def standard_cb_updates(cb, years): cb.update_params({ 'Simulation_Duration': 365 * years, 'x_Temporary_Larval_Habitat': 0.2, 'Base_Population_Scale_Factor': 0.1, }) cb.update_params({ # Demographics 'Birth_Rate_Dependence': 'FIXED_BIRTH_RATE', "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER", "Demographics_Filenames": ['single_node_demographics.json'], # Individual/Node Properties "Disable_IP_Whitelist": 1, "Enable_Vital_Dynamics": 1, "Enable_Birth": 1, 'Enable_Default_Reporting': 1, # Misc 'logLevel_default': 'ERROR', 'Enable_Demographics_Other': 0 }) # Set climate set_climate_constant(cb)
def prepare_malariatherapy_configbuilder(config_path, immunity_forcing=True, years=1): # Setup ------------------------------------------------------------------------------------------- cb = DTKConfigBuilder.from_files(config_path) cb.update_params({ 'Vector_Species_Names': [], 'Simulation_Duration': 365 * years, 'Demographics_Filenames': ['Malariatherapy_demographics.json'] }) set_climate_constant(cb) # Add source of infection (challenge bite or forced EIR) ------------------------------------------ add_challenge_trial(cb, start_day=0) # ---- CUSTOM REPORTS ---- add_patient_report(cb) return cb
return None if __name__ == "__main__": expname = 'vector_genetics_single_node_no_introgression' sim_duration = 365 * 10 num_seeds = 50 SetupParser('HPC') cb = DTKConfigBuilder.from_defaults('VECTOR_SIM') set_climate_constant(cb) set_species_param(cb, 'arabiensis', 'Larval_Habitat_Types', {"CONSTANT": 11250000000}) set_species_param(cb, 'arabiensis', 'Male_Life_Expectancy', 5) set_species_param(cb, 'arabiensis', 'Adult_Life_Expectancy', 10) set_species_param(cb, 'arabiensis', 'Transmission_Rate', 0.5) set_species_param(cb, 'arabiensis', 'Indoor_Feeding_Fraction', 1.0) set_species_param(cb, 'funestus', 'Larval_Habitat_Types', {"CONSTANT": 11250000000}) set_species_param(cb, 'funestus', 'Male_Life_Expectancy', 5) set_species_param(cb, 'funestus', 'Adult_Life_Expectancy', 10) set_species_param(cb, 'funestus', 'Transmission_Rate', 0.5) set_species_param(cb, 'funestus', 'Indoor_Feeding_Fraction', 1.0) ########################## VECTOR GENETICS ####################################################
def test_bad_climate_param(self): self.assertRaises( Exception, lambda: set_climate_constant(self.cb, Not_A_Climate_Parameter=26))
def test_constant_climate(self): set_climate_constant(self.cb, Base_Air_Temperature=26, Base_Rainfall=3) self.assertEqual(self.cb.get_param('Climate_Model'), 'CLIMATE_CONSTANT') self.assertEqual(self.cb.get_param('Base_Air_Temperature'), 26) self.assertEqual(self.cb.get_param('Base_Rainfall'), 3)