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)
