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Update TB consumables to use item names not packages (#1536)
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* update tb consumables to use item names and not packages. include optional items

* edit facility level to 1b for xpert testing (previously was level 2)

* test runs

---------

Co-authored-by: Tim Hallett <39991060+tbhallett@users.noreply.github.com>
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@tdm32 @tbhallett
tdm32 and tbhallett authored Dec 5, 2024
1 parent cb6cd8e commit 2d76315
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Showing 2 changed files with 37 additions and 17 deletions.
10 changes: 5 additions & 5 deletions src/scripts/hiv/projections_jan2023/analysis_logged_deviance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@

# %% Run the simulation
start_date = Date(2010, 1, 1)
end_date = Date(2022, 1, 1)
popsize = 5000
end_date = Date(2014, 1, 1)
popsize = 25000

# scenario = 1

Expand All @@ -51,7 +51,7 @@
"tlo.methods.tb": logging.INFO,
"tlo.methods.demography": logging.INFO,
# "tlo.methods.demography.detail": logging.WARNING,
# "tlo.methods.healthsystem.summary": logging.INFO,
"tlo.methods.healthsystem.summary": logging.INFO,
# "tlo.methods.healthsystem": logging.INFO,
# "tlo.methods.healthburden": logging.INFO,
},
Expand All @@ -70,7 +70,7 @@
resourcefilepath=resourcefilepath,
service_availability=["*"], # all treatment allowed
mode_appt_constraints=1, # mode of constraints to do with officer numbers and time
cons_availability="default", # mode for consumable constraints (if ignored, all consumables available)
cons_availability="all", # mode for consumable constraints (if ignored, all consumables available)
ignore_priority=False, # do not use the priority information in HSI event to schedule
capabilities_coefficient=1.0, # multiplier for the capabilities of health officers
use_funded_or_actual_staffing="actual", # actual: use numbers/distribution of staff available currently
Expand All @@ -89,7 +89,7 @@
# set the scenario
sim.modules["Hiv"].parameters["do_scaleup"] = True
sim.modules["Hiv"].parameters["scaleup_start_year"] = 2019
# sim.modules["Tb"].parameters["scenario"] = scenario
sim.modules["Tb"].parameters["first_line_test"] = 'xpert'
# sim.modules["Tb"].parameters["scenario_start_date"] = Date(2010, 1, 1)
# sim.modules["Tb"].parameters["scenario_SI"] = "z"

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44 changes: 32 additions & 12 deletions src/tlo/methods/tb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -681,16 +681,24 @@ def get_consumables_for_dx_and_tx(self):

# TB Sputum smear test
# assume that if smear-positive, sputum smear test is 100% specific and sensitive
self.item_codes_for_consumables_required['sputum_test'] = \
hs.get_item_codes_from_package_name("Microscopy Test")
self.item_codes_for_consumables_required['sputum_test'] = hs.get_item_code_from_item_name("ZN Stain")
self.item_codes_for_consumables_required['sputum_container'] = hs.get_item_code_from_item_name(
"Sputum container")
self.item_codes_for_consumables_required['slides'] = hs.get_item_code_from_item_name(
"Microscope slides, lime-soda-glass, pack of 50")
self.item_codes_for_consumables_required['gloves'] = hs.get_item_code_from_item_name(
"Gloves, exam, latex, disposable, pair")

self.sim.modules['HealthSystem'].dx_manager.register_dx_test(
tb_sputum_test_smear_positive=DxTest(
property='tb_inf',
target_categories=["active"],
sensitivity=p["sens_sputum_smear_positive"],
specificity=p["spec_sputum_smear_positive"],
item_codes=self.item_codes_for_consumables_required['sputum_test']
item_codes=self.item_codes_for_consumables_required['sputum_test'],
optional_item_codes=[self.item_codes_for_consumables_required['sputum_container'],
self.item_codes_for_consumables_required['slides'],
self.item_codes_for_consumables_required['gloves']]
)
)
self.sim.modules['HealthSystem'].dx_manager.register_dx_test(
Expand All @@ -699,13 +707,16 @@ def get_consumables_for_dx_and_tx(self):
target_categories=["active"],
sensitivity=0.0,
specificity=1.0,
item_codes=self.item_codes_for_consumables_required['sputum_test']
item_codes=self.item_codes_for_consumables_required['sputum_test'],
optional_item_codes=[self.item_codes_for_consumables_required['sputum_container'],
self.item_codes_for_consumables_required['slides'],
self.item_codes_for_consumables_required['gloves']]
)
)

