Working snapshot using SimpleVaccine for main vax.

emodpy_typhoid/interventions/typhoid_vaccine.py

@@ -27,6 +27,29 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
     intervention.Changing_Effect.Decay_Time_Constant = decay_constant
     return intervention
 
+def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=6935.0 ):
+    """
+     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.
+
+     Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Acquisition".
+         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.
+
+     Returns:
+         SimpleVaccine: A fully configured instance of the SimpleVaccine intervention with the specified parameters.
+     """
+
+    intervention = s2c.get_class_with_defaults( "SimpleVaccine", camp.schema_path )
+    #intervention.Mode = mode
+    intervention.Waning_Config = s2c.get_class_with_defaults( "WaningEffectBoxExponential" )
+    intervention.Waning_Config.Initial_Effect = efficacy
+    intervention.Waning_Config.Box_Duration = constant_period
+    intervention.Waning_Config.Decay_Time_Constant = decay_constant
+    return intervention
+
 def new_triggered_intervention( 
         camp, 
         efficacy=0.82,
@@ -65,6 +88,47 @@ def new_triggered_intervention(
 
     return event
 
+def new_routine_immunization( 
+        camp, 
+        efficacy=0.82,
+        mode="Acquisition",
+        constant_period=0,
+        decay_constant=6935.0,
+        start_day=1, 
+        child_age=9*30,
+        coverage=1.0, 
+        node_ids=None,
+        property_restrictions_list=[],
+        co_event=None # expansion slot
+    ):
+    """
+    Create a new birth-triggered SimpleVaccine intervention based on specified parameters.
+
+    Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Acquisition".
+         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.
+         start_day (int, optional): The day on which the intervention starts. Default is 1.
+         coverage (float, optional): Demographic coverage of the intervention. Default is 1.0.
+         node_ids (list, optional): List of node IDs where the intervention is applied. Default is None.
+         property_restrictions_list (list, optional): List of property restrictions for the intervention. Default is an empty list.
+         co_event (None, optional): Expansion slot for future use.
+
+     Returns:
+         TriggeredCampaignEvent: An instance of a triggered campaign event with the TyphoidVaccine intervention.
+    """
+    iv = new_vax( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
+    delay = {
+            "Delay_Period_Min": child_age-7,
+            "Delay_Period_Max": child_age+7
+            }
+
+    event = common.TriggeredCampaignEvent( camp, Start_Day=start_day, Triggers=["Births"], Demographic_Coverage=coverage, Intervention_List=[ iv ], Node_Ids=node_ids, Property_Restrictions=property_restrictions_list, Event_Name="9-Month 'Typhoid' Vax", Delay=delay )
+
+    return event
+
 def new_scheduled_intervention( 
         camp, 
         efficacy=0.82,

examples/vaccination/example.py

@@ -16,12 +16,16 @@
 # emodpy
 from emodpy.emod_task import EMODTask
 import emodpy.emod_task 
-emodpy.emod_task.dev_mode = True
+#emodpy.emod_task.dev_mode = True
 import emod_api.interventions.common as comm 
 #comm.old_adhoc_trigger_style = False
 
 import manifest
 
+BASE_YEAR=2010
+SIMULATION_DURATION_IN_YEARS=12
+CAMP_START_YEAR=2019
+
 def update_sim_bic(simulation, value):
     simulation.task.config.parameters.Base_Infectivity_Constant = value*0.1
     return {"Base_Infectivity": value}
@@ -30,28 +34,56 @@ def update_sim_random_seed(simulation, value):
     simulation.task.config.parameters.Run_Number = value
     return {"Run_Number": value}
 
+def year_to_days( year ):
+    return ( (year-BASE_YEAR)*365 )
+
 def set_param_fn( config ):
     config.parameters.Simulation_Type = "TYPHOID_SIM"
-    config.parameters.Simulation_Duration = 50*365.0
+    config.parameters.Simulation_Duration = SIMULATION_DURATION_IN_YEARS*365.0
     config.parameters.Base_Individual_Sample_Rate = 0.2
 
