contraception health impacts: scenario

src/scripts/contraception/scenarios/run_analysis_co_health_impacts_no_diseases.py

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+"""
+This file defines a batch run to get sims results to be used by the analysis_contraception_plot_table.
+Run on the remote batch system using:
+```tlo batch-submit src/scripts/contraception/scenarios/run_analysis_co_health_impacts_no_diseases.py```
+or locally using:
+```tlo scenario-run src/scripts/contraception/scenarios/run_analysis_co_health_impacts_no_diseases.py```
+
+# TODO: update
+SCENARIO SETTINGS
+-----------------
+used modules:
+* Demography
+* HealthSystem
+    - cons_availability="all", i.e. all consumables are assumed to be always available,
+    - disable=False, i.e. the health system is disabled (hence no constraints and no logging) and every HSI event runs
+* Contraception, for which SimplifiedPregnancyAndLabour is used
+    - use_interventions=False/True according to what we need (False => without interventions,
+    True => interventions since 2023)
+* DummyHivModule (a supporting module required by Contraception module)
+
+logging above warning level:
+* contraception:
+    - INFO if only analysis_all_calibration or figs but not the table from analysis_contraception_plot_table required,
+    - DEBUG if tabel from analysis_contraception_plot_table required.
+* demography: INFO.
+NB. For analysis_all_calibration this is enough only if analysis_hsi_descriptions are not required, and the analysis
+needs to be changed accordingly to run properly. We use an adjusted analysis_all_calibration script, stored in the
+EvaJ/contraception_2023-02_inclPR807/AnalysisAllCalib_Contraception branch.
+
+# TODO: update
+CONTRACEPTION PAPER (Eva J et al. 2023):
+---------------------------------------
+- 1 draw & 1 run/per draw with 250K initial_population_size
+- use_interventions=False/True for simulation without/with interventions,
+- for analysis_all_calibration adjusted in the branch
+EvaJ/contraception_2023-02_inclPR807/AnalysisAllCalib_Contraception with the analysis_hsi_descriptions excluded (Fig 2):
+    2010-2099 simulated with contraception logging at the level INFO (a job to simulate that many years with DEBUG
+    logging fails)
+- for analysis_contraception_plot_table (Fig 3, Fig 4, Tab 4, and Fig A6.1):
+    2010-2050 simulated with contraception logging at the level DEBUG
+"""
+
+from tlo import Date, logging
+from tlo.methods import (
+    alri,
+    cardio_metabolic_disorders,
+    care_of_women_during_pregnancy,
+    contraception,
+    demography,
+    depression,
+    diarrhoea,
+    enhanced_lifestyle,
+    epi,
+    healthburden,
+    healthseekingbehaviour,
+    healthsystem,
+    hiv,
+    labour,
+    malaria,
+    newborn_outcomes,
+    postnatal_supervisor,
+    pregnancy_supervisor,
+    stunting,
+    symptommanager,
+    tb,
+    wasting,
+)
+from tlo.scenario import BaseScenario
+
+
+class RunAnalysisCo(BaseScenario):
+    def __init__(self):
+        super().__init__(
+            seed=0,
+            start_date=Date(2010, 1, 1),
+            end_date=Date(2030, 12, 31),
+            initial_population_size=2_000,  # selected size for the Tim C at al. 2023 paper: 250K
+            number_of_draws=1,  # <- one scenario
+            runs_per_draw=1,  # <- repeated this many times
+        )
+
+    def log_configuration(self):
+        return {
+            'filename': 'run_analysis_co_health_impacts_no_diseases',  # <- (specified only for local running)
+            'directory': './outputs',  # <- (specified only for local running)
+            'custom_levels': {
+                '*': logging.WARNING,
+                "tlo.methods.demography": logging.INFO,
+                "tlo.methods.demography.detail": logging.INFO,
+                "tlo.methods.depression": logging.INFO,
+                "tlo.methods.contraception": logging.INFO,
+                "tlo.methods.healthsystem.summary": logging.INFO,
+                "tlo.methods.healthburden": logging.INFO,
+                "tlo.methods.hiv": logging.INFO,
+                "tlo.methods.labour": logging.INFO,
+                "tlo.methods.labour.detail": logging.INFO,
+                "tlo.methods.malaria": 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,
+                "tlo.methods.tb": logging.INFO,
+            }
+        }
+
+    def modules(self):
+        return [
+            demography.Demography(resourcefilepath=self.resources),
+            contraception.Contraception(resourcefilepath=self.resources,
+                                        use_interventions=False,  # default: False
+                                        # interventions_start_date=Date(2016, 1, 1),  # if needs to be changed
+                                        # the default date is Date(2023, 1, 1)
+                                        ),
+            enhanced_lifestyle.Lifestyle(resourcefilepath=self.resources),
+            healthburden.HealthBurden(resourcefilepath=self.resources),
+            symptommanager.SymptomManager(resourcefilepath=self.resources),
+            healthsystem.HealthSystem(resourcefilepath=self.resources,
+                                      mode_appt_constraints=1,
+                                      cons_availability='all'),
+            newborn_outcomes.NewbornOutcomes(resourcefilepath=self.resources),
+            pregnancy_supervisor.PregnancySupervisor(resourcefilepath=self.resources),
+            care_of_women_during_pregnancy.CareOfWomenDuringPregnancy(resourcefilepath=self.resources),
+            labour.Labour(resourcefilepath=self.resources),
+            postnatal_supervisor.PostnatalSupervisor(resourcefilepath=self.resources),
+            healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=self.resources),
+
+            # Register all the modules that are reference in the maternal perinatal health suite (including their
+            # dependencies)
+            alri.Alri(resourcefilepath=self.resources),
+            hiv.Hiv(resourcefilepath=self.resources),
+            tb.Tb(resourcefilepath=self.resources),
+            malaria.Malaria(resourcefilepath=self.resources),
+            cardio_metabolic_disorders.CardioMetabolicDisorders(resourcefilepath=self.resources),
+            depression.Depression(resourcefilepath=self.resources),
+            stunting.Stunting(resourcefilepath=self.resources),
+            wasting.Wasting(resourcefilepath=self.resources),
+            diarrhoea.Diarrhoea(resourcefilepath=self.resources),
+            epi.Epi(resourcefilepath=self.resources)
+        ]
+
+    def draw_parameters(self, draw_number, rng):
+        return {
+            'PregnancySupervisor': {'analysis_year': 2023},
+            'Labour': {'analysis_year': 2023},
+        }
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+
+    scenario_run([__file__])