def sample_anthrop_and_outdoor(cb, species, anthropophily, outdoor) :
update_species_param(cb, species, 'Anthropophily', anthropophily)
update_species_param(cb, species, 'Indoor_Feeding_Fraction', 1-outdoor)
return { '%s_Anthropophily' % species : anthropophily,
'%s_Outdoor_Fraction' % species : outdoor}
def update_vector_params(cb):
set_params_by_species(cb.params, ['minimus', 'dirus'])
update_species_param(cb,
'minimus',
'Larval_Habitat_Types', {'WATER_VEGETATION': 2e7},
overwrite=True)
update_species_param(cb,
'minimus',
'Acquire_Modifier',
0.8,
overwrite=False)
update_species_param(cb,
'minimus',
'Adult_Life_Expectancy',
25,
overwrite=False) # target: 12
update_species_param(cb,
'dirus',
'Larval_Habitat_Types', {
'CONSTANT': 1e7,
'TEMPORARY_RAINFALL': 7e7
},
overwrite=True)
update_species_param(cb,
'dirus',
'Adult_Life_Expectancy',
30,
overwrite=False) # target: 14
update_species_param(cb, 'minimus', 'Anthropophily', 0.5, overwrite=False)
update_species_param(cb, 'dirus', 'Anthropophily', 0.5, overwrite=False)
capacity_dist_per_year = {
"Times": [0, 1, 245, 275, 364],
"Values": [0.2, 0.2, 0.7, 3, 3]
}
linear_spline = {
"LINEAR_SPLINE": {
"Capacity_Distribution_Number_Of_Years": 1,
"Capacity_Distribution_Over_Time": capacity_dist_per_year,
"Max_Larval_Capacity": 3e7
}
}
update_species_param(cb,
'minimus',
'Larval_Habitat_Types',
linear_spline,
overwrite=False)
from dtk.vector.species import set_larval_habitat
from simtools.SetupParser import SetupParser
from spline_functions import *
# from .spline_functions import get_spline_values_for_all_params, get_annual_representative_spline, \
# get_representative_spline_multipiers
from dtk.interventions.novel_vector_control import add_ATSB
from ATSBEntoCalibSite import ATSBEntoCalibSite
# Which simtools.ini block to use for this calibration
SetupParser.default_block = 'HPC'
# Start from a base MALARIA_SIM config builder
# This config builder will be modify by the different sites defined below
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
update_species_param(cb, 'gambiae', 'Indoor_Feeding_Fraction', 0.5)
update_species_param(cb, 'funestus', 'Indoor_Feeding_Fraction', 0.9)
update_species_param(cb, 'gambiae', 'Vector_Sugar_Feeding_Frequency', 'VECTOR_SUGAR_FEEDING_EVERY_DAY', overwrite=False)
update_species_param(cb, 'gambiae', 'Anthropophily', 0.8)
update_species_param(cb, 'gambiae', 'Adult_Life_Expectancy', 20)
datadir = 'C:\\Users\\jkurlander\\Dropbox (IDM)'
# List of sites we want to calibrate on
throwaway = 1
species = 'gambiae'
reference_fname = 'cluster_mosquito_counts_per_house_by_month.csv'
reference_spline = 'Multi_year_calibration_by_HFCA_180404/best_180409/Panjane_funestus.csv'
irs_fn = os.path.join(datadir,
'Malaria Team Folder/projects/Mozambique/entomology_calibration/cluster_all_irs_events_pyrethroid_2014.csv')
itn_fn = os.path.join(datadir,
exp_name = 'atsb_killing_coverage_test'
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb, 'Namawala')
species = 'gambiae'
cb.update_params({
'Config_Name': 'ATSB_Test_Namawala',
'Simulation_Duration': 365,
'Vector_Species_Names': [species]
})
update_species_param(cb,
species,
'Vector_Sugar_Feeding_Frequency',
'VECTOR_SUGAR_FEEDING_EVERY_DAY',
overwrite=False)
def atsb_fn(cb, coverage, killing):
killing_cfg = [{
"Species": 'funestus',
"Killing_Config": {
"class": "WaningEffectMapLinearSeasonal",
"Initial_Effect": 1.0,
"Durability_Map": {
"Times": [0.0, 90.0, 91.0, 300.0, 301.0, 365.0],
"Values": [1.0, 1.0, 0.01, 0.01, 1.0, 1.0]
}