def add_summary_report(cb, start_day=0):
summary_report_fn(start=start_day + 1,
interval=1.0,
description='Daily_Report',
age_bins=[5.0, 15.0, 100.0])(cb)
return None
def add_summary_report(cb, start_day=0):
'''
Add daily summary report to output
:param cb: config builder
:param start_day: start day for report
:return: None
'''
summary_report_fn(start=start_day+1, interval=1.0, description='Daily_Report',
age_bins=[5.0, 10.0, 100.0])(cb)
return None
def get_setup_functions(self):
setup_fns = super(SugungumAgeSeasonCalibSiteBabies,
self).get_setup_functions()
setup_fns.append(config_setup_fn(duration=365 *
2)) # 60 years (with leap years)
setup_fns.append(
summary_report_fn(
start=365,
interval=365.0 / 12,
description='Monthly_Report',
parasitemia_bins=[0.0, 16.0, 70.0, 409.0, 4000000.0],
age_bins=[1.0, 4.0, 8.0, 18.0, 28.0, 43.0, 400000.0]))
setup_fns.append(site_input_eir_fn(self.name, birth_cohort=True))
setup_fns.append(lambda cb: cb.update_params({
'Demographics_Filenames':
['Calibration\\birth_cohort_demographics_babies.json'],
'Age_Initialization_Distribution_Type':
'DISTRIBUTION_SIMPLE',
'Base_Population_Scale_Factor':
10,
'Birth_Rate_Dependence':
'FIXED_BIRTH_RATE',
"Death_Rate_Dependence":
"NONDISEASE_MORTALITY_OFF",
'Enable_Birth':
1,
'Enable_Vital_Dynamics':
1,
'Maternal_Antibodies_Type':
'SIMPLE_WANING',
}))
return setup_fns
def get_setup_functions(self):
setup_fns = super(DapelogoInfCalibSite, self).get_setup_functions()
setup_fns.append(config_setup_fn(duration=365 *
5)) # 60 years (with leap years)
setup_fns.append(survey_report_fn(days=15, interval=1.0))
setup_fns.append(
summary_report_fn(
interval=365.0 / 12,
description='Monthly_Report',
parasitemia_bins=[0, 50, 500, 5000, 50000, 5000000],
age_bins=[5, 15, 100]))
setup_fns.append(
add_treatment_fn(start=0,
drug=['Artemether'],
targets=[{
'trigger': 'NewClinicalCase',
'coverage': 1,
'seek': 0.15,
'rate': 0.3
}]))
setup_fns.append(site_input_eir_fn(self.name, birth_cohort=True))
setup_fns.append(lambda cb: cb.update_params({
'Demographics_Filenames':
['Calibration\\birth_cohort_demographics.compiled.json']
}))
return setup_fns
def get_setup_functions(self):
return [
config_setup_fn(duration=21915), # 60 years (with leap years)
summary_report_fn(interval=30, description='Monthly_Report'
), # TODO: reconcile with 365/12 monthly EIR
add_treatment_fn(),
site_input_eir_fn(self.name, birth_cohort=True)
]
def get_setup_functions(self):
setup_fns = super(NdiopCalibSite, self).get_setup_functions()
setup_fns.append(config_setup_fn(duration=365 * 70 + 1)) # 60 years (with leap years)
setup_fns.append(summary_report_fn(start=0, interval=365.0, age_bins=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 60, 100]))
setup_fns.append(site_input_eir_fn(self.name, birth_cohort=True))
setup_fns.append(add_treatment_fn(start=0, drug=['Artemether'],
targets=[{'trigger': 'NewClinicalCase',
'coverage': 1, 'seek': 0.5, 'rate': 0.3}]))
setup_fns.append(update_params({'Demographics_Filenames': ['Calibration\\birth_cohort_demographics.compiled.json']}))
return setup_fns
def get_setup_functions(self):
setup_fns = super(RafinMarkeAgeSeasonCalibSite,
self).get_setup_functions()
setup_fns.append(config_setup_fn(duration=365 *
70)) # 60 years (with leap years)
setup_fns.append(
summary_report_fn(
interval=365.0 / 12,
description='Monthly_Report',
#parasitemia_bins=[0.0, 16.0, 70.0, 409.0, 4000000.0],
age_bins=[1.0, 4.0, 8.0, 18.0, 28.0, 43.0, 400000.0]))
setup_fns.append(site_input_eir_fn(self.name, birth_cohort=True))
setup_fns.append(
update_params({
'Demographics_Filenames':
['Calibration\\birth_cohort_demographics.compiled.json']
}))
return setup_fns
def get_setup_functions(self):
setup_fns = super(DapelogoInfectiousnessCalibSite,
self).get_setup_functions()
setup_fns.append(config_setup_fn(duration=365 *
70)) # 60 years (with leap years)
setup_fns.append(
summary_report_fn(
interval=365.0 / 12,
description='Monthly_Report',
parasitemia_bins=[0, 0.5, 5, 50, 500, 5000, 50000, 500000],
infection_bins=[0, 5, 20, 50, 80, 100],
age_bins=[5, 15, 100]))
setup_fns.append(site_input_eir_fn(self.name, birth_cohort=True))
setup_fns.append(lambda cb: cb.update_params({
'Demographics_Filenames':
['Calibration\\birth_cohort_demographics.compiled.json'],
'Antigen_Switch_Rate_LOG':
-9.530186548,
'Base_Gametocyte_Production_Rate':
0.024177457,
'Falciparum_MSP_Variants':
6,
'Falciparum_Nonspecific_Types':
56,
'Falciparum_PfEMP1_Variants':
1473,
'Gametocyte_Stage_Survival_Rate':
0.667841154,
'MSP1_Merozoite_Kill_Fraction':
0.444193352,
'Max_Individual_Infections':
3,
'Nonspecific_Antigenicity_Factor':
0.262812768
}))
return setup_fns
def get_setup_functions(self):
return [
config_setup_fn(duration=21915), # 60 years (with leap years)
summary_report_fn(interval=365),
site_input_eir_fn(self.name, birth_cohort=True)
]
def get_setup_functions(self):
return [
summary_report_fn(start=50*365),
lambda cb: cb.update_params( { 'logLevel_LarvalHabitatMultiplier' : 'WARNING'})
]
