add TB culture HSI

src/scripts/comparison_of_horizontal_and_vertical_programs/scenario_definitions.py

@@ -15,7 +15,7 @@ def YEAR_OF_CHANGE_FOR_HSS(self) -> int:
     @property
     def YEAR_OF_CHANGE_FOR_HTM(self) -> int:
         """Year in which HIV, TB, Malaria scale-up changes are made."""
-        return 2019
+        return 2015  # <-- todo changing this to 2015, to match Tara's run. Also note that it's not the same as the Year of change for the HSS
 
     def baseline(self) -> Dict:
         """Return the Dict with values for the parameter changes that define the baseline scenario. """
@@ -39,6 +39,11 @@ def baseline(self) -> Dict:
             },
         )
 
+    def baseline_mode1(self) -> Dict:
+        """Return the Dict with values for the parameter changes that define the baseline scenario when using Mode 1.
+        """
+        return get_parameters_for_status_quo()  # <-- Parameters that have been the calibration targets
+
     def double_capacity_at_primary_care(self) -> Dict:
         return {
             'HealthSystem': {
@@ -126,7 +131,7 @@ def hiv_scaleup(self) -> Dict:
         """The parameters for the scale-up of the HIV program"""
         return {
             "Hiv": {
-                'type_of_scaleup': 'max',  # <--- using MAXIMUM SCALE-UP as an experiment
+                'type_of_scaleup': 'max',  # <--- todo: using MAXIMUM SCALE-UP as an experiment
                 'scaleup_start_year': self.YEAR_OF_CHANGE_FOR_HTM,
             }
         }
@@ -135,7 +140,7 @@ def tb_scaleup(self) -> Dict:
         """The parameters for the scale-up of the TB program"""
         return {
             "Tb": {
-                'type_of_scaleup': 'max',  # <--- using MAXIMUM SCALE-UP as an experiment
+                'type_of_scaleup': 'max',  # <--- todo: using MAXIMUM SCALE-UP as an experiment
                 'scaleup_start_year': self.YEAR_OF_CHANGE_FOR_HTM,
             }
         }
@@ -144,7 +149,7 @@ def malaria_scaleup(self) -> Dict:
         """The parameters for the scale-up of the Malaria program"""
         return {
             'Malaria': {
-                'type_of_scaleup': 'max',  # <--- using MAXIMUM SCALE-UP as an experiment
+                'type_of_scaleup': 'max',  # <--- todo: using MAXIMUM SCALE-UP as an experiment
                 'scaleup_start_year': self.YEAR_OF_CHANGE_FOR_HTM,
             }
         }

src/scripts/comparison_of_horizontal_and_vertical_programs/scenario_vertical_programs_with_and_without_hss.py

@@ -27,10 +27,10 @@ def __init__(self):
         self.seed = 0
         self.start_date = Date(2010, 1, 1)
         self.end_date = Date(2031, 1, 1)
-        self.pop_size = 100_000
+        self.pop_size = 50_000  # <--- todo: N.B. very small population size
         self._scenarios = self._get_scenarios()
         self.number_of_draws = len(self._scenarios)
-        self.runs_per_draw = 3  # <--- todo: N.B. Very small number of repeated run, to be efficient for now
+        self.runs_per_draw = 1  # <--- todo: N.B. Very small number of repeated run, to be efficient for now
 
     def log_configuration(self):
         return {

src/scripts/comparison_of_horizontal_and_vertical_programs/scenario_vertical_programs_with_and_without_hss_consumables_available.py

