Add test switching functionality

crcsim/agent.py

@@ -872,6 +872,23 @@ def choose_tests(self):
         self.diagnostic_test = self.params["diagnostic_test"]
         self.surveillance_test = self.params["surveillance_test"]
 
+        if self.params["use_variable_routine_test"]:
+            # If the simulation is using variable routine tests, then we do not pick
+            # a single routine test for each person. Instead, we will refer to the
+            # routine_testing_year and routine_test_by_year parameters to determine
+            # which test to use each year. This allows a person to switch tests during
+            # their lifetime. We still assign the routine_test attribute here to
+            # avoid errors from yearly actions that expect a person to have a routine
+            # test attribute.
+            starting_test = self.params["routine_test_by_year"][0]
+            self.routine_test = starting_test
+            self.out.add_routine_test_chosen(
+                person_id=self.id,
+                test_name=starting_test,
+                time=self.scheduler.time,
+            )
+            return
+
         # Choose the routine test based on proportions specified in
         # parameters file.
         #
@@ -903,6 +920,7 @@ def choose_tests(self):
                 self.out.add_routine_test_chosen(
                     person_id=self.id,
                     test_name=test,
+                    time=self.scheduler.time,
                 )
                 break
 
@@ -1576,6 +1594,29 @@ def handle_ongoing_treatment(self, message="Ongoing treatment"):
             )
 
     def handle_yearly_actions(self, message="Conduct yearly actions"):
+        if self.params["use_variable_routine_test"]:
+            # If the simulation is using variable routine tests, then the parameters
+            # specify a single routine test that every person in the simulation will
+            # use for each testing year. This allows a person to switch tests during
+            # their lifetime. In this case, we assign the routine test for each year
+            # rather than choosing a single routine test at initiatilization.
+            #
+            # Note that indexing self.params["routine_testing_year"] will always
+            # return the min/max testing year, because crcsim.parameters raises an
+            # error if this parameter is not sorted in increasing order.
+            if (
+                self.scheduler.time >= self.params["routine_testing_year"][0]
+                and self.scheduler.time <= self.params["routine_testing_year"][-1]
+            ):
+                self.routine_test = self.params["variable_routine_test"](
+                    self.scheduler.time
+                )
+                self.out.add_routine_test_chosen(
+                    person_id=self.id,
+                    test_name=self.routine_test,
+                    time=self.scheduler.time,
+                )
+
         self.do_tests()
 
         self.scheduler.add_event(

crcsim/analysis.py

@@ -423,12 +423,25 @@ def summarize(self):
 
         # Number of times each test was adopted for routine screening
         routine_tests_chosen = self.raw_output[
-            self.raw_output.record_type.eq("test_chosen")
+            self.raw_output.record_type.eq("test_chosen") & self.raw_output.time.eq(0)
         ]
         for rt in self.params["routine_tests"]:
             rt_chosen = routine_tests_chosen[routine_tests_chosen.test_name.eq(rt)]
             replication_output_row[f"{rt}_adopted"] = len(rt_chosen.index)
 
+        # Number of years each routine test was used
+        # (if test variable routine test was enabled in the simulation)
+        if self.params["use_variable_routine_test"]:
+            rt_years = self.raw_output[
+                self.raw_output.record_type.eq("test_chosen")
+                & self.raw_output.time.gt(0)
+            ]
+            rt_years_grouped = rt_years.groupby(["test_name"]).agg(
+                count=("time", "count")
+            )
+            for ix, row in rt_years_grouped.iterrows():
+                replication_output_row[f"{ix}_available_as_routine"] = row["count"]
+
         # Number of times each test was performed for routine screening
         # and number of times per thousand unscreened and undiagnosed 40-year-olds
         routine_tests = tests[tests.role.eq(str(TestingRole.ROUTINE))]
@@ -970,11 +983,11 @@ def compute_pop_rates(self, status_arrays: list):
         """
         # Sum all of the person status arrays to get an array of counts of the number of
         # people in each status for each year.
-        statuses: np.ndarray = sum(status_arrays)
+        status_array: np.ndarray = sum(status_arrays)
 
         # Convert to DataFrame so we can index by column name
         statuses = pd.DataFrame(
-            statuses,
+            status_array,
             columns=[
                 "alive",
                 "crc_death",

crcsim/output.py

@@ -137,13 +137,14 @@ def add_expected_lifespan(self, person_id: Any, time: float):
             {"record_type": "lifespan", "person_id": person_id, "time": time}
         )
 
-    def add_routine_test_chosen(self, person_id: Any, test_name: str):
+    def add_routine_test_chosen(self, person_id: Any, test_name: str, time: float):
         self.rows.append(
             {
                 "record_type": "test_chosen",
                 "person_id": person_id,
                 "test_name": test_name,
                 "role": TestingRole.ROUTINE,
+                "time": time,
             }
         )
 

crcsim/parameters.py

@@ -64,4 +64,23 @@ def load_params(file):
                 y=params[f"death_rate_{race}_{sex}_rates"],
             )
 
+    if params["use_variable_routine_test"]:
+        params["variable_routine_test"] = StepFunction(
+            x=params["routine_testing_year"], y=params["routine_test_by_year"]
+        )
+        for test_name, test_params in params["tests"].items():
+            # Indexing 0 and -1 here safely returns the min and max testing years,
+            # because initializing the StepFunction raises an error if the testing
+            # years are not sorted in increasing order.
+            if test_params["routine_start"] != params["routine_testing_year"][0]:
+                raise ValueError(
+                    f"routine_start for {test_name} does not equal the first year"
+                    " of routine testing specified in routine_testing_year."
+                )
+            if test_params["routine_end"] != params["routine_testing_year"][-1]:
+                raise ValueError(
+                    f"routine_start for {test_name} does not equal the last year"
+                    " of routine testing specified in routine_testing_year."
+                )
+
     return params

parameters.json

@@ -106,6 +106,9 @@
   "diagnostic_test": "Colonoscopy",
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 0.00002,
+  "use_variable_routine_test": true,
+  "routine_testing_year": [           50,            51,            52,            53,            54,            55,            56,            57,            58,            59,            60,    61,    62,    63,    64,    65,    66,    67,    68,    69,    70,    71,    72,    73,    74,    75 ],
+  "routine_test_by_year": ["Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "Colonoscopy", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT", "FIT" ],
 
   "cost_discount_age": 50,
   "cost_discount_rate": 0.03,