def sweep_coverages(cb, coverage):
add_health_seeking(cb,
start_day=0,
drug=['DHA', 'Piperaquine'],
targets=[{
'trigger': 'NewClinicalCase',
'coverage': coverage[0],
'agemin': 0,
'agemax': 5,
'seek': 1,
'rate': 0.3
}, {
'trigger': 'NewClinicalCase',
'coverage': coverage[1],
'agemin': 10,
'agemax': 200,
'seek': 1,
'rate': 0.3
}, {
'trigger': 'NewSevereCase',
'coverage': 0.30,
'agemin': 0,
'agemax': 200,
'seek': 1,
'rate': 0.3
}]),
return {'coverage_pair': coverage}
def fn(self, cb):
with open(self.reffname) as fin:
cov = json.loads(fin.read())
for hscov in cov['hscov']:
targets = [{
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 15,
'agemax': 200,
'seek': hscov['coverage'],
'rate': 0.3
}, {
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 0,
'agemax': 15,
'seek': min([1, hscov['coverage'] * 1.5]),
'rate': 0.3
}, {
'trigger': 'NewSevereCase',
'coverage': 1,
'seek': 0.8,
'rate': 0.5
}]
add_health_seeking(cb,
start_day=self.start,
targets=targets,
nodes={
'Node_List': hscov['nodes'],
"class": "NodeSetNodeList"
})
def add_healthseeking_by_coverage(cb, coverage=1.0, rate=0.15, drugname="AL"):
drugs = {
"AL": ["Artemether", "Lumefantrine"],
"DP": ["DHA", "Piperaquine"]
}
add_health_seeking(cb,
targets=[{
"trigger": "NewClinicalCase",
"coverage": coverage,
"agemin": 0,
"agemax": 100,
"seek": 1.0,
"rate": rate
}],
drug=drugs[drugname],
dosing="FullTreatmentNewDetectionTech",
nodes={"class": "NodeSetAll"},
repetitions=1,
tsteps_btwn_repetitions=365,
broadcast_event_name="Received_Treatment")
return {
"CM_Coverage": coverage,
"CM_Daily_Prob": rate,
"CM_Drug": drugname
}
def fn(self, cb):
add_health_seeking(
cb,
start_day=self.start,
drug=self.drug,
targets=self.targets,
nodes=self.nodes,
drug_ineligibility_duration=self.durg_ineligibility_duration,
node_property_restrictions=self.node_property_restrictions)
cb.update_params({'PKPD_Model': 'CONCENTRATION_VERSUS_TIME'})
def seasonal_health_seeking(self, cb):
with open(self.fname) as fin:
cov = json.loads(fin.read())
for i, hscov in enumerate(cov[self.channel]):
code = 'group%d' % i
ad_cov = hscov['coverage']
kid_cov = min([1, hscov['coverage'] * 1.5])
sev_cov = 0.8
for start_month in range(len(self.scale_by_month)):
start_day = int(self.date +
np.cumsum(self.days_in_month)[start_month])
duration = self.days_in_month[start_month + 1]
scale = self.scale_by_month[start_month]
targets = [{
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 15,
'agemax': 200,
'seek': min([1, ad_cov * scale]),
'rate': 0.3
}, {
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 0,
'agemax': 15,
'seek': min([1, kid_cov * scale]),
'rate': 0.3
}, {
'trigger':
'NewSevereCase',
'coverage':
1,
'seek':
min([1, max([sev_cov * scale, kid_cov * scale])]),
'rate':
0.5
}]
add_health_seeking(cb,
start_day=start_day,
targets=targets,
duration=duration,
repetitions=self.duration_years + 1,
drug_ineligibility_duration=14,
node_property_restrictions=[{
self.prop_name:
code
}])
def fn(self, cb):
with open(self.reffname) as fin:
cov = json.loads(fin.read())
for hscov in cov['hscov']:
ad_cov = hscov['coverage']
kid_cov = min([1, hscov['coverage'] * 1.5])
sev_cov = 0.8
for start_month in range(len(self.scale_by_month)):
start_day = self.start + np.cumsum(
self.days_in_month)[start_month]
duration = self.days_in_month[start_month + 1]
scale = self.scale_by_month[start_month]
targets = [{
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 15,
'agemax': 200,
'seek': min([1, ad_cov * scale]),
'rate': 0.3
}, {
'trigger': 'NewClinicalCase',
'coverage': 1,
'agemin': 0,
'agemax': 15,
'seek': min([1, kid_cov * scale]),