@@ -0,0 +1,167 @@
+"""This Scenario file run the model under different assumptions for the HealthSystem and Vertical Program Scale-up
+
+Run on the batch system using:
+```
+tlo batch-submit
+ src/scripts/comparison_of_horizontal_and_vertical_programs/scenario_vertical_programs_with_and_without_hss.py
+```
+
+"""
+
+from pathlib import Path
+from typing import Dict
+
+from scripts.comparison_of_horizontal_and_vertical_programs.scenario_definitions import (
+    ScenarioDefinitions,
+)
+from tlo import Date, logging
+from tlo.analysis.utils import mix_scenarios
+from tlo.methods.fullmodel import fullmodel
+from tlo.methods.scenario_switcher import ImprovedHealthSystemAndCareSeekingScenarioSwitcher
+from tlo.scenario import BaseScenario
+
+
+class HTMWithAndWithoutHSS(BaseScenario):
+    def __init__(self):
+        super().__init__()
+        self.seed = 0
+        self.start_date = Date(2010, 1, 1)
+        self.end_date = Date(2031, 1, 1)
+        self.pop_size = 50_000  # <--- todo: N.B. very small population size
+        self._scenarios = self._get_scenarios()
+        self.number_of_draws = len(self._scenarios)
+        self.runs_per_draw = 1  # <--- todo: N.B. Very small number of repeated run, to be efficient for now
+
+    def log_configuration(self):
+        return {
+            'filename': 'htm_with_and_without_hss',
+            'directory': Path('./outputs'),
+            'custom_levels': {
+                '*': logging.WARNING,
+                'tlo.methods.demography': logging.INFO,
+                'tlo.methods.demography.detail': logging.WARNING,
+                'tlo.methods.healthburden': logging.INFO,
+                'tlo.methods.healthsystem': logging.WARNING,
+                'tlo.methods.healthsystem.summary': logging.INFO,
+                'tlo.methods.hiv': logging.INFO,
+                'tlo.methods.tb': logging.INFO,
+                'tlo.methods.malaria': logging.INFO,
+            }
+        }
+
+    def modules(self):
+        return (
+            fullmodel(resourcefilepath=self.resources)
+            + [ImprovedHealthSystemAndCareSeekingScenarioSwitcher(resourcefilepath=self.resources)]
+        )
+
+    def draw_parameters(self, draw_number, rng):
+        if draw_number < len(self._scenarios):
+            return list(self._scenarios.values())[draw_number]
+
+    def _get_scenarios(self) -> Dict[str, Dict]:
+        """Return the Dict with values for the parameters that are changed, keyed by a name for the scenario."""
+        # Load helper class containing the definitions of the elements of all the scenarios
+        scenario_definitions = ScenarioDefinitions()
+
+        # We are forcing consumables to be available for everything from 2015
+        consumables_all_available = {
+            'HealthSystem': {
+                'year_cons_availability_switch': 2015,
+                'cons_availability_postSwitch': 'all',
+            }
+        }
+
+        return {
+            "Baseline":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    consumables_all_available,
+                ),
+
+            # - - - FULL PACKAGE OF HEALTH SYSTEM STRENGTHENING - - -
+            "FULL HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.hss_package(),
+                    consumables_all_available,
+                ),
+
+            # **************************************************
+            # VERTICAL PROGRAMS WITH AND WITHOUT THE HSS PACKAGE
+            # **************************************************
+
+            # - - - HIV SCALE-UP WITHOUT HSS PACKAGE- - -
+            "HIV Programs Scale-up WITHOUT HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.hiv_scaleup(),
+                    consumables_all_available,
+                ),
+            # - - - HIV SCALE-UP *WITH* HSS PACKAGE- - -
+            "HIV Programs Scale-up WITH HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.hiv_scaleup(),
+                    scenario_definitions.hss_package(),
+                    consumables_all_available,
+                ),
+
+            # - - - TB SCALE-UP WITHOUT HSS PACKAGE- - -
+            "TB Programs Scale-up WITHOUT HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.tb_scaleup(),
+                    consumables_all_available,
+                ),
+            # - - - TB SCALE-UP *WITH* HSS PACKAGE- - -
+            "TB Programs Scale-up WITH HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.tb_scaleup(),
+                    scenario_definitions.hss_package(),
+                    consumables_all_available,
+                ),
+
+            # - - - MALARIA SCALE-UP WITHOUT HSS PACKAGE- - -
+            "Malaria Programs Scale-up WITHOUT HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.malaria_scaleup(),
+                    consumables_all_available,
+                ),
+            # - - - MALARIA SCALE-UP *WITH* HSS PACKAGE- - -
+            "Malaria Programs Scale-up WITH HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.malaria_scaleup(),
+                    scenario_definitions.hss_package(),
+                    consumables_all_available,
+                ),
+
+            # - - - HIV & TB & MALARIA SCALE-UP WITHOUT HSS PACKAGE- - -
+            "HIV/Tb/Malaria Programs Scale-up WITHOUT HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.hiv_scaleup(),
+                    scenario_definitions.tb_scaleup(),
+                    scenario_definitions.malaria_scaleup(),
+                    consumables_all_available,
+                ),
+            # - - - HIV & TB & MALARIA SCALE-UP *WITH* HSS PACKAGE- - -
+            "HIV/Tb/Malaria Programs Scale-up WITH HSS PACKAGE":
+                mix_scenarios(
+                    scenario_definitions.baseline(),
+                    scenario_definitions.hiv_scaleup(),
+                    scenario_definitions.tb_scaleup(),
+                    scenario_definitions.malaria_scaleup(),
+                    scenario_definitions.hss_package(),
+                    consumables_all_available,
+                ),
+        }
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+
+    scenario_run([__file__])