vivarium-public-health 2.1.0__py3-none-any.whl → 2.1.2__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.1.2"

vivarium_public_health/disease/state.py

@@ -11,10 +11,11 @@ from typing import Callable, Dict, List, Optional
 import numpy as np
 import pandas as pd
 from vivarium.framework.engine import Builder
-from vivarium.framework.lookup import LookupTableData
+from vivarium.framework.lookup import LookupTable, LookupTableData
 from vivarium.framework.population import PopulationView, SimulantData
+from vivarium.framework.randomness import RandomnessStream
 from vivarium.framework.state_machine import State, Transient, Transition, Trigger
-from vivarium.framework.values import list_combiner, union_post_processor
+from vivarium.framework.values import Pipeline, list_combiner, union_post_processor
 
 from vivarium_public_health.disease.transition import (
     ProportionTransition,
@@ -323,65 +324,41 @@ class DiseaseState(BaseDiseaseState):
         self.clock = builder.time.clock()
 
         prevalence_data = self.load_prevalence_data(builder)
-        self.prevalence = builder.lookup.build_table(
-            prevalence_data, key_columns=["sex"], parameter_columns=["age", "year"]
-        )
+        self.prevalence = self.get_prevalence(builder, prevalence_data)
 
         birth_prevalence_data = self.load_birth_prevalence_data(builder)
-        self.birth_prevalence = builder.lookup.build_table(
-            birth_prevalence_data, key_columns=["sex"], parameter_columns=["year"]
-        )
+        self.birth_prevalence = self.get_birth_prevalence(builder, birth_prevalence_data)
 
         dwell_time_data = self.load_dwell_time_data(builder)
-        self.dwell_time = builder.value.register_value_producer(
-            f"{self.state_id}.dwell_time",
-            source=builder.lookup.build_table(
-                dwell_time_data, key_columns=["sex"], parameter_columns=["age", "year"]
-            ),
-            requires_columns=["age", "sex"],
-        )
+        self.dwell_time = self.get_dwell_time_pipeline(builder, dwell_time_data)
 
         disability_weight_data = self.load_disability_weight_data(builder)
         self.has_disability = is_non_zero(disability_weight_data)
-        self.base_disability_weight = builder.lookup.build_table(
-            disability_weight_data, key_columns=["sex"], parameter_columns=["age", "year"]
-        )
-        self.disability_weight = builder.value.register_value_producer(
-            f"{self.state_id}.disability_weight",
-            source=self.compute_disability_weight,
-            requires_columns=["age", "sex", "alive", self.model],
+        self.base_disability_weight = self.get_base_disability_weight(
+            builder, disability_weight_data
         )
+
+        self.disability_weight = self.get_disability_weight_pipeline(builder)
+
         builder.value.register_value_modifier(
             "disability_weight", modifier=self.disability_weight
         )
 
         excess_mortality_data = self.load_excess_mortality_rate_data(builder)
         self.has_excess_mortality = is_non_zero(excess_mortality_data)
-        self.base_excess_mortality_rate = builder.lookup.build_table(
-            excess_mortality_data, key_columns=["sex"], parameter_columns=["age", "year"]
-        )
-        self.excess_mortality_rate = builder.value.register_rate_producer(
-            self.excess_mortality_rate_pipeline_name,
-            source=self.compute_excess_mortality_rate,
-            requires_columns=["age", "sex", "alive", self.model],
-            requires_values=[self.excess_mortality_rate_paf_pipeline_name],
-        )
-        paf = builder.lookup.build_table(0)
-        self.joint_paf = builder.value.register_value_producer(
-            self.excess_mortality_rate_paf_pipeline_name,
-            source=lambda idx: [paf(idx)],
-            preferred_combiner=list_combiner,
-            preferred_post_processor=union_post_processor,
+        self.base_excess_mortality_rate = self.get_base_excess_mortality_rate(
+            builder, excess_mortality_data
         )
+        self.excess_mortality_rate = self.get_excess_mortality_rate_pipeline(builder)
+        self.joint_paf = self.get_joint_paf(builder)
+
         builder.value.register_value_modifier(
             "mortality_rate",
             modifier=self.adjust_mortality_rate,
             requires_values=[self.excess_mortality_rate_pipeline_name],
         )
 
-        self.randomness_prevalence = builder.randomness.get_stream(
-            f"{self.state_id}_prevalent_cases"
-        )
+        self.randomness_prevalence = self.get_randomness_prevalence(builder)
 
     #################
     # Setup methods #
@@ -393,12 +370,55 @@ class DiseaseState(BaseDiseaseState):
         else:
             return builder.data.load(f"{self.cause_type}.{self.state_id}.prevalence")
 
+    def get_prevalence(
+        self, builder: Builder, prevalence_data: LookupTableData
+    ) -> LookupTable:
+        """Builds a LookupTable for the prevalence of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        prevalence_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the prevalence of this state.
+        """
+        return builder.lookup.build_table(
+            prevalence_data, key_columns=["sex"], parameter_columns=["age", "year"]
+        )
+
     def load_birth_prevalence_data(self, builder: Builder) -> LookupTableData:
         if "birth_prevalence" in self._get_data_functions:
             return self._get_data_functions["birth_prevalence"](builder, self.state_id)
         else:
             return 0
 
+    def get_birth_prevalence(
+        self, builder: Builder, birth_prevalence_data: LookupTableData
+    ) -> LookupTable:
+        """
+        Builds a LookupTable for the birth prevalence of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        birth_prevalence_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the birth prevalence of this state.
+        """
+        return builder.lookup.build_table(
+            birth_prevalence_data, key_columns=["sex"], parameter_columns=["year"]
+        )
+
     def load_dwell_time_data(self, builder: Builder) -> LookupTableData:
         if "dwell_time" in self._get_data_functions:
             dwell_time = self._get_data_functions["dwell_time"](builder, self.state_id)
@@ -414,6 +434,17 @@ class DiseaseState(BaseDiseaseState):
 
         return dwell_time
 
+    def get_dwell_time_pipeline(
+        self, builder: Builder, dwell_time_data: LookupTableData
+    ) -> Pipeline:
+        return builder.value.register_value_producer(
+            f"{self.state_id}.dwell_time",
+            source=builder.lookup.build_table(
+                dwell_time_data, key_columns=["sex"], parameter_columns=["age", "year"]
+            ),
+            requires_columns=["age", "sex"],
+        )
+
     def load_disability_weight_data(self, builder: Builder) -> LookupTableData:
         if "disability_weight" in self._get_data_functions:
             disability_weight = self._get_data_functions["disability_weight"](
@@ -429,6 +460,35 @@ class DiseaseState(BaseDiseaseState):
 
         return disability_weight
 
+    def get_base_disability_weight(
+        self, builder: Builder, disability_weight_data: LookupTableData
+    ) -> LookupTable:
+        """
+        Builds a LookupTable for the base disability weight of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        disability_weight_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the disability weight of this state.
+        """
+        return builder.lookup.build_table(
+            disability_weight_data, key_columns=["sex"], parameter_columns=["age", "year"]
+        )
+
+    def get_disability_weight_pipeline(self, builder: Builder) -> Pipeline:
+        return builder.value.register_value_producer(
+            f"{self.state_id}.disability_weight",
+            source=self.compute_disability_weight,
+            requires_columns=["age", "sex", "alive", self.model],
+        )
+
     def load_excess_mortality_rate_data(self, builder: Builder) -> LookupTableData:
         if "excess_mortality_rate" in self._get_data_functions:
             return self._get_data_functions["excess_mortality_rate"](builder, self.state_id)
@@ -439,6 +499,48 @@ class DiseaseState(BaseDiseaseState):
                 f"{self.cause_type}.{self.state_id}.excess_mortality_rate"
             )
 
+    def get_base_excess_mortality_rate(
+        self, builder: Builder, excess_mortality_data: LookupTableData
+    ) -> LookupTable:
+        """
+        Builds a LookupTable for the base excess mortality rate of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        excess_mortality_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the base excess mortality rate of this state.
+        """
+        return builder.lookup.build_table(
+            excess_mortality_data, key_columns=["sex"], parameter_columns=["age", "year"]
+        )
+
+    def get_excess_mortality_rate_pipeline(self, builder: Builder) -> Pipeline:
+        return builder.value.register_rate_producer(
+            self.excess_mortality_rate_pipeline_name,
+            source=self.compute_excess_mortality_rate,
+            requires_columns=["age", "sex", "alive", self.model],
+            requires_values=[self.excess_mortality_rate_paf_pipeline_name],
+        )
+
+    def get_joint_paf(self, builder: Builder) -> Pipeline:
+        paf = builder.lookup.build_table(0)
+        return builder.value.register_value_producer(
+            self.excess_mortality_rate_paf_pipeline_name,
+            source=lambda idx: [paf(idx)],
+            preferred_combiner=list_combiner,
+            preferred_post_processor=union_post_processor,
+        )
+
+    def get_randomness_prevalence(self, builder: Builder) -> RandomnessStream:
+        return builder.randomness.get_stream(f"{self.state_id}_prevalent_cases")
+
     ##################
     # Public methods #
     ##################

