Added restarting PrEP.

src/hivpy/prep.py

@@ -648,9 +648,10 @@ def continue_prep(self, pop: Population, time_step):
         """
         Update PrEP usage for people continuing PrEP.
         """
-        # people who have used prep before but not started this time step
+        # people who have used prep before but not yet started this time step
         eligible = pop.get_sub_pop(AND(COND(col.EVER_PREP, op.eq, True),
                                        COND(col.PREP_JUST_STARTED, op.eq, False),
+                                       COND(col.LAST_PREP_STOP_DATE, op.eq, None),
                                        OR(COND(col.LAST_TEST_DATE, op.ne, pop.date),
                                           AND(COND(col.LAST_TEST_DATE, op.eq, pop.date),
                                               COND(col.HIV_DIAGNOSED, op.eq, False)))))
@@ -728,6 +729,63 @@ def calc_current_prep(self, prep_type, favoured_prep, size):
 
         return prep
 
+    def restart_prep(self, pop: Population, time_step):
+        """
+        Update PrEP usage for people restarting PrEP.
+        """
+        # people who have used prep before and previously stopped using it
+        eligible = pop.get_sub_pop(AND(COND(col.EVER_PREP, op.eq, True),
+                                       COND(col.LAST_PREP_STOP_DATE, op.lt, pop.date),
+                                       COND(col.LAST_TEST_DATE, op.eq, pop.date)))
+
+        if len(eligible) > 0:
+            # starting prep outcomes
+            prep_types = pop.transform_group([col.FAVOURED_PREP_TYPE], self.calc_restarting_prep,
+                                             sub_pop=eligible, dropna=True)
+            # people who are restarting prep
+            restarting_prep_pop = pop.apply_bool_mask(prep_types.notnull(), eligible)
+
+            if len(restarting_prep_pop) > 0:
+                # set prep types
+                pop.set_present_variable(col.PREP_TYPE, prep_types, restarting_prep_pop)
+                pop.set_present_variable(col.PREP_JUST_STARTED, True, restarting_prep_pop)
+                # set start dates
+                pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, restarting_prep_pop)
+                self.set_prep_first_start_date(
+                    pop, restarting_prep_pop, PrEPType.Oral, col.FIRST_ORAL_START_DATE)
+                self.set_prep_first_start_date(
+                    pop, restarting_prep_pop, PrEPType.Cabotegravir, col.FIRST_CAB_START_DATE)
+                self.set_prep_first_start_date(
+                    pop, restarting_prep_pop, PrEPType.Lenacapavir, col.FIRST_LEN_START_DATE)
+                self.set_prep_first_start_date(
+                    pop, restarting_prep_pop, PrEPType.VaginalRing, col.FIRST_VR_START_DATE)
+                # set continuous use
+                pop.set_present_variable(col.CONT_ON_PREP, time_step, restarting_prep_pop)
+                pop.set_present_variable(col.CONT_ACTIVE_ON_PREP, time_step, restarting_prep_pop)
+                # increment cumulative use
+                self.set_prep_cumulative_cont(
+                    pop, restarting_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
+                self.set_prep_cumulative_cont(
+                    pop, restarting_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
+                self.set_prep_cumulative_cont(
+                    pop, restarting_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
+                self.set_prep_cumulative_cont(
+                    pop, restarting_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)
+                # unset stop date
+                pop.set_present_variable(col.LAST_PREP_STOP_DATE, None, restarting_prep_pop)
+
+    def calc_restarting_prep(self, favoured_prep, size):
+        """
+        Returns PrEP types for people restarting PrEP.
+        Individual preferences and availability are taken into account.
+        """
+        # outcomes
+        r = rng.uniform(size=size)
+        restarting = r < self.prob_prep_restart
+        prep = [favoured_prep if r else None for r in restarting]
+
+        return prep
+
     def prep_usage(self, pop: Population, time_step):
         """
         Update PrEP usage for people starting, continuing, switching, restarting, and stopping PrEP.
@@ -736,3 +794,5 @@ def prep_usage(self, pop: Population, time_step):
         self.start_prep(pop, time_step)
         # continuing prep
         self.continue_prep(pop, time_step)
+        # restarting prep
+        self.restart_prep(pop, time_step)

src/tests/test_prep.py

@@ -833,3 +833,34 @@ def test_continuing_prep():
                 (pop.data[col.PREP_TYPE] == PrEPType.VaginalRing)) |
                ((pop.data[col.CUMULATIVE_PREP_VR] == time_step) ==
                 (pop.data[col.LAST_PREP_STOP_DATE] == pop.date)))
+
+
+def test_restarting_prep():
+    N = 100
+    time_step = timedelta(months=1)
+    pop = Population(size=N, start_date=date(5000, 1, 1))
+    pop.prep.date_prep_intro = [date(2000), date(3000), date(4000), date(5000)]
+    pop.data[col.EVER_PREP] = True
+    pop.data[col.LAST_PREP_STOP_DATE] = pop.date - time_step
+    pop.data[col.PREP_JUST_STARTED] = False
+    pop.data[col.CONT_ON_PREP] = timedelta(months=0)
+    pop.data[col.CONT_ACTIVE_ON_PREP] = timedelta(months=0)
+    pop.data[col.LAST_TEST_DATE] = pop.date
+    pop.data[col.PREP_TYPE] = None
+    # everyone is taking their favoured prep type
+    pop.data[col.FAVOURED_PREP_TYPE] = [PrEPType.Oral, PrEPType.Cabotegravir,
+                                        PrEPType.Lenacapavir, PrEPType.VaginalRing] * (N // 4)
+    # 50% chance to restart prep
+    pop.prep.prob_prep_restart = 0.5
+
+    pop.prep.restart_prep(pop, time_step)
+    # expecting 90% of people to restart prep
+    no_on_prep = sum(pop.data[col.LAST_PREP_STOP_DATE].isnull())
+    mean = N * pop.prep.prob_prep_restart
+    stdev = sqrt(mean * (1 - pop.prep.prob_prep_restart))
+    assert mean - 3 * stdev <= no_on_prep <= mean + 3 * stdev
+    # check continuous prep usage
+    assert all((pop.data[col.CONT_ON_PREP] == time_step) ==
+               (pop.data[col.LAST_PREP_STOP_DATE].isnull()))
+    assert all((pop.data[col.CONT_ACTIVE_ON_PREP] == time_step) ==
+               (pop.data[col.LAST_PREP_STOP_DATE].isnull()))