'rate': 0.3
}, {
'trigger':
'NewSevereCase',
'coverage':
1,
'seek':
min([1, max([sev_cov * scale, kid_cov * scale])]),
'rate':
0.5
}]
add_health_seeking(cb,
start_day=start_day,
targets=targets,
duration=duration,
repetitions=-1,
drug_ineligibility_duration=14,
nodes={
'Node_List': hscov['nodes'],
"class": "NodeSetNodeList"
})
def configure_health_seeking(cb, pull_from_serialization, village_nodes, set_forest_HS=True) :
if pull_from_serialization :
add_health_seeking(cb, start_day=0,
drug=['Artemether', 'Lumefantrine'],
nodes=village_nodes,
targets=[
{'trigger': 'NewClinicalCase', 'coverage': 0.8, 'agemin': 0, 'agemax': 10, 'seek': 1,
'rate': 0.3},
{'trigger': 'NewClinicalCase', 'coverage': 0.7, 'agemin': 10, 'agemax': 100, 'seek': 1,
'rate': 0.3},
{'trigger': 'NewSevereCase', 'coverage': 0.95, 'agemin': 0, 'agemax': 100, 'seek': 1,
'rate': 0.3}],
ind_property_restrictions=[{'ForestGoing' : 'HatesForest'}]
)
if set_forest_HS :
add_health_seeking(cb, start_day=0,
drug=['Artemether', 'Lumefantrine'],
nodes=village_nodes,
targets=[
{'trigger': 'NewClinicalCase', 'coverage': 0.4, 'seek': 1, 'rate': 0.2}],
ind_property_restrictions=[{'ForestGoing': 'LovesForest'}]
)
else :
add_health_seeking(cb, start_day=0,
drug=['Artemether', 'Lumefantrine'],
nodes=village_nodes,
targets=[
{'trigger': 'NewClinicalCase', 'coverage': 0.4, 'agemin': 0, 'agemax': 5, 'seek': 1,
'rate': 0.3},
{'trigger': 'NewClinicalCase', 'coverage': 0.2, 'agemin': 5, 'agemax': 100, 'seek': 1,
'rate': 0.3},
{'trigger': 'NewSevereCase', 'coverage': 0.5, 'agemin': 0, 'agemax': 100, 'seek': 1,
'rate': 0.3}]
)
def add_simple_hs(cb, u5_hs_rate, o5_hs_rate=-1, start_day=1, duration=-1):
if o5_hs_rate == -1:
o5_hs_rate = u5_hs_rate * 0.5
target_list = [{
'trigger': 'NewClinicalCase',
'coverage': u5_hs_rate,
'agemin': 0,
'agemax': 5,
'seek': 1,
'rate': 0.3
}, {
'trigger': 'NewClinicalCase',
'coverage': o5_hs_rate,
'agemin': 5,
'agemax': 100,
'seek': 1,
'rate': 0.3
}, {
'trigger': 'NewSevereCase',
'coverage': 0.9,
'agemin': 0,
'agemax': 5,
'seek': 1,
'rate': 0.5
}, {
'trigger': 'NewSevereCase',
'coverage': 0.8,
'agemin': 5,
'agemax': 100,
'seek': 1,
'rate': 0.5
}]
add_health_seeking(cb,
start_day=start_day,
targets=target_list,
drug=['Artemether', 'Lumefantrine'],
duration=duration)
def add_simple_hs(cb, u5_hs_rate, o5_hs_rate=-1):
if o5_hs_rate == -1:
o5_hs_rate = u5_hs_rate * 0.5
add_health_seeking(cb,
start_day=1,
targets=[{'trigger': 'NewClinicalCase',
'coverage': u5_hs_rate,
'agemin': 0,
'agemax': 5,
'seek': 1,
'rate': 0.3},
{'trigger': 'NewClinicalCase',
'coverage': o5_hs_rate,
'agemin': 5,
'agemax': 100,
'seek': 1,
'rate': 0.3},
{'trigger': 'NewSevereCase',
'coverage': 0.9,
'agemin': 0,
'agemax': 5,
'seek': 1,
'rate': 0.5},
{'trigger': 'NewSevereCase',
'coverage': 0.8,
'agemin': 5,
'agemax': 100,
'seek': 1,
'rate': 0.5}],
drug=['Artemether', 'Lumefantrine'],
dosing='FullTreatmentNewDetectionTech')
return {"u5_hs_rate": u5_hs_rate,
"o5_hs_rate": o5_hs_rate}
def add_hs(cb, events_df):
hs_field_list = [
"cov_newclin_youth", "cov_newclin_adult", "cov_severe_youth",
"cov_severe_adult", "duration"
]
binned_intervene_events, binned_and_grouped, data_fields = try_campaign_compression(
events_df, hs_field_list)
for table, group in binned_and_grouped:
table_dict = dict(zip((data_fields), table))
node_list = sorted(group['grid_cell'])
node_dict = {"class": "NodeSetNodeList", "Node_List": node_list}
add_health_seeking(cb,
start_day=table_dict['simday'],
targets=[{
'trigger':
'NewClinicalCase',
'coverage':
float(table_dict['cov_newclin_youth']),
'agemin':
0,
