def run_phase_1(model, region, n_samples, params):
model_class = import_from('epidemics.' + model, 'Model')
params['country'] = region
print('[Phase 1] Running {}'.format(region))
a = model_class(**params)
a.sample(n_samples)
a.propagate()
a.save()
a.plot_intervals(ns=20)
def propagation(model, region, phase_3_path):
n_samples = 1
dataFolder = phase_3_path
params = {
'dataFolder': dataFolder,
'preprocess': True,
'nThreads': 12,
'nPropagation': 100,
'futureDays': 2,
'nValidation': 0,
'percentages': [0.5, 0.95, 0.99],
'silent': False
}
model_class = import_from('epidemics.' + model, 'Model')
params['country'] = region
a = model_class(**params)
a.load_parameters(phase_3_path + '/_korali_samples/')
a.propagate()
a.save()
a.plot_intervals(ns=20)
type=int,
default=0,
help=
'Use that many data from the end of the data list to validate the prediction.'
)
parser.add_argument('--percentages',
'-p',
nargs='+',
type=float,
default=[0.5, 0.95, 0.99],
help='Percentages for confidence intervals.')
parser.add_argument('--silent',
action='store_true',
help='No output on screen.')
parser.add_argument('--silentPlot',
'-sp',
action='store_true',
help='Close plot window after plot.')
args = parser.parse_args()
x = copy.deepcopy(args)
del x.compModel
del x.nSamples
del x.nGenerations
model_class = import_from('epidemics.' + args.compModel, 'Model')
a = model_class(**vars(x))
a.least_squares(args.nGenerations)
default='switzerland',
help='Country from which to retrieve data./')
parser.add_argument('--lastDay',
'-ld',
default='2020-06-15',
help='Last day of data sequence in format %Y-%m-%d./')
parser.add_argument('--silentPlot',
'-sp',
action='store_true',
help='Close plot window after plot.')
parser.add_argument('--preprocess',
'-pre',
type=bool,
default=False,
help='Preprocessing.')
args = parser.parse_args()
obs = []
obs.append('infections')
obs.append('deaths')
x = copy.deepcopy(args)
x.observations = obs
model_class = import_from('epidemics.country.reparam.sird_int.nbin', 'Model')
a = model_class(**vars(x))
a.fit_curve()