     #config.parameters.Enable_Birth = 0 # temporary
     #config.parameters.Minimum_End_Time = 90 
     # cover up for default bugs in schema
-    config.parameters.Base_Year = 2000
+    config.parameters.Base_Year = BASE_YEAR
     config.parameters.Inset_Chart_Reporting_Start_Year = 1900 
     config.parameters.Inset_Chart_Reporting_Stop_Year = 2050 
     config.parameters.Enable_Demographics_Reporting = 0 
     #config.parameters.Report_Event_Recorder_Events = [ "VaccineDistributed" ]
     #config.parameters["Custom_Events"] = [ "VaccineDistributed" ]
+    #config.parameters.Typhoid_Immunity_Memory = 36500
+    #config.parameters.Config_Name = "149_Typhoid"
+
+    config.parameters.Report_Typhoid_ByAgeAndGender_Start_Year = 2010
+    config.parameters.Report_Typhoid_ByAgeAndGender_Stop_Year = 2020
+    config.parameters.Typhoid_3year_Susceptible_Fraction = 0
+    config.parameters.Typhoid_6month_Susceptible_Fraction = 0
+    config.parameters.Typhoid_6year_Susceptible_Fraction = 0
+    config.parameters.Typhoid_Acute_Infectiousness = 13435
+    config.parameters.Typhoid_Carrier_Probability = 0.108
+    config.parameters.Typhoid_Carrier_Removal_Year = 2500
+    config.parameters.Typhoid_Chronic_Relative_Infectiousness = 0.241
+    config.parameters.Typhoid_Contact_Exposure_Rate = 0.06918859049226553
+    config.parameters.Typhoid_Environmental_Exposure_Rate = 0.06169346985005757
+    config.parameters.Typhoid_Environmental_Cutoff_Days = 157.20690133538764
+    config.parameters.Typhoid_Environmental_Peak_Start = 355.0579483941714
+    config.parameters.Typhoid_Environmental_Ramp_Down_Duration = 112.30224910440123
+    config.parameters.Typhoid_Environmental_Ramp_Up_Duration = 39.540475369174146
+    config.parameters.Typhoid_Exposure_Lambda = 7.0
+    config.parameters.Typhoid_Prepatent_Relative_Infectiousness = 0.5
+    config.parameters.Typhoid_Protection_Per_Infection = 0.98
+    config.parameters.Typhoid_Subclinical_Relative_Infectiousness = 1
+    config.parameters.Typhoid_Symptomatic_Fraction = 0.07
+
+    #config.parameters.x_Birth = 1.2
 
     # when using 2018 binary
     import emodpy_typhoid.config as config_utils
     config_utils.cleanup_for_2018_mode( config )
     return config
 
 
-def build_camp( start_day=1, vax_eff = 0.82 ):
+def build_camp( start_day_offset=1, vax_eff = 0.82 ):
     """
     Build a campaign input file for the DTK using emod_api. 
     """
@@ -61,27 +93,35 @@ def build_camp( start_day=1, vax_eff = 0.82 ):
     print(f"Telling emod-api to use {manifest.schema_file} as schema.")
     camp.set_schema( manifest.schema_file )
 
-    event = ob.new_intervention( camp, timestep=1, cases=1 )
-    camp.add( event )
+    for x in range( 10 ):
+        event = ob.new_intervention( camp, timestep=1+x, cases=1 )
+        camp.add( event )
 
     import emodpy_typhoid.interventions.typhoid_vaccine as tv
     import emod_api.interventions.common as comm 
-    #event = tv.new_triggered_intervention(camp, start_day=1, triggers=['Births'], coverage=1.0, node_ids=None, property_restrictions_list=[], co_event=None)
-    #camp.add( event )
-    #event = tv.new_scheduled_intervention(camp, start_day=10*365, coverage=1.0, node_ids=None, property_restrictions_list=[], co_event=None)
-    #camp.add( event )
-    tv_iv = tv.new_intervention( camp, efficacy=vax_eff )
+    ria = tv.new_routine_immunization( camp,
+            efficacy=vax_eff,
+            start_day=year_to_days( CAMP_START_YEAR )+start_day_offset
+        )
+
+    """
     notification_iv = comm.BroadcastEvent( camp, "VaccineDistributed" )
-            #"Delay_Distribution": "FIXED_DURATION",
     vax_plus_msg = comm.MultiInterventionDistributor( camp, [ tv_iv, notification_iv ] )
-    delay_dict = {
-            "Delay_Period_Min": 265,
-            "Delay_Period_Max": 275
-            }
+    """
     #event = comm.triggered_campaign_event_with_optional_delay( camp, start_day=1, intervention=[tv_iv,notification_iv], triggers=["Births"], delay=delay_dict )
-    event = comm.triggered_campaign_event_with_optional_delay( camp, start_day=start_day, intervention=tv_iv, triggers=["Births"], delay=delay_dict )
-    #event = comm.triggered_campaign_event_with_optional_delay( camp, start_day=1, intervention=vax_plus_msg, triggers=["Births"], delay=delay_dict )
-    camp.add( event )
+    camp.add( ria )
+
+    tv_iv = tv.new_vax( camp,
+            efficacy=vax_eff 
+        )
+    one_time_campaign = comm.ScheduledCampaignEvent( camp,
+                Start_Day=year_to_days( CAMP_START_YEAR )+start_day_offset,
+                Intervention_List=[tv_iv],
+                Demographic_Coverage=0.72,
+                Target_Age_Min=0.75,
+                Target_Age_Max=15
+        )
+    camp.add( one_time_campaign )
 
