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'}) ]