force_apply=True # Set to True to re-download and call "apply" again
)
]
#
# ***************************** END PRINCIPAL SECTION OF THIS EXAMPLE ****************************
#
# dtk analyze compatibility
site = sites[0]
analyzers = site.analyzers
# Restrict to only those params that are initially active
params = [p for p in params if p['Dynamic']]
plotters = [LikelihoodPlotter(), OptimToolPlotter()]
# Setting up our model configuration from templates
dir_path = os.path.dirname(os.path.realpath(__file__))
template_files_dir = os.path.join(dir_path, 'Templates')
static_files_dir = os.path.join(dir_path, 'Static')
demog = DemographicsTemplate.from_file(
os.path.join(static_files_dir, 'Rakai_Demographics_With_Properties.json'))
demog_pfa = DemographicsTemplate.from_file(
os.path.join(template_files_dir, 'PFA_Overlay.json'))
demog_acc = DemographicsTemplate.from_file(
os.path.join(template_files_dir, 'Accessibility_and_Risk_IP_Overlay.json'))
demog_asrt = DemographicsTemplate.from_file(
os.path.join(template_files_dir, 'Risk_Assortivity_Overlay.json'))
referenceData = 'C:/Users/jkurlander/Dropbox (IDM)/Malaria Team Folder/projects/atsb/Reference_data/HLCIntervention.csv'
hfca = 'Kangaba'
sites = [ATSBEntoCalibSite(species, hfca=hfca, throwaway=throwaway,
reference_fname = referenceData)]
# WaningEffectMapPiecewise (Seasonal), WaningEffectConstant, WaningEffectExponential, WaningEffectBoxExponential
Class = "WaningEffectConstant"
expname = 'Mali ATSB Calibration ' + str(Class) + ' HLC'
max_iterations = 5
max_diff = 0.5
max_frac_diff = 0.05
# The default plotters used in an Optimization with OptimTool
# plotters = [LikelihoodPlotter(combine_sites=True),
plotters = [SiteDataPlotter(num_to_plot=20, combine_sites=True),
OptimToolPlotter() # OTP must be last because it calls gc.collect()
]
#############################################################################################################
ref = sites[0].analyzers[0].reference.copy()
duration = 1#int(max(ref.reset_index()['Month'])/12) + 1
params = [
{
#% of mosquitoes killed per day
'Name': 'KillingProfile',
'Dynamic': True,
'Guess': 0.0337,
'Min': 0.0,
# This config builder will be modify by the different sites defined below
cb = CMSConfigBuilder.from_files(
model_file='base/core-model-with-age-groups.emodl',
config_file='base/with-age-groups.cfg')
try:
cb.set_collection_id('CMS 0.82 Pre-release')
except SimulationAssets.InvalidCollection:
cb.set_experiment_executable('../inputs/compartments/compartments.exe')
cb.set_dll_root('../inputs/compartments')
# List of sites we want to calibrate on
sites = [CMSSite()]
# The default plotters used in an Optimization with OptimTool
plotters = [OptimToolPlotter()]
params = [{
'Name': 'initial_S_A04',
'Dynamic': True,
'Guess': 4879554,
'Min': 4800000,
'Max': 4900000
}, {
'Name': 'initial_I_A04',
'Dynamic': True,
'Guess': 7608,
'Min': 2000,
'Max': 10000
}]