HIV testing for the symptomatic

src/hivpy/circumcision.py

@@ -159,15 +159,24 @@ def update_vmmc(self, pop, time_step):
                 pop.data.loc[uncirc_male_population, col.VMMC] = circumcision
 
                 # chance to get vmmc after a negative HIV test
-                pop.hiv_testing.update_vmmc_after_test(pop, time_step)
+                self.update_vmmc_after_test(pop, time_step)
 
                 # newly circumcised males get the current date set as their circumcision date
                 new_circ_males = pop.get_sub_pop([(col.CIRCUMCISED, op.eq, True),
                                                   (col.CIRCUMCISION_DATE, op.eq, None)])
                 pop.data.loc[new_circ_males, col.CIRCUMCISION_DATE] = self.date
 
-                # standard HIV testing after circumcision
-                pop.hiv_testing.update_post_vmmc_testing(pop)
+    def calc_circ_outcomes(self, age_group, size):
+        """
+        Uses the circumcision probability for a given
+        age group to return VMMC outcomes.
+        """
+        prob_circ = self.calc_prob_circ(age_group)
+        # outcomes
+        r = rng.uniform(size=size)
+        circumcision = r < prob_circ
+
+        return circumcision
 
     def calc_prob_circ(self, age_group):
         """
@@ -207,14 +216,23 @@ def calc_prob_circ(self, age_group):
 
         return min(prob_circ, 1)
 
-    def calc_circ_outcomes(self, age_group, size):
+    def update_vmmc_after_test(self, pop, time_step):
         """
-        Uses the circumcision probability for a given
-        age group to return VMMC outcomes.
+        Update VMMC in individuals that tested HIV negative last time step.
         """
-        prob_circ = self.calc_prob_circ(age_group)
-        # outcomes
-        r = rng.uniform(size=size)
-        circumcision = r < prob_circ
-
-        return circumcision
+        if self.circ_after_test:
+            # select uncircumcised men tested last timestep
+            tested_uncirc_male_pop = pop.get_sub_pop([(col.SEX, op.eq, SexType.Male),
+                                                      (col.CIRCUMCISED, op.eq, False),
+                                                      (col.HIV_DIAGNOSED, op.eq, False),
+                                                      (col.LAST_TEST_DATE, op.eq, pop.date - time_step),
+                                                      (col.HARD_REACH, op.eq, False),
+                                                      (col.AGE, op.le, self.max_vmmc_age)])
+            # continue if eligible men are present this timestep
+            if len(tested_uncirc_male_pop) > 0:
+                # calculate post-test vmmc outcomes
+                r = rng.uniform(size=len(tested_uncirc_male_pop))
+                circumcision = r < self.prob_circ_after_test
+                # assign outcomes
+                pop.set_present_variable(col.CIRCUMCISED, circumcision, tested_uncirc_male_pop)
+                pop.set_present_variable(col.VMMC, circumcision, tested_uncirc_male_pop)

src/hivpy/column_names.py

@@ -51,6 +51,7 @@
 STI = "sti"                                     # bool: True if has sexually transmitted infection (non HIV), false o/w (TODO: DUMMIED)
 
 HARD_REACH = "hard_reach"                       # bool: True if person is reluctant to test for HIV (also affects PrEP and VMMC), but will still test if symptomatic or in antenatal care
+TEST_MARK = "test_mark"                         # bool: True if a person has been marked for testing this time step
 EVER_TESTED = "ever_tested"                     # bool: True if person has ever been tested for HIV
 LAST_TEST_DATE = "last_test_date"               # None | datetime.date: date of last HIV test
 NSTP_LAST_TEST = "nstp_last_test"               # int: number of short term condomless sex partners since last test (DUMMY)

src/hivpy/data/hiv_testing.yaml

@@ -1,6 +1,7 @@
-# years during which HIV testing begins
-date_start_anc_testing: 2003.5
-date_start_testing: 2009
+# year during which HIV testing begins
+date_start_testing: 2003.5
+# year after which rate of testing starts increasing
+date_rate_testing_incr: 2009
 
 # starting probability for first tests
 init_rate_first_test: 0
@@ -24,17 +25,28 @@ prob_anc_test_trim3: 0.1
 # probability of being tested after delivery
 prob_test_postdel: 0.95
 
+# probability of being tested based on symptoms
+prob_test_non_hiv_symptoms: 0.01
+prob_test_who4: 0.1
+prob_test_tb: 0.1
+prob_test_non_tb_who3: 0.05
+
 # affects testing probability based on number of partners
 test_targeting:
   Value: [1, 1.25, 1.5]
   Probability: [0.2, 0.6, 0.2]
 
-# year during which testing probability plateaus
-date_test_rate_plateau:
+# years during which testing probability plateaus
+date_general_testing_plateau:
   Value: [2011.5, 2013.5, 2015.5, 2017.5, 2019.5]
   Probability: [0.1, 0.1, 0.2, 0.3, 0.3]
+date_targeted_testing_plateau: 2015
 
 # multiplier for testing probability
 an_lin_incr_test:
   Value: [0.0001, 0.0005, 0.003, 0.01, 0.02, 0.03]
   Probability: [0.2, 0.25, 0.35, 0.1, 0.05, 0.05]
+
+# multiplier for symptomatic testing probability
+incr_test_rate_sympt:
+  Value: [1.05, 1.10, 1.15, 1.20, 1.25]

src/hivpy/hiv_status.py

@@ -95,10 +95,10 @@ def init_HIV_variables(self, population: Population):
         population.init_variable(col.X4_VIRUS, False)
 
         population.init_variable(col.WHO3_EVENT, False)
-        population.init_variable(col.NON_TB_WHO3, False)
-        population.init_variable(col.TB, False)
+        population.init_variable(col.NON_TB_WHO3, False, n_prev_steps=1)
+        population.init_variable(col.TB, False, n_prev_steps=2)
         population.init_variable(col.TB_DIAGNOSED, False)
-        population.init_variable(col.ADC, False)
+        population.init_variable(col.ADC, False, n_prev_steps=1)
         population.init_variable(col.C_MENINGITIS, False)
         population.init_variable(col.C_MENINGITIS_DIAGNOSED, False)
         population.init_variable(col.SBI, False)