vivarium_public_health/population/mortality.py

@@ -128,6 +128,19 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_all_cause_mortality_rate(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load all cause mortality rate data and build a lookup table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the all cause mortality rate.
+        """
         acmr_data = builder.data.load("cause.all_causes.cause_specific_mortality_rate")
         return builder.lookup.build_table(
             acmr_data, key_columns=["sex"], parameter_columns=["age", "year"]
@@ -135,6 +148,19 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_life_expectancy(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load life expectancy data and build a lookup table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the life expectancy.
+        """
         life_expectancy_data = builder.data.load(
             "population.theoretical_minimum_risk_life_expectancy"
         )
@@ -142,6 +168,20 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_raw_unmodeled_csmr(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load unmodeled cause specific mortality rate data and build a lookup
+        table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the unmodeled csmr.
+        """
         unmodeled_causes = builder.configuration.unmodeled_causes
         raw_csmr = 0.0
         for idx, cause in enumerate(unmodeled_causes):

vivarium_public_health/risks/effect.py

@@ -121,12 +121,40 @@ class RiskEffect(Component):
         return builder.value.get_value(self.exposure_pipeline_name)
 
     def get_relative_risk_source(self, builder: Builder) -> LookupTable:
+        """
+        Get the relative risk source for this risk effect model.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A lookup table containing the relative risk data for this risk
+            effect model.
+        """
         relative_risk_data = get_relative_risk_data(builder, self.risk, self.target)
         return builder.lookup.build_table(
             relative_risk_data, key_columns=["sex"], parameter_columns=["age", "year"]
         )
 
     def get_population_attributable_fraction_source(self, builder: Builder) -> LookupTable:
+        """
+        Get the population attributable fraction source for this risk effect model.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A lookup table containing the population attributable fraction data
+            for this risk effect model.
+        """
         paf_data = get_population_attributable_fraction_data(builder, self.risk, self.target)
         return builder.lookup.build_table(
             paf_data, key_columns=["sex"], parameter_columns=["age", "year"]

vivarium_public_health/treatment/scale_up.py

@@ -127,6 +127,20 @@ class LinearScaleUp(Component):
         return get_endpoint("start"), get_endpoint("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.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A tuple of lookup tables returning the values at the start and end
+            of the scale-up period.
+        """
         scale_up_config = builder.configuration[self.configuration_key]["value"]
 
         def get_endpoint_value(endpoint_type: str) -> LookupTable:
@@ -172,6 +186,23 @@ 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.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        endpoint_type
+            The type of endpoint to get the value for. Allowed values are
+            "start" and "end".
+
+        Returns
+        -------
+        LookupTable
+            A lookup table returning the value at the start or end of the
+            scale-up period.
+        """
         if endpoint_type == "start":
             endpoint_data = builder.data.load(f"{self.treatment}.exposure")
         elif endpoint_type == "end":

{vivarium_public_health-2.1.0.dist-info → vivarium_public_health-2.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium-public-health
-Version: 2.1.0
+Version: 2.1.2
 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-2.1.0.dist-info → vivarium_public_health-2.1.2.dist-info}/RECORD

