Albrja/mic 5748/lbwsg

src/vivarium_gates_mncnh/components/__init__.py

@@ -1,4 +1,5 @@
 from vivarium_gates_mncnh.components.antenatal_care import AntenatalCare
+from vivarium_gates_mncnh.components.lbwsg import LBWSGRiskEffect
 from vivarium_gates_mncnh.components.maternal_disorders import MaternalDisorder
 from vivarium_gates_mncnh.components.mortality import (
     MaternalDisordersBurden,

src/vivarium_gates_mncnh/components/lbwsg.py

@@ -0,0 +1,30 @@
+from vivarium.framework.engine import Builder
+from vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation import (
+    LBWSGRiskEffect as LBWSGRiskEffect_,
+)
+from vivarium_public_health.utilities import get_lookup_columns
+
+
+class LBWSGRiskEffect(LBWSGRiskEffect_):
+    """Subclass of LBWSGRiskEffect to expose the PAF pipeline to be accessable by other components."""
+
+    def setup(self, builder: Builder) -> None:
+        # Paf pipeline needs to be registered before the super setup is called
+        self.paf = builder.value.register_value_producer(
+            "paf",
+            source=self.lookup_tables["population_attributable_fraction"],
+            component=self,
+            required_resources=get_lookup_columns(
+                [self.lookup_tables["population_attributable_fraction"]]
+            ),
+        )
+        super().setup(builder)
+
+    # NOTE: We will be manually handling the paf effect so the target_paf_pipeline
+    # has not been created and will throw a warning
+    def register_paf_modifier(self, builder: Builder) -> None:
+        builder.value.register_value_modifier(
+            self.target_paf_pipeline_name,
+            modifier=self.paf,
+            component=self,
+        )

src/vivarium_gates_mncnh/components/mortality.py

@@ -207,13 +207,20 @@ def setup(self, builder: Builder) -> None:
         self.location = get_location(builder)
 
         self.all_cause_mortality_rate = builder.value.register_value_producer(
-            "all_cause_mortality_rate",
+            "all_causes.cause_specific_mortality_rate",
             source=self.lookup_tables["all_cause_mortality_rate"],
             component=self,
-            requires_columns=get_lookup_columns(
+            required_resources=get_lookup_columns(
                 [self.lookup_tables["all_cause_mortality_rate"]]
             ),
         )
+        # Modify ACMR pipeline with CSMR for neonatal causes
+        self.death_in_age_group = builder.value.register_value_producer(
+            "death_in_age_group_probability",
+            source=self.all_cause_mortality_rate,
+            component=self,
+            required_resources=[self.all_cause_mortality_rate],
+        )
 
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         pop_update = pd.DataFrame(
@@ -234,7 +241,7 @@ def on_time_step(self, event: Event) -> None:
 
         pop = self.population_view.get(event.index)
         alive_children = pop.loc[pop[COLUMNS.CHILD_ALIVE] == "alive"]
-        mortality_rates = self.all_cause_mortality_rate(alive_children.index)
+        mortality_rates = self.death_in_age_group(alive_children.index)
         # Convert to rates to probability
         if self._sim_step_name() == SIMULATION_EVENT_NAMES.EARLY_NEONATAL_MORTALITY:
             duration = 7 / 365.0

src/vivarium_gates_mncnh/data/extra_gbd.py

@@ -8,23 +8,6 @@
 from vivarium_gates_mncnh.data import utilities
 
 
-@vi_utils.cache
-def load_lbwsg_exposure(location: str):
-    entity = utilities.get_entity(data_keys.LBWSG.EXPOSURE)
-    location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
-        gbd_id_type="rei_id",
-        gbd_id=entity.gbd_id,
-        source=gbd_constants.SOURCES.EXPOSURE,
-        location_id=location_id,
-        year_id=2021,
-        sex_id=gbd_constants.SEX.MALE + gbd_constants.SEX.FEMALE,
-        age_group_id=164,  # Birth prevalence
-        release_id=gbd_constants.RELEASE_IDS.GBD_2021,
-    )
-    return data
-
-
 @vi_utils.cache
 def get_maternal_disorder_yld_rate(key: str, location: str) -> pd.DataFrame:
     entity = utilities.get_entity(key)

src/vivarium_gates_mncnh/data/loader.py

@@ -66,7 +66,7 @@ def get_data(
         data_keys.PREGNANCY.RAW_INCIDENCE_RATE_ECTOPIC: load_raw_incidence_data,
         data_keys.LBWSG.DISTRIBUTION: load_metadata,
         data_keys.LBWSG.CATEGORIES: load_metadata,
-        data_keys.LBWSG.EXPOSURE: load_lbwsg_exposure,
+        data_keys.LBWSG.EXPOSURE: load_standard_data,
         data_keys.LBWSG.RELATIVE_RISK: load_lbwsg_rr,
         data_keys.LBWSG.RELATIVE_RISK_INTERPOLATOR: load_lbwsg_interpolated_rr,
         data_keys.LBWSG.PAF: load_standard_data,
@@ -257,28 +257,6 @@ def load_scaling_factor(
     return preg_inc
 
 
-def load_lbwsg_exposure(
-    key: str, location: str, years: Optional[Union[int, str, list[int]]] = None
-) -> pd.DataFrame:
-    entity = utilities.get_entity(data_keys.LBWSG.EXPOSURE)
-    data = extra_gbd.load_lbwsg_exposure(location)
-    # This category was a mistake in GBD 2019, so drop.
-    extra_residual_category = vi_globals.EXTRA_RESIDUAL_CATEGORY[entity.name]
-    data = data.loc[data["parameter"] != extra_residual_category]
-    idx_cols = ["location_id", "sex_id", "parameter"]
-    data = data.set_index(idx_cols)[vi_globals.DRAW_COLUMNS]
-
-    # Sometimes there are data values on the order of 10e-300 that cause
-    # floating point headaches, so clip everything to reasonable values
-    data = data.clip(lower=vi_globals.MINIMUM_EXPOSURE_VALUE)
-
-    # normalize so all categories sum to 1
-    total_exposure = data.groupby(["location_id", "sex_id"]).transform("sum")
-    data = (data / total_exposure).reset_index()
-    data = reshape_to_vivarium_format(data, location)
-    return data
-
-
 def load_anc_proportion(
     key: str, location: str, years: Optional[Union[int, str, list[int]]] = None
 ) -> pd.DataFrame:

src/vivarium_gates_mncnh/model_specifications/model_spec.yaml

@@ -5,6 +5,10 @@ plugins:
             builder_interface: vivarium_gates_mncnh.plugins.time.TimeInterface
 
 components:
+    vivarium_public_health:
+        risks:
+            - LBWSGRisk()
+
     vivarium_gates_mncnh:
         components:
             - AgelessPopulation("population.scaling_factor")
@@ -17,14 +21,15 @@ components:
             - MaternalDisorder("maternal_sepsis_and_other_maternal_infections")
             - MaternalDisordersBurden()
             - NeonatalMortality()
+            - LBWSGRiskEffect('cause.all_causes.cause_specific_mortality_rate')
             # Add model observers below here
             - ANCObserver()
             - MaternalDisordersBurdenObserver()
 
 configuration:
     input_data:
         input_draw_number: 0
-        artifact_path: "/mnt/team/simulation_science/pub/models/vivarium_gates_mncnh/artifacts/mortality/ethiopia.hdf"
+        artifact_path: "/mnt/team/simulation_science/pub/models/vivarium_gates_mncnh/artifacts/neonatal/ethiopia.hdf"
     interpolation:
         order: 0
         extrapolate: True