'agemax':
5,
'seek':
1,
'rate':
0.3
}, {
'trigger':
'NewClinicalCase',
'coverage':
float(table_dict['cov_newclin_adult']),
'agemin':
5,
'agemax':
100,
'seek':
1,
'rate':
0.3
}, {
'trigger':
'NewSevereCase',
'coverage':
float(table_dict['cov_severe_youth']),
'agemin':
0,
'agemax':
5,
'seek':
1,
'rate':
0.5
}, {
'trigger':
'NewSevereCase',
'coverage':
float(table_dict['cov_severe_adult']),
'agemin':
5,
'agemax':
100,
'seek':
1,
'rate':
0.5
}],
drug=['Artemether', 'Lumefantrine'],
dosing='FullTreatmentNewDetectionTech',
nodes=node_list,
duration=table_dict['duration'])
vector_stats_report = 0
malaria_summary_report = 0
add_reporters(cb, vector_genetics_report=vector_genetics_report)
############################## HEALTH SEEKING ###########################################
# Health seeking
add_health_seeking(cb,
targets=[{'trigger': 'NewClinicalCase',
'coverage': 0.5,
'agemin': 0,
'agemax': 100,
'seek': 1,
'rate': 0.3},
{'trigger': 'NewSevereCase',
'coverage': 0.8,
'agemin': 0,
'agemax': 100,
'seek': 1,
'rate': 0.5}
],
drug=['Artemether', 'Lumefantrine'],
start_day=0,
broadcast_event_name='Received_Treatment')
##########################################################################################
run_sim_args = {'config_builder': cb,
'exp_name': exp_name,
'exp_builder': builder}
def add_intervention(cb, intervention, coverage, target, ivm_duration) :
IPR = [{'HomeVillage' : 'Village1'}] if target == 'vill1' else None
if intervention == 'ivermectin_to_forest' :
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage, start_days=[365],
trigger_condition_list=['Immigrating'],
nodeIDs=forest_nodes,
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_to_forest' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365],
repetitions=1,
trigger_condition_list=['Immigrating'],
nodeIDs=forest_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_MDA' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365 + 152],
repetitions=3, tsteps_btwn_repetitions=30,
nodeIDs=village_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_ivermectin_MDA' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365 + 152],
repetitions=3, tsteps_btwn_repetitions=30,
nodeIDs=village_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
nodeIDs=village_nodes,
target_residents_only=False
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 51, 'agemax': 200, 'gender': 'Female'},
nodeIDs=village_nodes,
target_residents_only=False
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 5, 'agemax': 12, 'gender': 'Female'},
nodeIDs=village_nodes,
target_residents_only=False
)
elif intervention == 'ivermectin_MDA' :
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 51, 'agemax': 200, 'gender': 'Female'},
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 5, 'agemax': 12, 'gender': 'Female'},
target_residents_only=False,
ind_property_restrictions=IPR
)
forest_HS_coverage = coverage if intervention == 'forest_HS' else 0.4
add_health_seeking(cb, start_day=0,
drug=['Artemether', 'Lumefantrine'],
nodes=village_nodes,
targets=[
{'trigger': 'NewClinicalCase', 'coverage': forest_HS_coverage, 'seek': 1, 'rate': 0.2}],
ind_property_restrictions=[{'ForestGoing': 'LovesForest'}]
)
event_trigger_list=['Received_Treatment']
if 'ivermectin' in intervention :
event_trigger_list.append('Received_Ivermectin')
if 'drug' in intervention :
event_trigger_list.append('Received_Campaign_Drugs')
add_event_counter_report(cb, event_trigger_list=event_trigger_list)
return { 'intervention' : intervention,
'coverage' : coverage,
'target' : target,
'IVM duration' : ivm_duration}
