from typing import List
import emod_api.campaign as camp
import emodpy_hiv.interventions.outbreak as ob
import emodpy_hiv.interventions.reftracker as rt
import emod_api.interventions.common as comm
import emod_api.interventions.utils as utils
from emodpy_hiv import *
[docs]def reset( camp ):
"""
Utility function to clear out the campaign object, mostly useful to test. This function is not auto-imported
with the module like the rest of the functions in this submodule. Caller has to explicitly import
emodpy_hiv.interventions.cascade_helpers.
Args:
camp: emod_api.campaign object.
Returns:
None.
"""
del( camp.campaign_dict["Events"][:] )
[docs]def seed_infection( camp, timestep, coverage ):
"""
Seed an infection by time and %age of population infected.
"""
event = ob.new_intervention( timestep=timestep, camp=camp, coverage=coverage )
# have to be careful with having first in a wrapped function. This removes all other events.
camp.add( event )
# TODO: need to decide: use kwargs or custom pass-through params that go to TriggerdCampaignEvent (e.g. target_age_max)
[docs]def triggered_event_common(camp, in_trigger, out_iv, coverage=1.0, target_sex="All",
property_restrictions: List[str] = None, event_name="", node_ids: List[int] = None,
start_day: int = 1, target_age_min: float = 0, target_age_max: float = 365*200, delay: float = None):
"""
Parameterized utility function used by rest of functions in this submodule; listens for a trigger (signal)
and distributes an intervention (or list thereof) as a result, based on coverage and targeting.
Args:
camp: The central campaign accumulator, from emod_api.campaign.
in_trigger: The trigger aka signal for the event. E.g., "NewInfection"
out_iv: The output intervention of the event.
coverage (float): The coverage of the event (default is 1.0).
target_sex (str): The target sex for the event (default is "All").
property_restrictions (list[str]): A list of IP restrictions in "Risk:HIGH" format.
None means no restrictions.
event_name (str): The name of the event (default is an empty string).
node_ids: (list[int]) A list of node ids to apply the event to. None means all nodes.
start_day: (int) The model simulation time to start the event.
Returns:
New campaign event.
"""
out_ivs = out_iv if isinstance(out_iv, list) else [out_iv]
in_triggers = in_trigger if isinstance(in_trigger, list) else [in_trigger]
event = comm.TriggeredCampaignEvent(camp, Start_Day=start_day, Event_Name=event_name,
Nodeset_Config=utils.do_nodes(camp.schema_path, node_ids=node_ids),
Triggers=in_triggers, Intervention_List=out_ivs, Demographic_Coverage=coverage,
Target_Gender=target_sex, Property_Restrictions=property_restrictions,
Target_Age_Min=target_age_min, Target_Age_Max=target_age_max, Delay=delay)
# TODO: ask, should we ALWAYS pop these targeting configs? I think not, once they are implemented...
event.Event_Coordinator_Config.pop("Targeting_Config", None)
event.Event_Coordinator_Config.Intervention_Config.pop("Targeting_Config", None)
event['Event_Name'] = event_name # TODO: This should be in emod-api comm.TriggeredCampaignEvent, right?
camp.add(event)
# An alias for triggered_event_common.
add_triggered_event = triggered_event_common
[docs]def add_scheduled_event(camp, out_iv, coverage=1.0, target_sex="All",
property_restrictions: List[str] = None, event_name="", node_ids: List[int] = None,
start_day: int = 1):
out_ivs = out_iv if isinstance(out_iv, list) else [out_iv]
event = comm.ScheduledCampaignEvent(camp, Start_Day=start_day, Event_Name=event_name,
Nodeset_Config=utils.do_nodes(camp.schema_path, node_ids=node_ids),
Intervention_List=out_ivs, Demographic_Coverage=coverage,
Target_Gender=target_sex, Property_Restrictions=property_restrictions)
# TODO: ck4, needed? (following two lines)
event.Event_Coordinator_Config.pop("Targeting_Config", None)
event.Event_Coordinator_Config.Intervention_Config.pop("Targeting_Config", None)
event['Event_Name'] = event_name # TODO: This should be in emod-api comm.TriggeredCampaignEvent, right?