@@ -1,12 +1,12 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=Xybt2skBZamGMNlLuOX1IG-h4uIxqUDGAO8MIGWrJac,22
+vivarium_public_health/_version.py,sha256=UiuBcRXPtXxPUBDdp0ZDvWl0U9Db1kMNfT3oAfhxqLg,22
 vivarium_public_health/utilities.py,sha256=_X9sZQ7flsi2sVWQ9zrf8GJw8QwZsPZm3NUjx1gu7bM,2555
 vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
 vivarium_public_health/disease/model.py,sha256=7xFGo6JqPjQjm2VUZ3u3ThXWSzmitTOCZ8N9PTTL6MU,8253
 vivarium_public_health/disease/models.py,sha256=uiB2qUlxBsPPPmHJ8Cgot_T1ItZ8RYSNVOBtxtn93Y0,3478
 vivarium_public_health/disease/special_disease.py,sha256=gl8aK0z6afCxiCZxgJafLe4xmbR91zk3079hsi2pUAw,14751
-vivarium_public_health/disease/state.py,sha256=yZ76I4mRHfa-KG2lhCJZpVWkgxip0j6r3AkQD5SpTzg,21165
+vivarium_public_health/disease/state.py,sha256=TBbUQ8zALN5BdpJM2WPUYYhlZ4xcu-UXKc3rOZUj72Y,24403
 vivarium_public_health/disease/transition.py,sha256=Or5nucRzeGG-UuE_CGkPZ9qE35-Ed9I9LWHj4rjknCc,5334
 vivarium_public_health/metrics/__init__.py,sha256=bWAvvdCm_7RPIazo12qFohA2x5-_EV6ceV8IhKS37sk,209
 vivarium_public_health/metrics/disability.py,sha256=zm0vAG00wj44CHjYGdT2_pebgARa3XXIerrR06t80rc,3984
@@ -25,12 +25,12 @@ vivarium_public_health/population/__init__.py,sha256=17rtbcNVK5LtCCxAex7P7Q_vYpw
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=qNsZjvaJ7Et8_Kw7JNyRshHHRA3pEQMM4TSqCp48Gr4,9092
 vivarium_public_health/population/base_population.py,sha256=U9FibBoPuYWvUqPFCUIVwjBxQVuhTb58cUy-2EJSzio,15345
 vivarium_public_health/population/data_transformations.py,sha256=M1qZlDyWGQsVR33LtrKW2ts1OIXOT2TYoQEtjzXQ_1k,21804
-vivarium_public_health/population/mortality.py,sha256=Cv7OSSPLb6e9N0TaEBKz2mPbmDWVk3eEpdaKrzXQu6M,9004
+vivarium_public_health/population/mortality.py,sha256=w1Oxb958LjUkNwxJ0vdA3TZndpeNiaH3d7RukLas_oQ,10085
 vivarium_public_health/risks/__init__.py,sha256=XvX12RgD0iF5PBoc2StsOhxJmK1FP-RaAYrjIT9MfDs,232
 vivarium_public_health/risks/base_risk.py,sha256=6D7YlxQOdQm-Kw5_vjpQmFqU7spF-lTy14WEEefRQlA,6494
 vivarium_public_health/risks/data_transformations.py,sha256=-nEbytxaQEB1zaAacA46A3WATeKle2FvrnePx-NPCeg,19602
 vivarium_public_health/risks/distributions.py,sha256=EYMjhOmci4O7orU2-qQ55uOzqplqByn4GokbKgcZgfQ,10800
-vivarium_public_health/risks/effect.py,sha256=chpFI4UGqO_uaUjB9LCCPaHeVorHeYv0sTjXzphdwPo,6555
+vivarium_public_health/risks/effect.py,sha256=GH_n5j6RQY-DdV0hSH-_Qo10lXVZRdMyANh6wfrLtiI,7295
 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=G8-KMklSwd2Sl29oMX8WFPKKv1tBtRUOqLuAmoxOos0,18027
 vivarium_public_health/testing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -38,10 +38,10 @@ vivarium_public_health/testing/mock_artifact.py,sha256=T6Fw0rSEGfDr7Lqq-YxcJBmZt
 vivarium_public_health/testing/utils.py,sha256=bbAEGw5kRzVB_80uc5u5mp47NMj2xD6Nw7vlEsT_-Wg,2199
 vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=iPKFN3VjfiMy_XvN94UqM-FUrGuI0ULwmOdAGdOepYQ,1979
-vivarium_public_health/treatment/scale_up.py,sha256=zTPMfKG38dGBj14QpBeLlmUixx1y_XIMElmTpkklydA,6714
+vivarium_public_health/treatment/scale_up.py,sha256=7QKBgAII4dwkds9gdbQ5d6oDaD02iwcQCVcYRN-B4Mg,7573
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=VwZ7t90zzfGoBusduIvcE4lDe5zTvzmHiUNB3u2I52Y,2339
-vivarium_public_health-2.1.0.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-2.1.0.dist-info/METADATA,sha256=qmXdDtOXL1ZEE6zsUdDGG8CUPAvloE3-oQzToUduRnA,3430
-vivarium_public_health-2.1.0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-vivarium_public_health-2.1.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-2.1.0.dist-info/RECORD,,
+vivarium_public_health-2.1.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-2.1.2.dist-info/METADATA,sha256=3LZgXExgpesqC24nJKzasGyEaGqiS9NVAmbuVUNMEAM,3430
+vivarium_public_health-2.1.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+vivarium_public_health-2.1.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-2.1.2.dist-info/RECORD,,

{vivarium_public_health-2.1.0.dist-info → vivarium_public_health-2.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any