Updated testing date variables for better clarity.

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
@@ -35,10 +36,11 @@ 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_specific_testing_plateau: 2015
 
 # multiplier for testing probability
 an_lin_incr_test:

src/hivpy/hiv_testing.py

@@ -15,9 +15,8 @@ def __init__(self, **kwargs):
         with importlib.resources.path("hivpy.data", "hiv_testing.yaml") as data_path:
             self.ht_data = HIVTestingData(data_path)
 
-        # FIXME: date_start_anc_testing currently unused, do we need this for anything?
-        self.date_start_anc_testing = self.ht_data.date_start_anc_testing
         self.date_start_testing = self.ht_data.date_start_testing
+        self.date_rate_testing_incr = self.ht_data.date_rate_testing_incr
         self.init_rate_first_test = self.ht_data.init_rate_first_test
         self.eff_max_freq_testing = self.ht_data.eff_max_freq_testing
         self.test_scenario = self.ht_data.test_scenario
@@ -33,7 +32,8 @@ def __init__(self, **kwargs):
         self.prob_test_tb = self.ht_data.prob_test_tb
         self.prob_test_non_tb_who3 = self.ht_data.prob_test_non_tb_who3
         self.test_targeting = self.ht_data.test_targeting.sample()
-        self.date_test_rate_plateau = self.ht_data.date_test_rate_plateau.sample()
+        self.date_general_testing_plateau = self.ht_data.date_general_testing_plateau.sample()
+        self.date_specific_testing_plateau = self.ht_data.date_specific_testing_plateau
         self.an_lin_incr_test = self.ht_data.an_lin_incr_test.sample()
         self.incr_test_rate_sympt = self.ht_data.incr_test_rate_sympt.sample()
 
@@ -79,16 +79,16 @@ def test_mark_hiv_symptomatic(self, pop):
         """
         Mark HIV symptomatic individuals to undergo testing this time step.
 
-        Note: If the simulation is started after 2015 (or if date_start_testing
-        is set to be after 2015) the HIV symptomatic testing probabilities
-        will not be updated and this function may not work as expected.
+        Note: If the simulation is started after date_specific_testing_plateau
+        (or if date_start_testing is set to be after date_specific_testing_plateau)
+        the HIV symptomatic testing probabilities will not be updated
+        and this function may not work as expected.
         """
         # testing occurs after a certain year
-        if (pop.date.year >= self.date_start_testing):
+        if (pop.date.year > self.date_start_testing):
 
             # update symptomatic test probabilities
-            # FIXME: where does this year come from? move to yaml later
-            if pop.date.year <= 2015:
+            if pop.date.year <= self.date_specific_testing_plateau:
                 self.prob_test_who4 = min(0.9, self.prob_test_who4 * self.incr_test_rate_sympt)
                 self.prob_test_tb = min(0.8, self.prob_test_tb * self.incr_test_rate_sympt)
                 self.prob_test_non_tb_who3 = min(0.7, self.prob_test_non_tb_who3 * self.incr_test_rate_sympt)
@@ -240,10 +240,9 @@ def test_mark_general_pop(self, pop):
             self.test_mark_sex_workers(pop)
 
             # update testing probabilities
-            self.rate_first_test = self.init_rate_first_test + (min(pop.date.year, self.date_test_rate_plateau)
-                                                                - self.date_start_testing) * self.an_lin_incr_test
-            self.rate_rep_test = (min(pop.date.year, self.date_test_rate_plateau)
-                                  - self.date_start_testing) * self.an_lin_incr_test
+            self.rate_rep_test = (min(pop.date.year, self.date_general_testing_plateau)
+                                  - self.date_rate_testing_incr) * self.an_lin_incr_test
+            self.rate_first_test = self.init_rate_first_test + self.rate_rep_test
 
             # general population ready for testing
             testing_population = pop.get_sub_pop(AND(COND(col.HARD_REACH, op.eq, False),

src/hivpy/hiv_testing_data.py

@@ -12,8 +12,8 @@ def __init__(self, filename):
         super().__init__(filename)
 
         try:
-            self.date_start_anc_testing = self.data["date_start_anc_testing"]
             self.date_start_testing = self.data["date_start_testing"]
+            self.date_rate_testing_incr = self.data["date_rate_testing_incr"]
             self.init_rate_first_test = self.data["init_rate_first_test"]
             self.eff_max_freq_testing = self.data["eff_max_freq_testing"]
             self.test_scenario = self.data["test_scenario"]
@@ -29,7 +29,8 @@ def __init__(self, filename):
             self.prob_test_tb = self.data["prob_test_tb"]
             self.prob_test_non_tb_who3 = self.data["prob_test_non_tb_who3"]
             self.test_targeting = self._get_discrete_dist("test_targeting")
-            self.date_test_rate_plateau = self._get_discrete_dist("date_test_rate_plateau")
+            self.date_general_testing_plateau = self._get_discrete_dist("date_general_testing_plateau")
+            self.date_specific_testing_plateau = self.data["date_specific_testing_plateau"]
             self.an_lin_incr_test = self._get_discrete_dist("an_lin_incr_test")
             self.incr_test_rate_sympt = self._get_discrete_dist("incr_test_rate_sympt")
 

