Vax dedup

emodpy_typhoid/interventions/typhoid_vaccine.py

@@ -25,7 +25,7 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
          constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
          decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
          expected_expiration (float, optional): The mean duration before efficacy becomes 0. If this is set to non-zero value, the constant_period and decay_constant are ignored. These are two different modes of waning.
-
+         deduplication_policy (string, optional): Defaults to 'replace'. Can also be 'combine'. 
 
      Returns:
          TyphoidVaccine: A fully configured instance of the TyphoidVaccine intervention with the specified parameters.
@@ -36,9 +36,10 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
     intervention.Mode = mode
     intervention.Changing_Effect = _get_waning( constant_period=constant_period, decay_constant=decay_constant, expected_expiration=expected_expiration ) 
     intervention.Changing_Effect.Initial_Effect = efficacy
+
     return intervention
 
-def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=0, expected_expiration=0 ):
+def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=0, expected_expiration=0, deduplication_policy="replace" ):
     """
      Create a new 'SimpleVaccine' intervention with specified parameters. If you use this function directly, you'll need to distribute the intervention with a function like ScheduledCampaignEvent or TriggeredCampaignEvent from emod_api.interventions.common.
 
@@ -64,6 +65,16 @@ def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_c
     else:
         raise ValueError( f"mode {mode} not recognized. Options are: 'Acquisition', 'Transmission', or 'All'." )
 
+    # replace: DAD=1, EIR=1
+    # combine: DAD=1, EIR=0
+    intervention.Dont_Allow_Duplicates = 1
+    if deduplication_policy == "replace":
+        intervention.Enable_Intervention_Replacement = 1
+    elif deduplication_policy == "combine":
+        intervention.Enable_Intervention_Replacement = 0
+    else:
+        raise ValueError( f"duplication_policy needs to be 'replace' or 'combine', not '{duplication_policy}'." )
+
     intervention.Waning_Config = _get_waning( constant_period=constant_period, decay_constant=decay_constant, expected_expiration=expected_expiration ) 
     intervention.Waning_Config.Initial_Effect = efficacy
     return intervention

examples/future_campaign/multi_sweep.py

@@ -94,14 +94,14 @@ def add_historical_vax( camp, ria_coverage=0.75, camp_coverage=0.75, efficacy=0.
         ria = tv.new_routine_immunization(camp,
                                           efficacy=efficacy,
                                           constant_period=0,
-                                          expected_expiration=expiration,
-                                          #decay_constant=values['decay_constant'],
+                                          #expected_expiration=expiration,
+                                          decay_constant=expiration,
                                           start_day=year_to_days(CAMP_START_YEAR),
                                           coverage=ria_coverage)
         tv_iv = tv.new_vax(camp,
                            efficacy=efficacy,
-                           expected_expiration=expiration,
-                           #decay_constant=values['decay_constant'],
+                           #expected_expiration=expiration,
+                           decay_constant=expiration,
                            constant_period=0)
 
         notification_iv = comm.BroadcastEvent(camp, "VaccineDistributed")
@@ -113,7 +113,7 @@ def add_historical_vax( camp, ria_coverage=0.75, camp_coverage=0.75, efficacy=0.
                                                         Demographic_Coverage=camp_coverage,
                                                         Target_Age_Min=0.75,
                                                         Target_Age_Max=15
-                                                        )
+                                                       )
         camp.add(one_time_campaign)
 
     #add_historical_vax( camp )
@@ -150,7 +150,10 @@ def add_vax_intervention(campaign, values, min_age=0.75, max_age=15, binary_immu
     import emodpy_typhoid.interventions.typhoid_vaccine as tv
     print(f"Telling emod-api to use {manifest.schema_file} as schema.")
     campaign.set_schema(manifest.schema_file)
-    camp_coverage = values['coverage']
+    if 'coverage' in values:
+        camp_coverage = values['coverage']
+    else:
+        camp_coverage = values['coverage_camp']
 
