Delete r0_calc.py

r0_calc.py

-import numpy as np
-from scipy import optimize as opt
-
-from covid.rdata import *
-from covid.model import CovidUKODE
-
-if __name__=='__main__':
-
-    K, _ = load_age_mixing('data/polymod_normal_df.rds')
-    T, _ = load_mobility_matrix('data/movement.rds')
-    np.fill_diagonal(T, 0.)
-    N, _ = load_population('data/pop.rds')
-
-    model = CovidUKODE(K, T, N)
-
-    print("R0 (beta=0.036) = ",  model.eval_R0({'beta1': 0.036, 'beta2': 0.33, 'gamma': 0.25}))
-    R0 = 2.4
-
-    def opt_fn(beta, R0):
-        r0, i = model.eval_R0({'beta1': beta, 'beta2': 0.33, 'gamma': 0.25}, 1e-9)
-        return (r0 - R0)**2
-
-    res = opt.minimize_scalar(opt_fn, args=R0)
-    print(res['x'])