Simp vax

emodpy_typhoid/config.py

@@ -8,5 +8,4 @@ def cleanup_for_2018_mode( config ):
     config.parameters.Infectious_Period_Distribution = "FIXED_DURATION" # hack
     config.parameters.Base_Incubation_Period = 1
     config.parameters.Base_Infectious_Period = 1
-    config.parameters["Listed_Events"] = []
 

emodpy_typhoid/interventions/typhoid_vaccine.py

@@ -27,6 +27,37 @@ 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" Can also be "Transmission" or "All".
+         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 )
+    if mode == "Acquisition":
+        intervention.Vaccine_Type = "AcquisitionBlocking"
+    elif mode == "Transmission":
+        intervention.Vaccine_Type = "TransmissionBlocking"
+    elif mode == "All":
+        intervention.Vaccine_Type = "General"
+    else:
+        raise ValueError( f"mode {mode} not recognized. Options are: 'Acquisition', 'Transmission', or 'All'." )
+
+    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 +96,49 @@ 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 delayed, birth-triggered SimpleVaccine intervention based on specified parameters. Does not add to campaign.
+
+    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 "Shedding".
+         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.
+         child_age (int, optional): The age of the person when they get the vaccine. Defaults to 9 months. Vaccines are actually distribute +/- 7 days.
+         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 )
+    age_min = max(0,child_age-7)
+    delay = {
+            "Delay_Period_Min": age_min,
+            "Delay_Period_Max": child_age+7
+            }
+
+    event = common.triggered_campaign_delay_event( camp, start_day=start_day, trigger="Births", delay=delay, intervention=iv, ip_targeting=property_restrictions_list, coverage=coverage )
+
+    return event
+
 def new_scheduled_intervention( 
         camp, 
         efficacy=0.82,