     if binary_immunity:
         tv_iv = tv.new_vax(campaign,
@@ -164,6 +167,12 @@ def add_vax_intervention(campaign, values, min_age=0.75, max_age=15, binary_immu
                        constant_period=0)
 
     notification_iv = comm.BroadcastEvent(campaign, "VaccineDistributed")
+    # NOTE: the order of interventions in Intervention_List matters. This is because multiple
+    # interventions are delivered using a MultiInterventionDistributor intervention and de-duplication
+    # operates on Intervention_Name, so that when we try to distribute this intervention 'package',
+    # the model looks at the name of the existing intervention, which is the vax, and the name of the
+    # 'package' here, which would be MultiInterventionDistributor. But there is code in emod_api which
+    # sets the MID name to the name of the first intervention in the list, which here will be SimpleVaccine.
     one_time_campaign = comm.ScheduledCampaignEvent(campaign,
                                                     Start_Day=year_to_days(FWD_CAMP_START_YEAR),
                                                     Intervention_List=[tv_iv, notification_iv],
@@ -286,15 +295,26 @@ def get_sweep_list_duration():
             sweep_list.append({'start_day_offset': c[0], 'efficacy': c[1], 'coverage': c[2], 'decay_constant': c[3]})
         return sweep_list
 
+    def get_sweep_list_just_one():
+        start_day_offset = [1]
+        vax_effs = [1]
+        decay = [3000]
+        cov = [0.75]
+        combinations = list(itertools.product(start_day_offset, vax_effs, cov, decay))
+        sweep_list = []
+        for c in combinations:
+            sweep_list.append({'start_day_offset': c[0], 'efficacy': c[1], 'coverage_camp': c[2], 'decay_constant': c[3]})
+        return sweep_list
+
     def get_sweep_list_from_csv():
         # This is wrong. Just load rows. Code is recreating. But have to stop work for now.
         import pandas as pd
         df = pd.load_csv( manifest.sweep_config )
         raise NotImplemented( "get_sweep_list_from_csv" )
 
     def get_config_sweep_list():
-        tac = [ 13435, 15320 ]
-        tel = [ 5.0, 7.0 ]
+        tac = [ 13435 ]
+        tel = [ 7.0 ]
         combinations = list(itertools.product(tac, tel))
         sweep_list = []
         for c in combinations:
@@ -307,7 +327,8 @@ def get_config_sweep_list():
             "Coverage": get_sweep_list_coverage,
             "Coverage_RIA": get_sweep_list_coverage_ria,
             "Coverage_Camp": get_sweep_list_coverage_camp,
-            "Vax_Duration": get_sweep_list_duration
+            "Vax_Duration": get_sweep_list_duration,
+            "Just_One": get_sweep_list_just_one
             }
 
     if sweep_choice not in sweep_selections.keys():
@@ -319,10 +340,7 @@ def get_config_sweep_list():
     else:
         avi_age_coverage = partial( add_vax_intervention, min_age=0, max_age=125 )
 
-    if binary_immunity:
-        avi_decay = partial( avi_age_coverage, binary_immunity=True )
-    else:
-        avi_decay = partial( avi_age_coverage, binary_immunity=False )
+    avi_decay = partial( avi_age_coverage, binary_immunity=binary_immunity )
 
     builders = get_sweep_builders(sweep_list, get_config_sweep_list(), add_vax_fn=avi_decay)
 
@@ -341,7 +359,7 @@ def get_config_sweep_list():
 if __name__ == "__main__":
     import emod_typhoid.bootstrap as dtk
 
-    dtk.setup(manifest.model_dl_dir)
+    #dtk.setup(manifest.model_dl_dir)
 
     import sys
-    run( sys.argv[1] if len(sys.argv)>1 else "Efficacy" )
+    run( sys.argv[1] if len(sys.argv)>1 else "Just_One", binary_immunity=False )

examples/future_campaign/requirements.txt

@@ -2,4 +2,4 @@
 emodpy-typhoid==0.0.6.dev0
 emodpy==1.22.0.dev3
 emod-api==1.31.0.dev1
-emod-typhoid==0.0.4.dev5
+emod-typhoid==0.0.4.dev7