def add_simple_rcd(campaign):
simple_rcd_event = add_drug_campaign(
campaign,
campaign_type='rfMSAT',
drug_code='AL',
diagnostic_type='BLOOD_SMEAR_PARASITES',
diagnostic_threshold=0,
start_days=[2],
coverage=0.7,
trigger_coverage=0.01,
listening_duration=1000)
campaign.add(simple_rcd_event)
def add_bednets(campaign):
# simple bednet from example
# bednet_distribution = Bednet(campaign,
# start_day=100,
# coverage=1.0,
# killing_eff=1.0,
# blocking_eff=1.0,
# usage_eff=1.0,
# node_ids=[1])
# campaign.add(bednet_distribution)
kariba_itn_age_dependence = {
'youth_cov': 0.65,
'youth_min_age': 5,
'youth_max_age': 20
}
kariba_itn_seasonal_dependence = {'min_cov': 0.5, 'max_day': 60}
kariba_itn_discard_rates = {
"Expiration_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
"Expiration_Period_Mean_1": 260,
"Expiration_Period_Mean_2": 2106,
"Expiration_Period_Proportion_1": 0.6
}
# Typical blocking and killing efficacy/waning are now code defaults!
fancier_bednet_distribution = UDBednet(
campaign,
start_day=100,
coverage=0.6,
age_dependence=kariba_itn_age_dependence,
seasonal_dependence=kariba_itn_seasonal_dependence,
discard_config=kariba_itn_discard_rates,
node_ids=[1])
fancier_bednet_distribution_with_birth_trigger = UDBednet(
campaign,
start_day=100,
coverage=0.6,
age_dependence=kariba_itn_age_dependence,
seasonal_dependence=kariba_itn_seasonal_dependence,
discard_config=kariba_itn_discard_rates,
triggers=["Births"],
node_ids=[1])
#fixme This was generating a bug. Test looking into this.
campaign.add(fancier_bednet_distribution)
campaign.add(fancier_bednet_distribution_with_birth_trigger)
def set_random_campaign_file(campaign_filename="campaign.json", campaign_template_filename= "campaign_template.json", debug = False):
durations = generate_durations(NUM_OF_BUCKETS, MAX_DURATION)
if sum(durations) != MAX_DURATION:
print( "total duration is {0}, expected {1}.\n".format(sum(durations), MAX_DURATION))
ip.durations = durations
rates = generate_rates(NUM_OF_BUCKETS,MAX_RATE)
ip.daily_import_pressures = rates
ip.nodes = [ 3, 5, 7 ]
print( "Calling ip.new_intervention_as_file." )
#camp_filename = ip.new_intervention_as_file(1, campaign_filename)
event = ip.new_intervention(1, durations, rates, [ 3, 5, 7 ] )
camp.add( event )
camp.save( campaign_filename )
if debug:
print("durations are : {}.\n".format(durations))
print("daily inport pressures are : {}.\n".format(rates))
return campaign_filename
def add_drug_interventions(campaign):
mda_event = add_drug_campaign(campaign,
campaign_type='MDA',
drug_code='DP',
start_days=[50],
coverage=0.5)
msat_event = add_drug_campaign(campaign,
campaign_type='MSAT',
drug_code='AL',
diagnostic_type='BLOOD_SMEAR_PARASITES',
diagnostic_threshold=0,
start_days=[75],
coverage=0.8)
# healthseeking_event = add_healthseeking()
#fixme couldn't find this function
campaign.add(mda_event)
campaign.add(msat_event)
def build_camp():
"""
Build a campaign input file for the DTK using emod_api.
Right now this function creates the file and returns the filename. If calling code just needs an asset that's fine.
"""
import emod_api.campaign as camp
import emodpy_covid.interventions.covid_vaccine as cv # will move to emodpy_covid
import emodpy_covid.interventions.complex_import as ci # will move to emodpy_measles
# This isn't desirable. Need to think about right way to provide schema (once)
cv.schema_path = manifest.schema_file
ci.schema_path = manifest.schema_file
print(f"Telling emod-api to use {manifest.schema_file} as schema.")
# importation pressure
event = cv.SimpleSample1(timestep=0)
camp.add(event, first=True)
# routine immunization
event = cv.SimpleSample2(timestep=365, coverage=0.5)
camp.add(event)
event = ci.ComplexImportationEvent(dips=[1. / 10],
durs=[20 * 365],
timestep=0)
camp.add(event)
# We are saving and reloading. Maybe there's an even better way? But even an outbreak seeding does not belong in the EMODTask.
filename = "campaign.json"
camp.save(filename)
print(f"Check for valid campaign file at: {filename}.")
return filename
def build_camp():
"""
Build a campaign input file for the DTK using emod_api.
Right now this function creates the file and returns the filename. If calling code just needs an asset that's fine.
"""
import emod_api.campaign as camp
import emodpy_measles.interventions.measles_vaccine as mv # will move to emodpy_measles
import emodpy_measles.interventions.complex_import as ci # will move to emodpy_measles
import emodpy_measles.interventions.simple_sia as sia # will move to emodpy_measles
import emodpy_measles as meas
# This isn't desirable. Need to think about right way to provide schema (once)
mv.schema_path = manifest.schema_file
ci.schema_path = manifest.schema_file
sia.schema_path = manifest.schema_file
print(f"Telling emod-api to use {manifest.schema_file} as schema.")
# importation pressure
event = ci.ComplexImportationEvent(dips=[1. / 10],
durs=[20 * 365],
timestep=0)
camp.add(event, first=True)
# routine immunization
event = mv.SimpleMCV1(timestep=0, coverage=0.5)
camp.add(event)
# SIAs
SIAs = meas.ConstructHistoricalCampaigns()
SIA_count = 0
for SIA in SIAs:
if (SIA.region == 'north') or (SIA.region) == 'all':
SIA_count += 1
event = sia.SimpleSIA(Event_Name=f'SIA_{SIA_count}',
timestep=SIA.startday.toordinal() -
SIA.startday.toordinal())
camp.add(event)
# We are saving and reloading. Maybe there's an even better way? But even an outbreak seeding does not belong in the EMODTask.
filename = "campaign_kb_example.json"
camp.save(filename)
print(f"Check for valid campaign file at: {filename}.")
return filename
def add_irs(campaign):
irs_spray_event = IRSHousingModification(campaign,
start_day=200,
coverage=0.8,
node_ids=[2])
campaign.add(irs_spray_event)