     return camp
 
@@ -92,8 +132,19 @@ def build_demog():
     import emodpy_typhoid.demographics.TyphoidDemographics as Demographics # OK to call into emod-api
 
     demog = Demographics.from_template_node( lat=0, lon=0, pop=10000, name=1, forced_id=1 )
-    wb_births_df = pd.read_csv( manifest.world_bank_dataset )
-    demog.SetEquilibriumVitalDynamicsFromWorldBank( wb_births_df=wb_births_df, country='Chile', year=2005 )
+    #wb_births_df = pd.read_csv( manifest.world_bank_dataset )
+    #demog.SetEquilibriumVitalDynamicsFromWorldBank( wb_births_df=wb_births_df, country='Chile', year=BASE_YEAR )
+    """
+    demog.AddAgeDependentTransmission( 
+            Age_Bin_Edges_In_Years = [0, 5, 20, 60, -1],
+            TransmissionMatrix = [
+                [1.0, 1.0, 1.0, 1.0],
+                [1.0, 1.0, 1.0, 1.0],
+                [1.0, 1.0, 1.0, 1.0],
+                [1.0, 1.0, 1.0, 1.0]
+            ]
+    )
+    """
     return demog
 
 
@@ -103,9 +154,14 @@ def run_test():
     platform = Platform("SLURM", node_group="idm_48cores", priority="Highest") 
 
     task = EMODTask.from_default2(config_path="config.json", eradication_path=manifest.eradication_path, campaign_builder=build_camp, demog_builder=build_demog, schema_path=manifest.schema_file, param_custom_cb=set_param_fn, ep4_custom_cb=None)
+    #task.config.parameters.Demographics_Filenames = [  "demographics.json", "TestDemographics_pak_updated.json" ]
+    task.config.parameters.Demographics_Filenames = [  "TestDemographics_pak_updated.json" ]
+    task.config.parameters.Death_Rate_Dependence = "NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER"
+    task.config.parameters.Birth_Rate_Dependence = "INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR"
 
     #print("Adding asset dir...")
     #task.common_assets.add_directory(assets_directory=manifest.reporters, relative_path="reporter_plugins")
+    task.common_assets.add_directory(assets_directory=manifest.assets_input_dir)
 
     task.set_sif( manifest.sif )
 
@@ -121,13 +177,14 @@ def update_campaign_start(simulation, value):
         simulation.task.create_campaign_from_callback(build_campaign_partial)
         return {"campaign_start_day": value}
 
-    #vax_effs = np.linspace(0,1.0,3) # 0.0, 0.5, 1.0
-    #builder.add_sweep_definition( update_campaign_efficacy, vax_effs )
-    start_days = np.linspace(1,3651,11) # 1, 366, etc.
-    builder.add_sweep_definition( update_campaign_start, start_days )
+    vax_effs = np.linspace(0,1.0,3) # 0.0, 0.5, 1.0
+    builder.add_sweep_definition( update_campaign_efficacy, vax_effs )
+    builder.add_sweep_definition( update_sim_random_seed, range(5) )
+    #start_day_offsets = np.linspace(0,60,7) # 1, 366, etc.
+    #builder.add_sweep_definition( update_campaign_start, start_day_offsets )
 
     # create experiment from builder
-    experiment  = Experiment.from_builder(builder, task, name="Typhoid Hello World") 
+    experiment  = Experiment.from_builder(builder, task, name="Typhoid Vax 101") 
     # The last step is to call run() on the ExperimentManager to run the simulations.
     experiment.run(wait_until_done=True, platform=platform)
 
@@ -136,8 +193,10 @@ def update_campaign_start(simulation, value):
     # download and plot some stuff.
     EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json" ] )
     task.cache_experiment_metadata_in_sql( experiment.uid )
+    import matplotlib
+    matplotlib.use( "TkAgg" )
     import emod_api.channelreports.plot_icj_means as plotter
-    chan_data = plotter.collect( str( experiment.uid ), "Infected" )
+    chan_data = plotter.collect( str( experiment.uid ), "Infected", tag="vax_efficacy=SWEEP" )
     plotter.display( chan_data, False, "Infected", str( experiment.uid ) )