# TB GeneXpert
self.item_codes_for_consumables_required['xpert_test'] = \
hs.get_item_codes_from_package_name("Xpert test")
hs.get_item_code_from_item_name("Xpert")

# sensitivity/specificity set for smear status of cases
self.sim.modules["HealthSystem"].dx_manager.register_dx_test(
Expand All @@ -714,7 +725,10 @@ def get_consumables_for_dx_and_tx(self):
target_categories=["active"],
sensitivity=p["sens_xpert_smear_positive"],
specificity=p["spec_xpert_smear_positive"],
item_codes=self.item_codes_for_consumables_required['xpert_test']
item_codes=self.item_codes_for_consumables_required['xpert_test'],
optional_item_codes=[self.item_codes_for_consumables_required['sputum_container'],
self.item_codes_for_consumables_required['slides'],
self.item_codes_for_consumables_required['gloves']]
)
)
self.sim.modules["HealthSystem"].dx_manager.register_dx_test(
Expand All @@ -723,13 +737,17 @@ def get_consumables_for_dx_and_tx(self):
target_categories=["active"],
sensitivity=p["sens_xpert_smear_negative"],
specificity=p["spec_xpert_smear_negative"],
item_codes=self.item_codes_for_consumables_required['xpert_test']
item_codes=self.item_codes_for_consumables_required['xpert_test'],
optional_item_codes=[self.item_codes_for_consumables_required['sputum_container'],
self.item_codes_for_consumables_required['slides'],
self.item_codes_for_consumables_required['gloves']]
)
)

# TB Chest x-ray
self.item_codes_for_consumables_required['chest_xray'] = {
hs.get_item_code_from_item_name("X-ray"): 1}
self.item_codes_for_consumables_required['chest_xray'] = hs.get_item_code_from_item_name("X-ray")
self.item_codes_for_consumables_required['lead_apron'] = hs.get_item_code_from_item_name(
"Lead rubber x-ray protective aprons up to 150kVp 0.50mm_each_CMST")

# sensitivity/specificity set for smear status of cases
self.sim.modules["HealthSystem"].dx_manager.register_dx_test(
Expand All @@ -738,7 +756,8 @@ def get_consumables_for_dx_and_tx(self):
target_categories=["active"],
sensitivity=p["sens_xray_smear_positive"],
specificity=p["spec_xray_smear_positive"],
item_codes=self.item_codes_for_consumables_required['chest_xray']
item_codes=self.item_codes_for_consumables_required['chest_xray'],
optional_item_codes=self.item_codes_for_consumables_required['lead_apron']
)
)
self.sim.modules["HealthSystem"].dx_manager.register_dx_test(
Expand All @@ -747,7 +766,8 @@ def get_consumables_for_dx_and_tx(self):
target_categories=["active"],
sensitivity=p["sens_xray_smear_negative"],
specificity=p["spec_xray_smear_negative"],
item_codes=self.item_codes_for_consumables_required['chest_xray']
item_codes=self.item_codes_for_consumables_required['chest_xray'],
optional_item_codes=self.item_codes_for_consumables_required['lead_apron']
)
)

Expand Down Expand Up @@ -1796,7 +1816,7 @@ def apply(self, person_id, squeeze_factor):
if self.facility_level == "1a":
self.sim.modules["HealthSystem"].schedule_hsi_event(
hsi_event=HSI_Tb_ScreeningAndRefer(
person_id=person_id, module=self.module, facility_level="2"
person_id=person_id, module=self.module, facility_level="1b"
),
topen=self.sim.date + DateOffset(days=1),
tclose=None,
Expand Down

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