src/hivpy/pregnancy.py

@@ -154,6 +154,7 @@ def update_antenatal_care(self, pop: Population):
         # get population that became pregnant this time step
         pregnant_population = pop.get_sub_pop([(col.PREGNANT, op.eq, True),
                                                (col.LAST_PREGNANCY_DATE, op.eq, pop.date)])
+        # FIXME: should be affected by date_start_testing and date_specific_testing_plateau
         # update probability of antenatal care attendance
         self.prob_anc = min(max(self.prob_anc, 0.1) + self.rate_test_anc_inc, 0.975)
 

src/tests/test_hiv_testing.py

@@ -32,7 +32,8 @@ def test_hiv_symptomatic_testing():
     pop.data[col.LAST_TEST_DATE] = None
     pop.data[pop.get_correct_column(col.ADC, dt=1)] = True
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.prob_test_who4 = 0.6
     pop.hiv_testing.prob_test_tb = 0.5
     pop.hiv_testing.prob_test_non_tb_who3 = 0.4
@@ -100,7 +101,8 @@ def test_non_hiv_symptomatic_testing():
     pop.data[col.LAST_TEST_DATE] = None
     pop.data[pop.get_correct_column(col.HIV_DIAGNOSED, dt=1)] = False
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.prob_test_non_hiv_symptoms = 1
     pop.hiv_testing.prob_test_who4 = 0.6
     pop.hiv_testing.prob_test_non_tb_who3 = 0.4
@@ -132,7 +134,8 @@ def test_general_sex_worker_testing():
     pop.data[col.HIV_DIAGNOSED] = False
     pop.data[col.LAST_TEST_DATE] = start_date - timedelta(days=150)
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.eff_max_freq_testing = 0
     pop.hiv_testing.sw_test_regularly = True
     pop.hiv_testing.covid_disrup_affected = False
@@ -167,9 +170,10 @@ def test_general_testing_conditions():
     pop.data[col.LAST_TEST_DATE] = date(2008, 1, 1)
     pop.data[col.NP_LAST_TEST] = 1
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.eff_max_freq_testing = 1
-    pop.hiv_testing.date_test_rate_plateau = 2015.5
+    pop.hiv_testing.date_general_testing_plateau = 2015.5
     pop.hiv_testing.an_lin_incr_test = 0.8
     pop.hiv_testing.no_test_if_np0 = False
     pop.hiv_testing.sw_test_regularly = False
@@ -211,9 +215,10 @@ def test_first_time_testers():
     pop.data[col.CIRCUMCISED] = False
     pop.data[col.CIRCUMCISION_DATE] = None
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.init_rate_first_test = 0.1
-    pop.hiv_testing.date_test_rate_plateau = 2015.5
+    pop.hiv_testing.date_general_testing_plateau = 2015.5
     pop.hiv_testing.an_lin_incr_test = 0.8
     pop.hiv_testing.no_test_if_np0 = False
     pop.hiv_testing.sw_test_regularly = False
@@ -245,9 +250,10 @@ def test_repeat_testers():
     pop.data[col.CIRCUMCISED] = False
     pop.data[col.CIRCUMCISION_DATE] = None
     # fixing some values
-    pop.hiv_testing.date_start_testing = 2009
+    pop.hiv_testing.date_start_testing = 2003.5
+    pop.hiv_testing.date_rate_testing_incr = 2009
     pop.hiv_testing.eff_max_freq_testing = 1
-    pop.hiv_testing.date_test_rate_plateau = 2015.5
+    pop.hiv_testing.date_general_testing_plateau = 2015.5
     pop.hiv_testing.an_lin_incr_test = 0.8
     pop.hiv_testing.no_test_if_np0 = False
     pop.hiv_testing.sw_test_regularly = False
@@ -282,10 +288,11 @@ def test_partner_reset_after_test():
         pop.data[col.NP_LAST_TEST] = 2
         pop.data[col.NSTP_LAST_TEST] = 1
         # fixing some values
-        pop.hiv_testing.date_start_testing = 2009
+        pop.hiv_testing.date_start_testing = 2003.5
+        pop.hiv_testing.date_rate_testing_incr = 2009
         pop.hiv_testing.eff_max_freq_testing = 1
         pop.hiv_testing.init_rate_first_test = 0.1
-        pop.hiv_testing.date_test_rate_plateau = 2015.5
+        pop.hiv_testing.date_general_testing_plateau = 2015.5
         pop.hiv_testing.an_lin_incr_test = 0.8
         pop.hiv_testing.no_test_if_np0 = False
         pop.hiv_testing.sw_test_regularly = False
@@ -319,9 +326,10 @@ def test_max_frequency_testing():
         pop.data[col.NP_LAST_TEST] = 1
         pop.data[col.NSTP_LAST_TEST] = 1
         # fixing some values
-        pop.hiv_testing.date_start_testing = 2009
+        pop.hiv_testing.date_start_testing = 2003.5
+        pop.hiv_testing.date_rate_testing_incr = 2009
         pop.hiv_testing.eff_max_freq_testing = index
-        pop.hiv_testing.date_test_rate_plateau = 2015.5
+        pop.hiv_testing.date_general_testing_plateau = 2015.5
         # guaranteed testing
         pop.hiv_testing.an_lin_incr_test = 1
         pop.hiv_testing.no_test_if_np0 = False