diff --git a/covid/python/seir.py b/covid/python/seir.py index 6411cb360493384b8132d1474d690ba59a6ac046..bcb3847e1913eb52aef4a722f55abe8e45200049 100644 --- a/covid/python/seir.py +++ b/covid/python/seir.py @@ -1,20 +1,14 @@ import numpy as np import matplotlib.pyplot as plt +import functools swiss = np.array([2.100350058, 3.150525088, 4.900816803, 6.534422404, 10.501750292, 13.302217036, 24.970828471, 31.271878646, 39.323220537, 43.640606768, 57.292882147, 76.079346558, 100.116686114, 131.271878646, 158.576429405, 256.709451575, 256.709451575, 268.378063011, 309.218203034, 353.325554259, 453.675612602]) swiss = np.array([18, 27, 42, 56, 90, 114, 214, 268, 337, 374, 491, 652, 858, 1125, 1359, 2200, 2200, 2300, 2650, 3028, 3888]) days = np.array(range(1,len(swiss)+1)) -R_0 = 4.26 -R_01 = 4.26 -R_02 = 1 - 1/R_01 - -Tinf = 7.0 -Tinc = 5.1 -N = 8000000.0 - -def seir(y, t): +def seir(y, t, R_0, Tinf, Tinc): + N = np.sum(y) y1 = np.zeros(4) y1[0] = - R_0 / Tinf * y[2] * y[0] / N y1[1] = R_0 / Tinf * y[2] * y[0] / N - 1.0 / Tinc * y[1] @@ -30,15 +24,23 @@ def rk4(F, y, t, dt): k4 = dt * F(y + k3, t + dt) return y + (k1 + 2 * (k2 + k3) + k4) / 6 -I0 = 0 -E0 = swiss[0] +R_0 = 4.26 +R_01 = 4.26 +R_02 = 1 - 1/R_01 + +Tinf = 7.0 +Tinc = 5.1 +N = 500000 + +I0 = 214 / 0.2 +E0 = 2000 R0 = 0 S0 = N-E0-I0 -t0 = -Tinc +t0 = 24 # max_t = 5*days[len(swiss)-1] max_t = 2000 -n_steps = 1000000 +n_steps = 100000 dt = max_t / n_steps y0 = np.array([S0, E0, I0, R0]) @@ -47,10 +49,11 @@ y_list = [y0] t_list = [t0] for i in range(0, n_steps): t = t_list[i] + dt - y1 = rk4(seir, y_list[i], t, dt) + foo = functools.partial(seir, R_0=R_0, Tinf=Tinf, Tinc=Tinc) + y1 = rk4(foo, y_list[i], t, dt) y_list.append(y1) t_list.append(t) - if (t >= 27 and t <= 67) or (t >= 98 and t <= 122) : + if (t > t0 and t <= t0 + 30) or (t >= t0 + 60 and t <= t0 + 90) : R_0 = R_02 else: R_0 = R_01 @@ -67,7 +70,7 @@ plt.semilogy(t, p[0], 'b') plt.semilogy(t, p[1], 'r') plt.semilogy(t, p[2], 'k') plt.semilogy(t, p[3], 'g') -plt.semilogy(days, swiss, 'k*') +# plt.semilogy(days, swiss, 'k*') plt.legend(['S', 'E', 'I', 'R', 'swiss']) plt.show()