Need non-HINT Blantyre.

examples/blantyre_noHINT/Blantyre_mortality_1year.csv

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+Age_Bin,1950,1951
+0-2,0.0059,0.0059
+2-5,0.0024,0.0024
+5-10,0.001,0.001
+10-20,0.0011,0.0011
+20-30,0.0016,0.0016
+30-40,0.0026,0.0026
+40-50,0.0052,0.0052
+50-65,0.0479,0.0479
+65,1000,1000

examples/blantyre_noHINT/example.py

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+#!/usr/bin/env python
+
+import pandas as pd
+import math
+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 manifest
+
+base_year=1917
+sim_years=122 # 100 OK
+initial_pop=9712
+
+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 set_param_fn( config ):
+    # sim nature, size and scope
+    config.parameters.Simulation_Type = "TYPHOID_SIM"
+    #config.parameters.Simulation_Type = "GENERIC_SIM" # for demographics
+    config.parameters.Enable_Environmental_Route = 1 # This should be implicit with TYPHOID_SIM; Fix in C++/G-O
+    config.parameters.Simulation_Duration = sim_years*365.0
+    #config.parameters.Enable_Skipping = 1  
+    config.parameters.Base_Individual_Sample_Rate = 0.25
+    #config.parameters.Base_Individual_Sample_Rate = 0.1
+
+    # demographics
+    #config.parameters.x_Birth = 3
+    #config.parameters.x_Other_Mortality = 100 # just to add some additional fertility
+
+    #config.parameters.Enable_Birth = 0 # temporary
+    #config.parameters.Minimum_End_Time = 90 
+    # cover up for default bugs in schema
+
+    #Comment some things out while doing GENERIC_SIM testing
+    def typhoid_report():
+        config.parameters.Base_Year = base_year # to 1960
+        config.parameters.Inset_Chart_Reporting_Start_Year = base_year
+        config.parameters.Inset_Chart_Reporting_Stop_Year = 2040
+        config.parameters.Report_Typhoid_ByAgeAndGender_Start_Year = 2040
+        config.parameters.Report_Typhoid_ByAgeAndGender_Stop_Year = 2041
+    typhoid_report()
+    def generic_infect(): # for demographics
+        config.parameters.Infectious_Period_Exponential = 10
+        config.parameters.Incubation_Period_Constant = 10
+        config.parameters.Base_Infectivity_Constant = 1
+    #generic_infect()
+
+
+    # reporting
+    config.parameters.Enable_Demographics_Reporting = 0 
+    #config.parameters.Enable_Property_Output = 1 
+    #config.parameters["logLevel_default"] = "INFO"
+
+    # typhoid
+    config.parameters.Node_Contagion_Decay_Rate = 0.056278
+    #config.parameters.Environmental_Incubation_Period = 1
+    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 # not in this schema
+    config.parameters.Typhoid_Chronic_Relative_Infectiousness = 0.241
+    config.parameters.Typhoid_Contact_Exposure_Rate = 0.05717751694664575
+    config.parameters.Typhoid_Environmental_Exposure_Rate = 0.04742897659197619
+    def seasonal_forcing_to():
+        config.parameters.Environmental_Cutoff_Days = 190.0 # not in this schema
+        config.parameters.Environmental_Peak_Start = 40.0
+        config.parameters.Environmental_Ramp_Down_Duration = 100.0
+        config.parameters.Environmental_Ramp_Up_Duration = 28.0
+    #seasonal_forcing_to()
+    config.parameters.Typhoid_Exposure_Lambda = 5.19468669532742
+    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 = 0.049739494850446146
+
+    # overhead
+    config.parameters.pop( "Serialized_Population_Filenames" )
+    config.parameters.pop( "Serialization_Time_Steps" )
+
+    return config
+
+
+def build_camp():
+    """
+    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 )
+
+    def seed():
+        #ob.seed( camp, Start_Day=1, Coverage=0.01, Target_Props="Geographic:A", Tot_Rep=20, Rep_Interval=365, Honor_Immunity=True )
+        # 1 :: AllPlaces :: 50.0% :: OutbreakIndividual
+        ob.seed( camp, Start_Day=2, Coverage=0.5, Honor_Immunity=False )
+
+        # 730(x10/_365) :: AllPlaces :: 0.5% :: OutbreakIndividual
+        ob.seed( camp, Start_Day=730, Coverage=0.005, Tot_Rep=10, Rep_Interval=365, Honor_Immunity=False )
