Updated schistosomiasis model (#1587)

tdm32 · tbhallett · tamuri · web-flow · commit 9b8112d4a0b2 · 2025-07-11T15:05:48.000+01:00
Co-authored-by: Tim Hallett &lt;39991060+tbhallett@users.noreply.github.com&gt;
Co-authored-by: Asif Tamuri &lt;tamuri@gmail.com&gt;
diff --git a/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/MDA_historical_Coverage.csv b/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/MDA_historical_Coverage.csv
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diff --git a/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/MDA_prognosed_Coverage.csv b/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/MDA_prognosed_Coverage.csv
diff --git a/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/main.csv b/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/main.csv
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diff --git a/resources/ResourceFile_Schisto/District_Params_haematobium.csv b/resources/ResourceFile_Schisto/District_Params_haematobium.csv
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diff --git a/resources/ResourceFile_Schisto/ESPEN.csv b/resources/ResourceFile_Schisto/ESPEN.csv
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diff --git a/resources/ResourceFile_Schisto/InitialData_haematobium.csv b/resources/ResourceFile_Schisto/InitialData_haematobium.csv
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diff --git a/resources/ResourceFile_Schisto/MDA_historical_Coverage.csv b/resources/ResourceFile_Schisto/MDA_historical_Coverage.csv
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diff --git a/resources/ResourceFile_Schisto/MDA_prognosed_Coverage.csv b/resources/ResourceFile_Schisto/MDA_prognosed_Coverage.csv
diff --git a/resources/ResourceFile_Schisto/Parameters.csv b/resources/ResourceFile_Schisto/Parameters.csv
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diff --git a/resources/ResourceFile_Schisto/Symptoms.csv b/resources/ResourceFile_Schisto/Symptoms.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/CVD.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/CVD.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test Mode 1.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test Mode 1.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv
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diff --git a/src/scripts/profiling/run_profiling.py b/src/scripts/profiling/run_profiling.py
@@ -326,7 +326,7 @@ def run_profiling(
         additional_stats=additional_stats,
     )
     print("done")
-    
+
     # Write out logged profiling statistics
     logged_statistics_file = output_dir / f"{output_name}.logged-stats.csv"
     print(f"Writing {logged_statistics_file}", end="...", flush=True)
diff --git a/src/scripts/schistosomiasis/baseline_run.py b/src/scripts/schistosomiasis/baseline_run.py
@@ -0,0 +1,107 @@
+"""
+This file uses the calibrated parameters for prop_susceptible
+and runs with no MDA running
+outputs can be plotted against data to check calibration
+
+check the batch configuration gets generated without error:
+tlo scenario-run --draw-only src/scripts/schistosomiasis/baseline_run.py
+
+Run locally:
+tlo scenario-run src/scripts/schistosomiasis/baseline_run.py
+
+or execute a single run:
+tlo scenario-run src/scripts/schistosomiasis/baseline_run.py --draw 1 0
+
+Run on the batch system using:
+tlo batch-submit src/scripts/schistosomiasis/baseline_run.py
+
+"""
+
+import random
+
+from tlo import Date, logging
+from tlo.methods import (
+    alri,
+    bladder_cancer,
+    demography,
+    diarrhoea,
+    enhanced_lifestyle,
+    epi,
+    healthburden,
+    healthseekingbehaviour,
+    healthsystem,
+    hiv,
+    schisto,
+    simplified_births,
+    stunting,
+    symptommanager,
+    tb,
+    wasting,
+)
+from tlo.scenario import BaseScenario
+
+
+class TestScenario(BaseScenario):
+
+    def __init__(self):
+        super().__init__()
+        self.seed = random.randint(0, 50000)
+        self.start_date = Date(2010, 1, 1)
+
+        self.end_date = Date(2023, 12, 31)
+        self.pop_size = 64_000  # if equal_allocation_by_district, 64,000=2k per district
+        self.runs_per_draw = 3
+
+        self.mda_execute = True
+        self.single_district = False
+        self.equal_allocation_by_district = True
+
+        # Calculate the total number of combinations
+        self.number_of_draws = 1
+
+    def log_configuration(self):
+        return {
+            'filename': 'schisto_scenarios',
+            'directory': './outputs',
+            'custom_levels': {
+                '*': logging.WARNING,
+                "tlo.methods.hiv": logging.INFO,
+                "tlo.methods.enhanced_lifestyle": logging.INFO,
+                "tlo.methods.schisto": logging.INFO,
+                "tlo.methods.healthsystem.summary": logging.INFO,
+                "tlo.methods.healthburden": logging.INFO,
+            }
+        }
+
+    def modules(self):
+        return [
+            demography.Demography(resourcefilepath=self.resources,
+                                  equal_allocation_by_district=self.equal_allocation_by_district),
+            simplified_births.SimplifiedBirths(resourcefilepath=self.resources),
+            enhanced_lifestyle.Lifestyle(resourcefilepath=self.resources),
+            epi.Epi(resourcefilepath=self.resources),
+            healthburden.HealthBurden(resourcefilepath=self.resources),
+            healthsystem.HealthSystem(resourcefilepath=self.resources),
+            healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=self.resources),
+            symptommanager.SymptomManager(resourcefilepath=self.resources),
+            # diseases
+            alri.Alri(resourcefilepath=self.resources),
+            bladder_cancer.BladderCancer(resourcefilepath=self.resources),
+            diarrhoea.Diarrhoea(resourcefilepath=self.resources),
+            hiv.Hiv(resourcefilepath=self.resources),
+            schisto.Schisto(resourcefilepath=self.resources,
+                            mda_execute=self.mda_execute,
+                            single_district=self.single_district),
+            stunting.Stunting(resourcefilepath=self.resources),
+            tb.Tb(resourcefilepath=self.resources),
+            wasting.Wasting(resourcefilepath=self.resources),
+        ]
+
+    def draw_parameters(self, draw_number, rng):
+
+        return
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+    scenario_run([__file__])
diff --git a/src/scripts/schistosomiasis/schisto_single_run_local.py b/src/scripts/schistosomiasis/schisto_single_run_local.py
diff --git a/src/tlo/methods/demography.py b/src/tlo/methods/demography.py
diff --git a/src/tlo/methods/enhanced_lifestyle.py b/src/tlo/methods/enhanced_lifestyle.py
diff --git a/src/tlo/methods/schisto.py b/src/tlo/methods/schisto.py
diff --git a/tests/test_schisto.py b/tests/test_schisto.py

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