PYMv69I4zC6ciz4KILeBXWW_c8g,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
@@ -24,26 +24,26 @@ vivarium_public_health/population/data_transformations.py,sha256=QVh_63Wwg9BUkaQ
 vivarium_public_health/population/mortality.py,sha256=w7b_TUssHjRcnULdXu7MXKfZBjCrlYWbB94oO3JWogI,10264
 vivarium_public_health/results/__init__.py,sha256=XKuX9HTXUur1kpHM7zuMSnkJxlg-W7eMAPmh8LP9Xp4,281
 vivarium_public_health/results/columns.py,sha256=V-L3JgTcsk51Zx9PcUwSgaE1iZjuGyfZ8aShPjynadU,495
-vivarium_public_health/results/disability.py,sha256=DqSNI1CEdhNXy-mhTtuTXom22e6XGrvFoaeQwyBdlig,9872
-vivarium_public_health/results/disease.py,sha256=q5-g495tPbcs1zfApwoCTfkionAwQbCeXn3JigBUOIk,12526
-vivarium_public_health/results/mortality.py,sha256=Bo8l8CYcBmI6BsXl8l_7mPieGLzyUp3XeFBm497mThE,9652
-vivarium_public_health/results/observer.py,sha256=-VoOYOaT-vmxVNi0bxm3It0ZFdLIq8D9Ng28xO1JuLw,7143
+vivarium_public_health/results/disability.py,sha256=JQm3Q7CoGCT2AgxaoH6MKkvnq4xF83wfFmEvEOvTmvA,9876
+vivarium_public_health/results/disease.py,sha256=OwxhPrfDsCnCZSaw8Yiq2AnibWikoqI-gM7xDdhFLcM,12529
+vivarium_public_health/results/mortality.py,sha256=imH5OGze_rb0i60hmFs-JUjE6XXoH8Gt9wWeut0sk_M,9656
+vivarium_public_health/results/observer.py,sha256=SQmKL1OCs2gDS8clIuJvZ3WiuspMkGEVDhnuNMJAvHc,7300
 vivarium_public_health/results/risk.py,sha256=GS4qJVjW3MqsDeRDDac2etFQlqIluxOxIZFMy1Ytmp8,6622
-vivarium_public_health/results/simple_cause.py,sha256=jlrllbSiEIOrf69gQvrJww29uMrR8xzK_5TApu1Mxqg,724
+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-3.0.4.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-3.0.4.dist-info/METADATA,sha256=mVOUpc6PRXAW7lnKkJ3BRJPKHT3erLyQuS60qlMFUzU,4061
-vivarium_public_health-3.0.4.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
-vivarium_public_health-3.0.4.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-3.0.4.dist-info/RECORD,,
+vivarium_public_health-3.0.6.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.0.6.dist-info/METADATA,sha256=9R6AnfAPIZppi65fLRkAEMGemyS-yognH2oN1U9zS_g,4061
+vivarium_public_health-3.0.6.dist-info/WHEEL,sha256=uCRv0ZEik_232NlR4YDw4Pv3Ajt5bKvMH13NUU7hFuI,91
+vivarium_public_health-3.0.6.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.0.6.dist-info/RECORD,,

{vivarium_public_health-3.0.4.dist-info → vivarium_public_health-3.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.0.0)
+Generator: setuptools (74.1.1)
 Root-Is-Purelib: true
 Tag: py3-none-any