+    seed()
+
+    def vax_test():
+        import emodpy_typhoid.interventions.typhoid_vaccine as tv
+        event = tv.new_triggered_intervention(camp, start_day=20*365, 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=5*365, coverage=1.0, node_ids=None, property_restrictions_list=[], co_event=None)
+        #camp.add( event )
+
+    def seasonal_forcing_go():
+        # seasonal forcing
+        # G-O method
+        import emod_api.interventions.node_multiplier as nim
+        nim_iv = nim.new_intervention( camp, new_infectivity=0.0, profile="TRAP", rise_dur=227, peak_dur=19, fall_dur=11 )
+        #nim_iv.Transmission_Route = "ENVIRONMENTAL"
+
+        import emod_api.interventions.common as comm
+        event = comm.ScheduledCampaignEvent( camp, Start_Day=1, Intervention_List=[nim_iv], Number_Repetitions=-1, Timesteps_Between_Repetitions=365 )
+        camp.add( event )
+    seasonal_forcing_go()
+
+    def give_vax( start_year, age ):
+         import emodpy_typhoid.interventions.typhoid_vaccine as tv
+         event = tv.new_triggered_intervention(camp, start_day=(start_year-base_year)*365, triggers=['Births'], coverage=0.85, node_ids=None, property_restrictions_list=[], co_event="Vaccinated")
+         # TBD: use common.TriggeredCampaignEvent to use the delay. The above doesn't have delays.
+         camp.add( event )
+    give_vax( start_year=2017, age=0.75 )
+
+    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=initial_pop, 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=1960 ) # 1960 just coz it's earliest
+    demog.SetInitialAgeLikeSubSaharanAfrica()
+    inflection_year = 1960
+    #demog.SetFertilityOverTimeFromParams( years_region1=40, years_region2=(122-40), start_rate=0.025, inflection_rate=0.025, end_rate=0.007 )
+    yrs_region1 = inflection_year-base_year
+    yrs_region2 = max((sim_years-yrs_region1),0)
+
+    #demog.SetFertilityOverTimeFromParams( years_region1=yrs_region1, years_region2=yrs_region2, start_rate=0.1662, inflection_rate=0.1662, end_rate=0.0521 )
+    # 1917-1960( 43 years): high fert -- for typhoid, demog file should have absolute year values in it.
+    # years_region1=1960 (ish)
+    # years_region2=2015-1960=55
+    # stays at low value from 2017 to end
+    demog.SetFertilityOverTimeFromParams( years_region1=yrs_region1+base_year, years_region2=55, start_rate=0.1662, inflection_rate=0.1662, end_rate=0.0521 )
+    demog.SetMortalityOverTimeFromData( manifest.mortality_data, 0 )
+
+    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_from_py.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 = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None)
+
+    print("Adding asset dir...")
+    task.common_assets.add_directory(assets_directory=manifest.reporters, relative_path="reporter_plugins")
+
+    task.set_sif( manifest.sif )
+
+    # Create simulation sweep with builder
+    builder = SimulationBuilder()
+    builder.add_sweep_definition( update_sim_random_seed, range(10) )
+
+    # create experiment from builder
+    experiment  = Experiment.from_builder(builder, task, name="Typhoid Blantyre emodpy") 
+    # 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", "SpatialOutput_Prevalence.bin" ] )
+    task.cache_experiment_metadata_in_sql( experiment.uid )
+    import emod_api.channelreports.plot_icj_means as plotter
+    chan_data = plotter.collect( str( experiment.uid ), "Infected" )
+    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/blantyre_noHINT/from_files/dtk_centos.id

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+f1e6b032-47b7-ec11-a9f6-9440c9be2c51::Asset Collection

examples/blantyre_noHINT/manifest.py

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+import os
+requirements = "./requirements.txt"
+#model_dl_dir = "stash"
+model_dl_dir = "model-from-go"
+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.id"
+world_bank_dataset="../world_bank_dataset.csv"
+mortality_data="Blantyre_mortality_1year.csv"