MNH cohort

src/scripts/maternal_perinatal_analyses/cohort_analysis/cohort_interventions_scenario.py

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+import numpy as np
+import pandas as pd
+
+from pathlib import Path
+
+from tlo import Date, logging
+from tlo.methods import mnh_cohort_module
+from tlo.methods.fullmodel import fullmodel
+from tlo.scenario import BaseScenario
+
+
+class BaselineScenario(BaseScenario):
+    def __init__(self):
+        super().__init__()
+        self.seed = 562661
+        self.start_date = Date(2024, 1, 1)
+        self.end_date = Date(2025, 1, 2)
+        self.pop_size = 40_000
+        self.number_of_draws =6
+        self.runs_per_draw = 60
+
+    def log_configuration(self):
+        return {
+            'filename': 'block_intervention_big_run', 'directory': './outputs',
+            "custom_levels": {
+                "*": logging.WARNING,
+                "tlo.methods.demography": logging.INFO,
+                "tlo.methods.demography.detail": logging.INFO,
+                "tlo.methods.contraception": logging.INFO,
+                "tlo.methods.healthsystem.summary": logging.INFO,
+                "tlo.methods.healthburden": logging.INFO,
+                "tlo.methods.labour": logging.INFO,
+                "tlo.methods.labour.detail": logging.INFO,
+                "tlo.methods.newborn_outcomes": logging.INFO,
+                "tlo.methods.care_of_women_during_pregnancy": logging.INFO,
+                "tlo.methods.pregnancy_supervisor": logging.INFO,
+                "tlo.methods.postnatal_supervisor": logging.INFO,
+            }
+        }
+
+    def modules(self):
+        return [*fullmodel(resourcefilepath=self.resources,
+                           module_kwargs={'Schisto': {'mda_execute': False}}),
+                 mnh_cohort_module.MaternalNewbornHealthCohort(resourcefilepath=self.resources)]
+
+    def draw_parameters(self, draw_number, rng):
+
+        # if draw_number == 0:
+        #     return {'PregnancySupervisor': {
+        #             'analysis_year': 2024}}
+        #
+        # else:
+        interventions_for_analysis = ['iron_folic_acid', 'iron_folic_acid',
+                                      'post_abortion_care_core', 'post_abortion_care_core',
+                                      'ectopic_pregnancy_treatment', 'ectopic_pregnancy_treatment']
+
+        avail_for_draw = [0.0, 1.0,
+                          0.0, 1.0,
+                          0.0, 1.0,
+                          ]
+
+        return {'PregnancySupervisor': {
+                'analysis_year': 2024,
+                'interventions_analysis': True,
+                'interventions_under_analysis': [interventions_for_analysis[draw_number]],
+                'intervention_analysis_availability': avail_for_draw[draw_number]}}
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+    scenario_run([__file__])