Model 29.1 Anemia YLDs

src/vivarium_gates_mncnh/components/hemoglobin.py

@@ -56,12 +56,12 @@ def build_all_lookup_tables(self, builder: Builder) -> None:
             value_columns=["value"],
         )
 
-    def get_current_exposure(self, index: pd.Index) -> pd.Series:
-        propensity = self.propensity(index)
-        gbd_exposure = pd.Series(self.exposure_distribution.ppf(propensity), index=index)
-        return gbd_exposure - (
-            self.ifa_effect_size * self.ifa_coverage * self.lookup_tables["ANC1"](index)
-        )
+    # def get_current_exposure(self, index: pd.Index) -> pd.Series:
+    #     propensity = self.propensity(index)
+    #     gbd_exposure = pd.Series(self.exposure_distribution.ppf(propensity), index=index)
+    #     return gbd_exposure - (
+    #         self.ifa_effect_size * self.ifa_coverage * self.lookup_tables["ANC1"](index)
+    #     )
 
     def on_time_step_cleanup(self, event: Event) -> None:
         if self._sim_step_name() != SIMULATION_EVENT_NAMES.FIRST_TRIMESTER_ANC:

src/vivarium_gates_mncnh/components/observers.py

@@ -67,6 +67,7 @@ def register_stratifications(self, builder: Builder) -> None:
                     PREGNANCY_OUTCOMES.STILLBIRTH_OUTCOME,
                     PREGNANCY_OUTCOMES.LIVE_BIRTH_OUTCOME,
                     PREGNANCY_OUTCOMES.PARTIAL_TERM_OUTCOME,
+                    PREGNANCY_OUTCOMES.FULL_TERM_OUTCOME,
                 ]
             ),
             requires_columns=[COLUMNS.PREGNANCY_OUTCOME],
@@ -534,7 +535,7 @@ def configuration_defaults(self) -> dict[str, Any]:
             "stratification": {
                 self.get_configuration_name(): {
                     "exclude": [],
-                    "include": ["age_group"],
+                    "include": ["age_group", "pregnancy_outcome"],
                 },
             },
         }

src/vivarium_gates_mncnh/constants/paths.py

@@ -31,5 +31,5 @@
 
 # Update for new model results directory after model changes and runs
 # This should match the directory after /mnt/team/simulation_sicence/pub/models/vivarium_gates_mncnh/results/
-MODEL_RESULTS_DIR = "model26.0"
+MODEL_RESULTS_DIR = "model29.2"
 MODEL_NOTEBOOKS_DIR = BASE_DIR.parent.parent / "tests" / "model_notebooks"

src/vivarium_gates_mncnh/model_specifications/model_spec.yaml

@@ -37,7 +37,7 @@ components:
             - InterventionRiskEffect('azithromycin')
             - InterventionRiskEffect('misoprostol')
             - OralIronInterventionExposure() # IFA and MMS
-            - OralIronEffectOnHemoglobin()
+            # - OralIronEffectOnHemoglobin()
             - OralIronEffectOnStillbirth()
             - AdditiveRiskEffect('risk_factor.iron_folic_acid_supplementation', 'risk_factor.birth_weight.birth_exposure')
             - AdditiveRiskEffect('risk_factor.multiple_micronutrient_supplementation', 'risk_factor.birth_weight.birth_exposure')