camp.add(event)
[docs]def add_reference_tracked_event(camp,
out_iv,
time_value_map: dict,
event_name: str = '',
target_min_age: float = 0,
target_max_age: float = 200,
target_sex: str = 'All',
target_disease_state: str = None,
update_period: float = 30.4166666666667,
start_day: float = 1960.5,
node_ids: List[int] = None):
# out_ivs = out_iv if isinstance(out_iv, list) else [out_iv]
event = rt.DistributeIVByRefTrack(camp=camp,
Start_Day=start_day,
Intervention=out_iv,
TVMap=time_value_map,
node_ids=node_ids,
Target_Age_Min=target_min_age,
Target_Age_Max=target_max_age,
Target_Gender=target_sex,
Update_Period=update_period,
Event_Name=event_name,
Target_Disease_State=target_disease_state)
# event.Event_Name = event_name
event['Event_Name'] = event_name # TODO: This should be in emodpy-hiv rt.DistributeIVByRefTrack, right?
camp.add(event)
[docs]def add_choice( camp, sympto_signal="NewlySymptomatic", get_tested_signal="GetTested" ):
"""
Listen for a trigger. Defaults to 'NewlySymptomatic'. Then toss a fair coin; in case of heads,
Distribute diagnostic (and publish signal -- default is 'GetTested'; tails maybe it's just a cold ('Ignore').
Args:
camp: The central campaign accumulator, from emod_api.campaign.
sympto_signal (str): The signal or trigger we are listening for. Doesn't have to be anything to do with
symptomaticity but defaults to "NewlySymptomatic".
get_tested_signal (str): The signal/trigger published if coin toss is heads and person gets tested.
"""
actual_iv = randomchoice.new_diagnostic( camp, choices={ get_tested_signal: 0.5, "Ignore": 0.5 } )
triggered_event_common( camp, in_trigger=sympto_signal, out_iv=actual_iv, event_name="Decide_On_Testing" )
[docs]def add_test( camp, get_tested_signal="GetTested" ):
"""
Listen for get_tested_signal signal (defaults to "GetTested"). Then give HIV RapidDiagnostic test after a delay of 30 days.
Publish 'HIVPositiveTest' on +ve or 'HIVNegativeTest' on -ve.
"""
actual_iv = rapiddiag.new_diagnostic( camp, Positive_Event="HIVPositiveTest", Negative_Event="HIVNegativeTest" )
delayed_iv = comm.DelayedIntervention( camp, [ actual_iv ], Delay_Dict={ "Delay_Period_Constant": 30 } )
triggered_event_common( camp, get_tested_signal, delayed_iv, event_name="Test" )
[docs]def trigger_art_from_pos_test( camp, input_signal="HIVPositiveTest", output_signal="StartTreatment", lag_time=30 ):
"""
Listen for HIVPositiveTest trigger. Then Trigger ART. Note that Trigger ART isn't same as starting it.
"""
actual_iv = comm.BroadcastEvent( camp, output_signal )
delayed_iv = comm.DelayedIntervention( camp, [ actual_iv ], Delay_Dict={ "Delay_Period_Constant": lag_time } )
triggered_event_common( camp, input_signal, delayed_iv, event_name="NeedTreatment" )
[docs]def add_art_from_trigger( camp, signal="StartTreatment" ):
"""
Actually distribute ART if a StartTreatment signal/trigger is observed. Broadcast a StartedART signal synchronously.
"""
actual_iv = art.new_intervention(camp)
triggered_event_common( camp, signal, [ actual_iv ], event_name="ART on trigger" )
[docs]def trigger_art( camp, timestep, coverage, trigger="StartTreatment" ):
"""
Schedule a broadcast of StartTreatment (or equivalent), not based on any observed signals.
"""
trigger_event = comm.ScheduledCampaignEvent( camp, Start_Day=timestep, Demographic_Coverage=coverage, Event_Name="ART trigger", Nodeset_Config=utils.do_nodes(camp.schema_path, node_ids=[]), Intervention_List=[ comm.BroadcastEvent( camp, trigger ) ] )
trigger_event.Event_Coordinator_Config.pop( "Targeting_Config" )
camp.add( trigger_event )