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 }]