Updates to HIV module in line with newly received data (#1616)

tdm32 · mmsuarezcosta · web-flow · commit 36e36cc62e24 · 2026-02-09T17:04:26.000Z
* update recruitment for fsw - capped at 39,000 scaled by initial population size reduce RR for HIV for FSW * add hiv self-tests update prep for agyw poll add prep for fsw poll * modify death rates for people with HIV and TB, risk is 0.5 if no treatment, risk falls to 0.15 if on treatment * update AGYW - limit to age 25 max * logger for days on prep - AGYW and FSW VL logger * add parameter for selt-testing availability in policy * update retention on prep to 0.85 * add logger outputs for PY on PrEP and new VMMC * fix lm argument * update lm for lifestyle * linting * fix failing hiv test * update tolerance of hiv prevalence in test_hiv to match the uncertainty around the calibration targets * update test_hiv.py to fix failing test * merge in master * incoming changes from master * update spectrum projections for treatment cascade * update sheet with prob viral suppression, add adjustment for viral load testing starting in 2016. update prob_viral_suppression() with adjusted values allow 0.1% default each 3 months * remove parameter vs_adjustment * remove parameter treatment_initiation_adjustment * remove treatment_initiation_adjustment and vs_adjustment from improved healthcare seeking sheet * remove TB screening from HIV test appt following DHA advice * move HIV test from TB screening appt to TB treatment initiation appt following advice from DHA * update HIV treatment appt with TB screening appt * update childrens program data AIDSInfo update figures to use MPHIA 2020 * update UNAIDS data on children, treatment cascade and mortality fix failing assert * update plot functions * add new property for current ARV prescription length add ARV dispensation schedule varying by year, age, sex, pregnancy / BF adapt consumables checks for varying dispensation schedules check follow-up appt for tx and prep * add logger for multi-month dispensing by age/sex/pregnant/breastfeeding * update logger for MMD * add plot for MMD * fix to failing test * merge in master * update loggers * reduce prob retained on prep to 0.5 (from 0.85) * give prep to AGYW in status quo, randomly distribute amongst top 50% of high-risk AGYW * setup new scenarios for program simplification * prep in AGYW given randomly among 50% highest risk remove commented out code * update the scenarios for program simplification * update the scenarios for program simplification * correct reference to TB HSI for IPT in HIV module * fix dataframe copy warning * update division by 0 error * set up scenarios * Cherry-pick parameter_values Enhanced_Lifestyle from MIHPSA branch * Cherry-pick Enhanced_Lifestyle from MIHPSA branch * update enhanced_lifestyle.py * test runs * set up status quo local run * use only essential modules for test runs * add new parameters for TDF test * update IPT length and follow-up * tdf test switch added to scenarios * check scenarios * set up scenarios * update plots * check prep dispensation period * update output processing * set up scale-up scenario and add to runs * update scenario file * json * correct scaleup scenario which affected all scenarios * set up scenarios * update comment * new figures for epi outputs and HCW time * update figures * update plots * update hiv.py with VL testing, adherence counselling and oral/inj prep choice * clean up todo statements * update viral suppression probability using new logic for effects of viral load tests add adjustment for young adults having lower viral suppression rates * remove unneeded loggers * update adjustments to viral suppression rates by age, weight for ages 30+ to get average correct * update the logic around choice of TDF and VL test, check referral to adherence counselling and add delay * update VL test sensitivity * add HSI event for self-tests, positive result prompts referral for confirmatory testing at facility * update parameter list * set up scenarios * edit comment * set up scenarios * update scenarios * json * update scenarios update outputs * update scenarios update outputs * update output processing * remove hardcoding and param revamp * update scenario file to include proper labeling * update test_htm_scaleup.py to reflect changes in scaleup_parameters.py * update param labeling for calibration * remove addt hardcoded params * bring in changes to hiv.py from mihpsda branch * replace baseline art coverage file * update parameter values * update oral:inj prep ratio * oral prep 90 days dispensation * add scenario switch to injectable prep * update adjust_viral_load_suppression_rates_function * update testing rates in Reduce Testing scenario to match MIHPSA halfHTS * json * update spectrum_treatment_cascade.csv * test run * fix to prep type * test run setup * comment out schisto person days logging * remove warnings from equipment.py check tb logger for int to float conversion warnings * reset scenarios * change infant / child cotrim to oral suspension * additional plots for temporal trends * if no HIV test available, set blank footprint * remove scenarios for program simplification runs * accept todo statements as completed for updated ART coverage and the revised coverage estimates which incorporate viral load monitoring effect * clean up todo statements * remove criteria for TPT in PLHIV requiring residence in high-risk district * clean up comments * merge in PR #1742 and check conflicts * update reference to art coverage data for baseline * fixing low art coverage * test runs * remove duplicated parameters in malaria for rdt delays * linting * linting * isort * replace numbers with parameters * fix remaining todo statements * remove processing script * fix failing tests * remove hiv test check from test_tb.py as it no longer occurs during tb screening * allow warnings for equipment if item not recognised add hiv self test to priority policies * update improved healthcare seeking parameter names * update improved healthcare seeking parameter names * pull in new fixes from schisto updates PR #1787 * update schisto parameters to ensure read as floats pull in updates from master * fix conflict * improved_healthsystem_and_healthcare_seeking update the adjusted viral suppression on art column label * update param types for test_analysis checks * update treatment_id in priority policies * update treatment_id in priority policies * update treatment ID in priority policies * fix fsw parameters remove json * replace WASH logging in enhanced_lifestyle.py * fix typo in comment * add comments for test containers * rmeove magic numbers for 3hp and ipt dosage * clarify dict for vl testing availability * update tdf test results to bool * fix error in return statement * remove unneeded logger * remove unneeded logging * remove unneeded logging * fix missing comma * update test_tb to use the updated parameter for length IPT dispensation --------- Co-authored-by: mmsuarezcosta <mmsuarezcosta@gmail.com>
diff --git a/resources/ResourceFile_HIV/MPHIA_incidence2020.csv b/resources/ResourceFile_HIV/MPHIA_incidence2020.csv
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diff --git a/resources/ResourceFile_HIV/MPHIA_prevalence_art2020.csv b/resources/ResourceFile_HIV/MPHIA_prevalence_art2020.csv
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diff --git a/resources/ResourceFile_HIV/MoH_numbers_tests.csv b/resources/ResourceFile_HIV/MoH_numbers_tests.csv
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diff --git a/src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py b/src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py
@@ -0,0 +1,112 @@
+"""This Scenario file runs the model under different assumptions for the HIV program simplification
+
+
+check the batch configuration gets generated without error:
+tlo scenario-run --draw-only src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py
+
+Test the scenario starts running without problems:
+tlo scenario-run src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py
+
+or execute a single run:
+tlo scenario-run src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py --draw 1 0
+
+Run on the batch system using:
+tlo batch-submit src/scripts/hiv/program_simplification/analysis_hiv_program_simplification.py
+
+Display information about a job:
+tlo batch-job tlo_q1_demo-123 --tasks
+
+Download result files for a completed job:
+tlo batch-download calibration_script-2022-04-12T190518Z
+
+if running locally need to parse each folder
+tlo parse-log /Users/tmangal/PycharmProjects/TLOmodel/outputs/hiv_program_simplification-2025-07-24T160218Z/0/0
+
+"""
+
+from pathlib import Path
+from typing import Dict
+
+from scripts.hiv.program_simplification.scenario_definitions import ScenarioDefinitions
+from tlo import Date, logging
+from tlo.methods.fullmodel import fullmodel
+from tlo.scenario import BaseScenario
+
+
+class HIV_Progam_Elements(BaseScenario):
+    def __init__(self):
+        super().__init__()
+        self.seed = 10
+        self.start_date = Date(2010, 1, 1)
+        self.end_date = Date(2051, 1, 1)
+        self.pop_size = 100_000
+        self._scenarios = self._get_scenarios()
+        self.number_of_draws = len(self._scenarios)
+        self.runs_per_draw = 10
+
+    def log_configuration(self):
+        return {
+            'filename': 'hiv_program_simplification',
+            '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,
+            }
+        }
+
+    def modules(self):
+        return (
+            fullmodel(use_simplified_births=True,
+                      module_kwargs={"HealthSystem": {"equip_availability": 'all'}})
+        )
+
+    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."""
+
+        scenario_definitions = ScenarioDefinitions()
+
+        return {
+            "Status Quo": scenario_definitions.status_quo(),
+
+            "Reduce HIV testing": scenario_definitions.reduce_HIV_test(),
+
+            "Remove Viral Load Testing": scenario_definitions.remove_VL(),
+
+            "Target Viral Load Testing": scenario_definitions.target_VL(),
+
+            "Replace Viral Load Testing": scenario_definitions.replace_VL_with_TDF(),
+
+            "Remove PrEP for FSW": scenario_definitions.remove_prep_fsw(),
+
+            "Remove PrEP for AGYW": scenario_definitions.remove_prep_agyw(),
+
+            "Switch to injectable PrEP": scenario_definitions.switch_to_injectable_prep(),
+
+            "Remove TPT for PLHIV": scenario_definitions.remove_TPT(),
+
+            "Targeted TPT": scenario_definitions.target_TPT(),
+
+            "Remove VMMC": scenario_definitions.remove_vmmc(),
+
+            "Target All Elements": scenario_definitions.target_all(),
+
+            "Reduce All Elements": scenario_definitions.remove_all(),
+
+            "Program Scale-up": scenario_definitions.scaleup(),
+        }
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+
+    scenario_run([__file__])
diff --git a/src/scripts/hiv/program_simplification/scenario_definitions.py b/src/scripts/hiv/program_simplification/scenario_definitions.py
diff --git a/src/scripts/hiv/projections_jan2023/output_plots.py b/src/scripts/hiv/projections_jan2023/output_plots.py
diff --git a/src/tlo/methods/enhanced_lifestyle.py b/src/tlo/methods/enhanced_lifestyle.py
diff --git a/src/tlo/methods/hiv.py b/src/tlo/methods/hiv.py
diff --git a/src/tlo/methods/hiv_tb_calibration.py b/src/tlo/methods/hiv_tb_calibration.py
diff --git a/src/tlo/methods/malaria.py b/src/tlo/methods/malaria.py
diff --git a/src/tlo/methods/tb.py b/src/tlo/methods/tb.py
diff --git a/tests/test_hiv.py b/tests/test_hiv.py
diff --git a/tests/test_malaria.py b/tests/test_malaria.py
diff --git a/tests/test_tb.py b/tests/test_tb.py

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`@@ -0,0 +1,3 @@`
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	`2`	`+oid sha256:29021468af00211dd4c3d8876ac93cf0a8c5c4f401a9b1b5d941da0702e6e73f`
	`3`	`+size 2351`