Prevent people having Hiv_DecisionToContinueTreatment events at inappropriate times (#1129)

Author: tdm32

resources/ResourceFile_HIV.xlsx

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:b7613f565d446cdf31f7360cc3d72d2deae6545294a41d3b0580430bec63f7d5
-size 158138
+oid sha256:d20e316c9b00816da27cc8c104b70cec214787f0d96c80a437f8690806c5e2fb
+size 158196

src/scripts/hiv/projections_jan2023/analysis_full_model.py

@@ -23,14 +23,14 @@
 
 # %% Run the simulation
 start_date = Date(2010, 1, 1)
-end_date = Date(2018, 1, 1)
+end_date = Date(2020, 1, 1)
 popsize = 5000
-scenario = 0
+# scenario = 0
 
 # set up the log config
 # add deviance measure logger if needed
 log_config = {
-    "filename": "tb_transmission_runs",
+    "filename": "hiv_test_runs",
     "directory": outputpath,
     "custom_levels": {
         "*": logging.WARNING,
@@ -55,12 +55,11 @@
         "SymptomManager": {"spurious_symptoms": True},
         "HealthSystem": {"disable": False,
                          "service_availability": ["*"],
-                         "mode_appt_constraints": 0,  # no constraints, no squeeze factor
+                         "mode_appt_constraints": 1,
                          "cons_availability": "default",
                          "beds_availability": "all",
                          "ignore_priority": False,
-                         "use_funded_or_actual_staffing": "funded_plus",
-                         "capabilities_coefficient": 1.0},
+                         "use_funded_or_actual_staffing": "actual"},
     },
 ))
 

src/scripts/hiv/projections_jan2023/analysis_logged_deviance.py

@@ -35,9 +35,9 @@
 # %% Run the simulation
 start_date = Date(2010, 1, 1)
 end_date = Date(2015, 1, 1)
-popsize = 500
+popsize = 5000
 
-scenario = 1
+# scenario = 1
 
 # set up the log config
 log_config = {
@@ -69,11 +69,11 @@
     healthsystem.HealthSystem(
         resourcefilepath=resourcefilepath,
         service_availability=["*"],  # all treatment allowed
-        mode_appt_constraints=0,  # mode of constraints to do with officer numbers and time
+        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)
         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="funded_plus",  # actual: use numbers/distribution of staff available currently
+        use_funded_or_actual_staffing="actual",  # actual: use numbers/distribution of staff available currently
         disable=False,  # disables the healthsystem (no constraints and no logging) and every HSI runs
         disable_and_reject_all=False,  # disable healthsystem and no HSI runs
     ),
@@ -90,7 +90,7 @@
 # sim.modules["Hiv"].parameters["beta"] = 0.129671
 # sim.modules["Tb"].parameters["scaling_factor_WHO"] = 1.5
 # sim.modules["Tb"].parameters["scenario"] = scenario
-sim.modules["Tb"].parameters["scenario_start_date"] = Date(2010, 1, 1)
+# sim.modules["Tb"].parameters["scenario_start_date"] = Date(2010, 1, 1)
 # sim.modules["Tb"].parameters["scenario_SI"] = "z"
 
 # sim.modules["Tb"].parameters["rr_tb_hiv"] = 5  # default 13

src/scripts/hiv/projections_jan2023/output_plots.py

@@ -519,7 +519,7 @@ def make_plot(model=None, data_mid=None, data_low=None, data_high=None, title_st
 # latest_path = sim.log_filepath
 # tlo.methods.deviance_measure.log written after log file below:
 # outputs\deviance__2022-01-20T105927.log
-# latest_path = "outputs\tb_transmission_runs__2023-01-23T132304.log"
+latest_path = "outputs/hiv_test_runs__2023-11-03T160819.log"
 death_compare = compare_number_of_deaths(latest_path, resourcefilepath)
 
 # include all ages and both sexes

src/tlo/methods/hiv.py

@@ -126,6 +126,7 @@ def __init__(self, name=None, resourcefilepath=None, run_with_checks=False):
         "hv_last_test_date": Property(Types.DATE, "Date of last HIV test"),
         "hv_date_inf": Property(Types.DATE, "Date infected with HIV"),
         "hv_date_treated": Property(Types.DATE, "date hiv treatment started"),
+        "hv_date_last_ART": Property(Types.DATE, "date of last ART dispensation"),
     }
 
     PARAMETERS = {
@@ -374,6 +375,10 @@ def __init__(self, name=None, resourcefilepath=None, run_with_checks=False):
             Types.REAL,
             "probability of death if aids and tb, person on treatment for tb",
         ),
+        "dispensation_period_months": Parameter(
+            Types.REAL,
+            "length of prescription for ARVs in months, same for all PLHIV",
+        ),
     }
 
     def read_parameters(self, data_folder):
@@ -750,7 +755,7 @@ def split_into_vl_and_notvl(all_idx, prob):
         # all those on ART need to have event scheduled for continuation/cessation of treatment
         # this window is 1-90 days (3-monthly prescribing)
         for person in art_idx:
-            days = self.rng.randint(low=1, high=90, dtype=np.int64)
+            days = self.rng.randint(low=1, high=self.parameters['dispensation_period_months'] * 30.5, dtype=np.int64)
             self.sim.schedule_event(
                 Hiv_DecisionToContinueTreatment(person_id=person, module=self),
                 self.sim.date + pd.to_timedelta(days, unit="days"),
@@ -2438,6 +2443,12 @@ def apply(self, person_id, squeeze_factor):
         # Confirm that the person is diagnosed (this should not run if they are not)
         assert person["hv_diagnosed"]
 