examples/HINTy/example.py

@@ -0,0 +1,262 @@
+#!/usr/bin/env python
+
+import pandas as pd
+import numpy as np # just for linspace
+import pathlib # for a join
+from functools import partial
+
+# idmtools ...
+from idmtools.assets import Asset, AssetCollection  #
+from idmtools.builders import SimulationBuilder
+from idmtools.core.platform_factory import Platform
+from idmtools.entities.experiment import Experiment
+from idmtools_platform_comps.utils.python_requirements_ac.requirements_to_asset_collection import RequirementsToAssetCollection
+from idmtools_models.templated_script_task import get_script_wrapper_unix_task
+
+# emodpy
+from emodpy.emod_task import EMODTask
+import emodpy.emod_task 
+#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}
+
+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 = 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 = 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.Enable_Property_Output = 1 
+    config.parameters.Report_Event_Recorder_Events = [ "VaccineDistributed", "PropertyChange"]
+    config.parameters["Listed_Events"] = [ "VaccineDistributed" ] # old school
+    #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 = 2050
+    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_offset=1, vax_eff = 0.82 ):
+    """
+    Build a campaign input file for the DTK using emod_api. 
+    """
+    import emod_api.campaign as camp
+    import emod_api.interventions.outbreak as ob 
+
+    print(f"Telling emod-api to use {manifest.schema_file} as schema.")
+    camp.set_schema( manifest.schema_file )
+
+    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 
+    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" )
+    #event = comm.triggered_campaign_event_with_optional_delay( camp, start_day=1, intervention=[tv_iv,notification_iv], triggers=["Births"], delay=delay_dict )
+    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,notification_iv],
+                Demographic_Coverage=0.72,
+                Target_Age_Min=0.75,
+                Target_Age_Max=15
+        )
+    camp.add( one_time_campaign )
+
+    def migrate():
+        """
+        Use PropertyValueChanger to move some fraction between Rural and Urban over time.
+        """
+
+        def two_step():
+            rural_to_urban_pvc = comm.PropertyValueChanger( camp,
+                Target_Property_Key="Region",
+                Target_Property_Value="Urban",
+                Maximum_Duration=30,
+                Revert=1,
+            )
+            #rural_to_urban_pvc = comm.PropertyValueChanger( camp, ... )
+            event = comm.ScheduledCampaignEvent( camp,
+                    Start_Day=t,
+                    Intervention_List=[rural_to_urban_pvc],
+                    Demographic_Coverage=0.1,
+                    Property_Restrictions = "Region:Rural"
+                    #,Target_Age_Min=0.75,
+                    #,Target_Age_Max=15
+                )
+            camp.add( event )
+            """
+            # 1% Urban->Rural
+            comm.change_individual_property( camp,
+                    target_property_name="Region",
+                    target_property_value="Rural",
+                    start_day=t, coverage=0.01,
+                    ip_restrictions="Region:Urban" )
+            """
+
+        def one_step():
+            # 1% Rural->Urban
+            comm.change_individual_property( camp,
+                    target_property_name="Region",
+                    target_property_value="Urban",
+                    start_day=t, coverage=0.1, 
+                    ip_restrictions="Region:Rural" )
+
+        for t in np.linspace( 1, SIMULATION_DURATION_IN_YEARS*365, 20 ):
+            two_step()
+
+        #for t in np.linspace( 10*365, SIMULATION_DURATION_IN_YEARS*365, 3 ):
+
+    #migrate()
+    return camp
+
+def build_demog():
+    """
+    Build a demographics input file for the DTK using emod_api. 
+    """
+    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 )
+    # We're getting all our demographics from a static file overlay.
+
+    """
+    # This doesn't work right now but still want to leave in example of what we want to be able to do soon.
+    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]
+            ]
+    )
+    """
+    # 80% rural, 20% urban.
+    demog.AddIndividualPropertyAndHINT( Property="Region",
+            Values = [ "Rural", "Urban" ],
+            InitialDistribution = [ 0.8, 0.2 ],
+            TransmissionMatrix = [
+                            [ 1, 0.1 ],
+                            [ 0.1, 1 ]
+                        ],
+            EnviroTransmissionMatrix = [
+                            [ 1, 0.1 ],
+                            [ 0.1, 1 ]
+                        ]
+        )
+
+    return demog
+
+
+def run_test():
+    # Create a platform
+    # Show how to dynamically set priority and node_group
+    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)
+    # normally we don't force-set parameters at this point
+    task.config.parameters.Demographics_Filenames = [  "demographics.json", "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"
+    task.common_assets.add_directory(assets_directory=manifest.assets_input_dir)
+
+    task.set_sif( manifest.sif )
+
+    # Create simulation sweep with builder
+    builder = SimulationBuilder()
+    #builder.add_sweep_definition( update_sim_random_seed, range(1) )
+    def update_campaign_efficacy(simulation, value):
+        build_campaign_partial = partial(build_camp, vax_eff=value)
+        simulation.task.create_campaign_from_callback(build_campaign_partial)
+        return {"vax_efficacy": value}
+    def update_campaign_start(simulation, value):
+        build_campaign_partial = partial(build_camp, start_day=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 )
+    builder.add_sweep_definition( update_sim_random_seed, range(5) ) # keep at 1 for smoketesting
+    #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 Vax 101") 
+    # The last step is to call run() on the ExperimentManager to run the simulations.
+    experiment.run(wait_until_done=True, platform=platform)
+
+    task.handle_experiment_completion( experiment )
+
+    # 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", tag="vax_efficacy=SWEEP" )
+    plotter.display( chan_data, False, "Infected", str( experiment.uid ) )
+
+
+if __name__ == "__main__":
+    import emod_typhoid.bootstrap as dtk
+    dtk.setup( manifest.model_dl_dir )
+
+    run_test()

examples/HINTy/manifest.py

@@ -0,0 +1,9 @@
+import os
+requirements = "./requirements.txt"
+model_dl_dir = "stash2"
+schema_file=os.path.join(model_dl_dir, "schema.json")
+eradication_path=os.path.join(model_dl_dir, "Eradication")
+assets_input_dir="Assets"
+reporters=model_dl_dir
+sif="dtk_centos_2018.id"
+world_bank_dataset="../world_bank_dataset.csv"

examples/HINTy/requirements.txt

@@ -0,0 +1,4 @@
+emodpy-typhoid==0.0.5.dev0
+emodpy==1.22.0.dev3
+emod-api==1.31.0.dev0
+emod-typhoid==0.0.4.dev2

examples/vaccination/dtk_centos_2018.id

@@ -0,0 +1 @@
+79791913-ee50-ee11-aa0a-b88303911bc1::Asset Collection