+        # check whether person had Rx at least 3 months ago and is now due repeat prescription
+        # alternate routes into testing/tx may mean person already has recent ARV dispensation
+        if person['hv_date_last_ART'] >= (
+            self.sim.date - pd.DateOffset(months=self.module.parameters['dispensation_period_months'])):
+            return self.sim.modules["HealthSystem"].get_blank_appt_footprint()
+
         if art_status_at_beginning_of_hsi == "not":
 
             assert person[
@@ -2452,14 +2463,18 @@ def apply(self, person_id, squeeze_factor):
 
         # if ART is available (1st item in drugs_were_available dict)
         if drugs_were_available.get('art', False):
+            df.at[person_id, 'hv_date_last_ART'] = self.sim.date
+
             # If person has been placed/continued on ART, schedule 'decision about whether to continue on Treatment
             self.sim.schedule_event(
                 Hiv_DecisionToContinueTreatment(
                     person_id=person_id, module=self.module
                 ),
-                self.sim.date + pd.DateOffset(months=3),
+                self.sim.date + pd.DateOffset(months=self.module.parameters['dispensation_period_months']),
             )
+
         else:
+
             # logger for drugs not available
             person_details_for_tx = {
                 'age': person['age_years'],
@@ -2471,57 +2486,57 @@ def apply(self, person_id, squeeze_factor):
             }
             logger.info(key='hiv_arv_NA', data=person_details_for_tx)
 
-            # As drugs were not available, the person will default to being off ART (...if they were on ART at the
-            # beginning of the HSI.)
-            # NB. If the person was not on ART at the beginning of the HSI, then there is no need to stop them (which
-            #  causes a new AIDSOnsetEvent to be scheduled.)
-            self.counter_for_drugs_not_available += 1  # The current appointment is included in the count.
+        # As drugs were not available, the person will default to being off ART (...if they were on ART at the
+        # beginning of the HSI.)
+        # NB. If the person was not on ART at the beginning of the HSI, then there is no need to stop them (which
+        #  causes a new AIDSOnsetEvent to be scheduled.)
+        self.counter_for_drugs_not_available += 1  # The current appointment is included in the count.
 
-            if art_status_at_beginning_of_hsi != "not":
-                self.module.stops_treatment(person_id)
+        if art_status_at_beginning_of_hsi != "not":
+            self.module.stops_treatment(person_id)
 
-            p = self.module.parameters["probability_of_seeking_further_art_appointment_if_drug_not_available"]
+        p = self.module.parameters["probability_of_seeking_further_art_appointment_if_drug_not_available"]
 
-            if self.module.rng.random_sample() >= p:
+        if self.module.rng.random_sample() >= p:
 
-                # add in referral straight back to tx
-                # if defaulting, seek another treatment appointment in 6 months
+            # add in referral straight back to tx
+            # if defaulting, seek another treatment appointment in 6 months
+            self.sim.modules["HealthSystem"].schedule_hsi_event(
+                hsi_event=HSI_Hiv_StartOrContinueTreatment(
+                    person_id=person_id, module=self.module,
+                    facility_level_of_this_hsi="1a",
+                ),
+                topen=self.sim.date + pd.DateOffset(months=6),
+                priority=0,
+            )
+
+        else:
+            # If person 'decides to' seek another treatment appointment,
+            # schedule a new HSI appointment for next month
+            # NB. With a probability of 1.0, this will keep occurring,
+            # if person has already tried unsuccessfully to get ART at level 1a 2 times
+            #  then refer to level 1b
+            if self.counter_for_drugs_not_available <= 2:
+                # repeat attempt for ARVs at level 1a
                 self.sim.modules["HealthSystem"].schedule_hsi_event(
                     hsi_event=HSI_Hiv_StartOrContinueTreatment(
                         person_id=person_id, module=self.module,
-                        facility_level_of_this_hsi="1a",
+                        facility_level_of_this_hsi="1a"
                     ),
-                    topen=self.sim.date + pd.DateOffset(months=6),
+                    topen=self.sim.date + pd.DateOffset(months=1),
                     priority=0,
                 )
 
             else:
-                # If person 'decides to' seek another treatment appointment,
-                # schedule a new HSI appointment for next month
-                # NB. With a probability of 1.0, this will keep occurring,
-                # if person has already tried unsuccessfully to get ART at level 1a 2 times
-                #  then refer to level 1b
-                if self.counter_for_drugs_not_available <= 2:
-                    # repeat attempt for ARVs at level 1a
-                    self.sim.modules["HealthSystem"].schedule_hsi_event(
-                        hsi_event=HSI_Hiv_StartOrContinueTreatment(
-                            person_id=person_id, module=self.module,
-                            facility_level_of_this_hsi="1a"
-                        ),
-                        topen=self.sim.date + pd.DateOffset(months=1),
-                        priority=0,
-                    )
-
-                else:
-                    # refer to higher facility level
-                    self.sim.modules["HealthSystem"].schedule_hsi_event(
-                        hsi_event=HSI_Hiv_StartOrContinueTreatment(
-                            person_id=person_id, module=self.module,
-                            facility_level_of_this_hsi="2"
-                        ),
-                        topen=self.sim.date + pd.DateOffset(days=1),
-                        priority=0,
-                    )
+                # refer to higher facility level
+                self.sim.modules["HealthSystem"].schedule_hsi_event(
+                    hsi_event=HSI_Hiv_StartOrContinueTreatment(
+                        person_id=person_id, module=self.module,
+                        facility_level_of_this_hsi="2"
+                    ),
+                    topen=self.sim.date + pd.DateOffset(days=1),
+                    priority=0,
+                )
 
         # also screen for tb
         if "Tb" in self.sim.modules: