def model(districts, populations, cases, seed) -> NetworkedSIR:
max_ts = cases["date_reported"].max()
units = [
SIR(district, populations[i],
dT0 = len(cases[(cases.geo_reported == district) & (cases.date_reported == max_ts)]),
mobility = 0.000001)
for (i, district) in enumerate(districts)
]
return NetworkedSIR(units, random_seed=seed)
def model(districts, populations, cases, seed) -> NetworkedSIR:
units = [
SIR(district, populations[i],
dT0 = cases[i],
R0 = 0,
D0 = 0,
mobility = 0.000001)
for (i, district) in enumerate(districts)
]
return NetworkedSIR(units, random_seed=seed)
def run_simulation(school: SIR, nonschool: SIR):
for _ in range(30):
school.run(1)
nonschool.forward_epi_step(dB = 2*school.dT[-1]//3) # doesn't preserve population
dT_school = np.array(school.dT)
dT_nonschool = np.array(nonschool.dT)
dT = dT_school + dT_nonschool
var_up_school = np.array(school.upper_CI) - dT_school
var_dn_school = np.array(school.lower_CI) - dT_school
var_up_nonschool = np.array(nonschool.upper_CI) - dT_nonschool
var_dn_nonschool = np.array(nonschool.lower_CI) - dT_nonschool
dT_CI_l = dT - np.sqrt(var_dn_school**2 + var_dn_nonschool**2)
dT_CI_u = dT + np.sqrt(var_up_school**2 + var_up_nonschool**2)
return (dT[1:], dT_CI_l[1:], dT_CI_u[1:])
def models(seed, simulated_school_Rt = school_Rt):
school = SIR("school",
population = school_proportion * total_pop,
infectious_period = 6.25,
I0 = age_ts.sum(level = 0)["school"],
dT0 = age_ts.loc["school"][-1],
lower_CI = school_T_lb,
upper_CI = school_T_ub,
Rt0 = simulated_school_Rt,
random_seed = seed)
nonschool = SIR("nonschool",
population = (1 - school_proportion) * total_pop,
infectious_period = 5.0,
I0 = age_ts.sum(level = 0)["nonschool"],
dT0 = age_ts.loc["nonschool"][-1],
lower_CI = school_T_lb,
upper_CI = school_T_ub,
Rt0 = nonschool_Rt,
random_seed = seed)
return (school, nonschool)
geo_tag = f"{state}_{district}_"
dD0 = ts.loc[district].dD.loc[simulation_start]
I0 = max(0, (T_scaled - R - D))
print(district, I0, "extended IFR",
ts.loc[district].dD.cumsum()[simulation_start] / T_scaled,
"instantaneous IFR", dD0 / (gamma * I0))
# # run model forward with no vaccination
model = SIR(
name=district,
population=N_district,
dT0=np.ones(num_sims) *
(dT_conf_district_smooth[simulation_start] * T_ratio).astype(int),
Rt0=Rt[simulation_start],
I0=np.ones(num_sims) * I0,
R0=np.ones(num_sims) * R,
D0=np.ones(num_sims) * D,
mortality=ts.loc[district].dD.cumsum()[simulation_start] /
T_scaled if I0 == 0 else dD0 / (gamma * I0),
random_seed=0)
model.dD[0] = np.ones(num_sims)
param_tag = "novaccination"
ran_models[geo_tag + param_tag] = model
t = 0
while (model.Rt[-1].mean() > Rt_threshold) and (model.dT[-1].mean() > 0):
model.parallel_forward_epi_step()
print("::::", district, "no vax", t, np.mean(model.dT[-1]),
np.std(model.dT[-1]), model.Rt[-1].mean())
t += 1
var_dn_nonschool = np.array(nonschool.lower_CI) - dT_nonschool
dT_CI_l = dT - np.sqrt(var_dn_school**2 + var_dn_nonschool**2)
dT_CI_u = dT + np.sqrt(var_up_school**2 + var_up_nonschool**2)
return (dT[1:], dT_CI_l[1:], dT_CI_u[1:])
rt1_10x = run_simulation(*models(0, 1.10*school_Rt))
rt1_25x = run_simulation(*models(0, 1.25*school_Rt))
rt1_50x = run_simulation(*models(0, 1.50*school_Rt))
(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, T_pred, T_CI_upper, T_CI_lower, total_cases, new_cases_ts, anomalies, anomaly_dates)\
= analytical_MPVS(age_ts.sum(level = 1), CI = CI, smoothing = smoothing, totals = False)
MAK = SIR(name = "MAK", population = 1.339e6, dT0 = T_pred[-1], Rt0 = Rt_pred[-1], upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1], mobility = 0, random_seed = 0, I0 = age_ts.sum(level = 1).sum()).run(30)
plt.daily_cases(dates, T_pred, T_CI_upper, T_CI_lower, new_cases_ts, anomaly_dates, anomalies, CI,
prediction_ts = [
(MAK.dT[:-1], MAK.lower_CI[1:], MAK.upper_CI[1:], plt.PRED_PURPLE, "current social distancing"),
(*rt1_10x, "orange", "10% increase in school-age $R_t$"),
(*rt1_25x, "mediumseagreen", "25% increase in school-age $R_t$"),
(*rt1_50x, "hotpink", "50% increase in school-age $R_t$"),
])\
.xlabel("\ndate")\
.ylabel("cases\n")
# .title("\nMakassar Daily Cases - school reopening scenarios")\
# .annotate("\nBayesian training process on empirical data, with anomalies identified")
(_, r) = plt.xlim()
plt.xlim(left = pd.Timestamp("Sep 1, 2020"), right = r)
plt.ylim(bottom = 10, top = 1000)
def model(seed = 0):
return NetworkedSIR([SIR(
name = "SULSEL", population = 8_819_500,
dT0 = historical.iloc[-1][0], Rt0 = Rt_pred[-1], upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1],
mobility = 0, I0 = historical.sum()[0]
)], random_seed = seed)
logger.info("running province-level Rt estimate")
(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, T_pred, T_CI_upper, T_CI_lower, total_cases, new_cases_ts, anomalies, anomaly_dates)\
= analytical_MPVS(new_cases, CI = CI, smoothing = smoothing, totals = False)
plt.Rt(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, CI)\
.title("\nSouth Sulawesi: Reproductive Number Estimate")\
.xlabel("\ndate")\
.ylabel("$R_t$\n", rotation=0, labelpad=30)\
.annotate(f"\n{window}-day smoothing window, gamma-prior Bayesian estimation method")\
.show()
logger.info("running case-forward prediction")
prediction_period = 14*days
I0 = (~cases.confirmed.isna()).sum() - (~cases.recovered.isna()).sum() - (~cases.died.isna()).sum()
IDN = SIR(name = "IDN", population = 8_819_500, dT0 = T_pred[-1], Rt0 = Rt_pred[-1], upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1], mobility = 0, random_seed = 0, I0 = I0)\
.run(prediction_period)
plt.daily_cases(dates, T_pred, T_CI_upper, T_CI_lower, new_cases_ts, anomaly_dates, anomalies, CI,
prediction_ts = [
(IDN.dT[:-1], IDN.lower_CI[1:], IDN.upper_CI[1:], plt.PRED_PURPLE, "predicted cases")
])\
.title("\nSouth Sulawesi: Daily Cases")\
.xlabel("\ndate")\
.ylabel("cases\n")\
.annotate("\nBayesian training process on empirical data, with anomalies identified")\
.show()
# makassar estimates
mak_cases = cases[cases.regency == "Makassar"]
mak_new_cases = mak_cases.confirmed.value_counts().sort_index()
def model(seed):
return NetworkedSIR([SIR(name = state, population = pop, dT0 = T_pred[-1], Rt0 = Rt_pred[-1], mobility = 0, I0 = I0)], random_seed = seed)
import adaptive.plots as plt
from adaptive.models import SIR
from adaptive.estimators import analytical_MPVS, parametric_scheme_mcmc, branching_random_walk
from adaptive.smoothing import convolution
import numpy as np
import pandas as pd
import pymc3 as pm
sir_model = SIR("test",
population=500000,
I0=100,
dT0=20,
Rt0=1.01,
random_seed=0)
total_t = 0
schedule = [(1.01, 75), (1.4, 75), (0.9, 75)]
R0_timeseries = []
for (R0, t) in schedule:
R0_timeseries += [R0] * t
sir_model.Rt0 = R0
sir_model.run(t)
total_t += t
plt.plot(sir_model.dT)
plt.show()
plt.plot(R0_timeseries, "-", color="black", label="$R_0$")
plt.plot(sir_model.Rt, "-", color="dodgerblue", label="$R_t$")
plt.legend(framealpha=1, handlelength=1, loc="best")
plt.PlotDevice().xlabel("time").ylabel("reproductive rate").adjust(left=0.10,
bottom=0.15,
natl_cases = sum(province_cases.values())
logger.info("running national-level Rt estimate")
(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, T_pred, T_CI_upper, T_CI_lower, total_cases, new_cases_ts, anomalies, anomaly_dates)\
= analytical_MPVS(natl_cases, CI = CI, smoothing = smoothing)
plt.Rt(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, CI, ymin=0, ymax=4)\
.title("\nIndonesia: Reproductive Number Estimate")\
.xlabel("\ndate")\
.ylabel("$R_t$", rotation=0, labelpad=30)\
.annotate(f"\n{window}-day smoothing window, gamma-prior Bayesian estimation method")\
.show()
logger.info("running case-forward prediction")
IDN = SIR("IDN", 267.7e6, dT0 = T_pred[-1], Rt0 = Rt_pred[-1], mobility = 0, random_seed = 0).run(14)
logger.info("province-level projections")
migration = np.zeros((len(provinces), len(provinces)))
estimates = []
max_len = 1 + max(map(len, provinces))
with tqdm(provinces) as progress:
for (province, cases) in province_cases.items():
progress.set_description(f"{province :<{max_len}}")
(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, *_) = analytical_MPVS(cases, CI = CI, smoothing = smoothing)
apr_idx = np.argmax(dates > "31 Mar, 2020")
may_idx = np.argmax(dates >= "01 May, 2020")
max_idx = np.argmax(Rt_pred[apr_idx:may_idx])
apr_max_idx = apr_idx + max_idx
estimates.append((province, Rt_pred[-1], Rt_CI_lower[-1], Rt_CI_upper[-1], max(0, linear_projection(dates, Rt_pred, window, period = 2*weeks)), Rt_pred[apr_max_idx], Rt_CI_lower[apr_max_idx], Rt_CI_upper[apr_max_idx], dates[apr_max_idx], cases.iloc[-1][0]))
logger.info("running province-level Rt estimate")
(dates, RR_pred, RR_CI_upper, RR_CI_lower, T_pred, T_CI_upper, T_CI_lower, total_cases, new_cases_ts, anomalies, anomaly_dates)\
= analytical_MPVS(jakarta_cases, CI = CI, smoothing = smoothing, totals=False)
plt.Rt(dates, RR_pred[1:], RR_CI_upper[1:], RR_CI_lower[1:], CI)\
.title("\nDKI Jakarta: Reproductive Number Estimate")\
.xlabel("\ndate")\
.ylabel("$R_t$\n", rotation=0, labelpad=30)\
.annotate(f"\n{window}-day smoothing window, gamma-prior Bayesian estimation method")\
.show()
logger.info("running case-forward prediction")
prediction_period = 14*days
IDN = SIR(name = "IDN", population = 267.7e6, dT0 = T_pred[-1], Rt0 = RR_pred[-1], upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1], mobility = 0, random_seed = 0)\
.run(prediction_period)
plt.daily_cases(dates, T_pred[1:], T_CI_upper[1:], T_CI_lower[1:], new_cases_ts[1:], anomaly_dates, anomalies, CI,
prediction_ts = [
(IDN.dT[:-1], IDN.lower_CI[1:], IDN.upper_CI[1:], None, "predicted cases")
])\
.title("\nDKI Jakarta: Daily Cases")\
.xlabel("\ndate")\
.ylabel("cases\n")\
.annotate("\nBayesian training process on empirical data, with anomalies identified")\
.show()
logger.info("district-level projections")
district_cases = dkij.groupby(["district", "date_positiveresult"])["id"].count().sort_index()
districts = dkij.district.unique()
migration = np.zeros((len(districts), len(districts)))
# first, look at state level predictions
(dates, Rt_pred, Rt_CI_upper, Rt_CI_lower, T_pred, T_CI_upper, T_CI_lower,
total_cases, new_cases_ts, anomalies, anomaly_dates) = analytical_MPVS(
state_ts,
CI=CI,
smoothing=notched_smoothing(window=smoothing),
totals=False)
plt.Rt(dates, Rt_pred[1:], Rt_CI_upper[1:], Rt_CI_lower[1:], CI, ymin=0, ymax=3)\
.title("\nBihar: Reproductive Number Estimate (Covid19India Data)")\
.annotate(f"public data from {str(dates[0]).split()[0]} to {str(dates[-1]).split()[0]}")\
.xlabel("\ndate")\
.ylabel("$R_t$", rotation=0, labelpad=20)\
.show()
Bihar = SIR(name="Bihar",
population=99_000_000,
dT0=T_pred[-1],
Rt0=Rt_pred[-1],
mobility=0,
random_seed=0)
Bihar.run(14)
plt.daily_cases(dates, T_pred[1:], T_CI_upper[1:], T_CI_lower[1:], new_cases_ts[1:], anomaly_dates, anomalies, CI,
prediction_ts = [(Bihar.dT[:-1], Bihar.lower_CI[1:], Bihar.upper_CI[1:], None, "predicted cases")])\
.title("\nBihar: Daily Cases")\
.xlabel("\ndate")\
.ylabel("cases\n")\
.annotate("\nBayesian training process on empirical data, with anomalies identified")\
.show()
# now, do district-level estimation
policies = [RandomVaccineAssignment(daily_vax_doses, IN_age_ratios)]
else:
policies = [
RandomVaccineAssignment(daily_vax_doses, IN_age_ratios),
PrioritizedAssignment(daily_vax_doses, split_by_age(S),
[6, 5, 4, 3, 2, 1, 0], "mortality"),
PrioritizedAssignment(daily_vax_doses, split_by_age(S),
[1, 2, 3, 4, 0, 5, 6], "contactrate")
]
for vaccination_policy in policies:
model = SIR(name=state,
population=N,
dT0=np.ones(num_sims) *
(dT_conf_smooth[simulation_start] * T_ratio).astype(int),
Rt0=Rt[simulation_start] * N / (N - T_sero),
I0=np.ones(num_sims) * S,
R0=np.ones(num_sims) * R,
D0=np.ones(num_sims) * D,
random_seed=0)
t = 0
dVx = [np.zeros(len(IN_age_structure))]
# run vax rate forward 1 year, then until 75% of pop is recovered or vax
while (t <= 365) or ((t > 365) and
(model.R[-1].mean() +
(daily_vax_doses * t)) / N < immunity_threshold):
dVx.append(vaccination_policy.distribute_doses(model))
print("::::", state, vax_pct_annual_goal, vax_effectiveness,
vaccination_policy.name(), t, np.mean(model.dT[-1]),
T_scaled = dT_conf_smooth.cumsum()[simulation_start] * T_ratio
D, R = df.loc[simulation_start, "TT"]["total"][["deceased", "recovered"]]
S = N_natl - T_scaled - D - R
(Rt_dates, Rt_est, *_) = analytical_MPVS(T_ratio * dT_conf_smooth,
CI=CI,
smoothing=lambda _: _,
totals=False)
Rt = dict(zip(Rt_dates, Rt_est))
model = SIR(name=state,
population=N_natl,
dT0=np.ones(num_sims) *
(dT_conf_smooth[simulation_start] * T_ratio).astype(int),
Rt0=Rt[simulation_start],
I0=np.ones(num_sims) * (T_scaled - R - D),
R0=np.ones(num_sims) * R,
D0=np.ones(num_sims) * D,
mortality=mu_TN,
random_seed=0)
while np.mean(model.dT[-1]) > 0:
model.parallel_forward_epi_step()
pd.DataFrame(data = {
"date": [simulation_start + pd.Timedelta(n, "days") for n in range(len(model.dT))],
"dT" : [np.mean(_)/N_natl for _ in model.dT],
"dD" : [np.mean(_)/N_natl for _ in model.dD],
})\
.assign(month = lambda _: _.date.dt.month.astype(str) + "_" + _.date.dt.year.astype(str))\
.groupby("month")\
(Rt_dates, Rt_est, *_) = analytical_MPVS(T_ratio * dT_conf_district_smooth,
CI=CI,
smoothing=lambda _: _,
totals=False)
Rt = dict(zip(Rt_dates, Rt_est))
daily_rate = vax_pct_annual_goal / 365
daily_vax_doses = int(vax_effectiveness * daily_rate * N_district)
T_scaled = dT_conf_district_smooth.cumsum()[simulation_start] * T_ratio
model = SIR(
name=state,
population=N_district,
dT0=np.ones(num_sims) *
(dT_conf_district_smooth[simulation_start] * T_ratio).astype(int),
Rt0=Rt[simulation_start] * N_district / (N_district - T_scaled),
I0=np.ones(num_sims) * (T_scaled - R - D),
R0=np.ones(num_sims) * R,
D0=np.ones(num_sims) * D,
random_seed=0)
t = 0
dVx = [np.zeros(len(IN_age_structure))]
# run vax rate forward 1 year, then until 75% of pop is recovered or vax
while (t <= 365) or (
(t > 365) and
(model.R[-1].mean() +
(daily_vax_doses * t)) / N_district < immunity_threshold):
dVx.append(Multinomial.rvs(daily_vax_doses, IN_age_ratios))
model.S[-1] -= daily_vax_doses
# grab time series
R = df[state].loc[simulation_start, "total", "recovered"]
D = df[state].loc[simulation_start, "total", "deceased"]
# run Rt estimation on scaled timeseries
(Rt_dates, Rt_est, *_) = analytical_MPVS(T_ratio * dT_conf_smooth,
CI=CI,
smoothing=lambda _: _,
totals=False)
Rt = dict(zip(Rt_dates, Rt_est))
model = SIR(name=state,
population=N,
dT0=np.ones(num_sims) *
(dT_conf_smooth[simulation_start] * T_ratio).astype(int),
Rt0=Rt[simulation_start] * N / (N - T_sero),
I0=np.ones(num_sims) * (T_sero - R - D),
R0=np.ones(num_sims) * R,
D0=np.ones(num_sims) * D,
random_seed=0)
i = 0
print(
Rt[simulation_start], Rt[simulation_start] * N /
(N - T_ratio * T_conf_smooth[simulation_start]))
while np.mean(model.dT[-1]) > 0:
model.parallel_forward_epi_step(num_sims=num_sims)
i += 1
print(state, i, np.mean(model.dT[-1]), np.std(model.dT[-1]))
Rt_m = np.mean(Rt[(Rt.index >= "31 March, 2020") & (Rt.index <= "17 May, 2020")])[0]
Rt_v = np.mean(Rt[(Rt.index < "31 March, 2020")])[0]
print(" + Rt today:", Rt_pred[-1])
print(" + Rt_m :", Rt_m)
print(" + Rt_v :", Rt_v)
historical = pd.DataFrame({"smoothed": new_cases_ts}, index = dates)
plt.Rt(dates, Rt_pred, RR_CI_lower, RR_CI_upper, CI)\
.ylabel("$R_t$")\
.xlabel("date")\
.title(f"\n{state}: Reproductive Number Estimate")\
.annotate(f"public data from {str(dates[0]).split()[0]} to {str(dates[-1]).split()[0]}")\
.show()
I0 = (ts.loc[state].Hospitalized - ts.loc[state].Recovered - ts.loc[state].Deceased).sum()
state_model = SIR(name = state, population = pop, dT0 = T_pred[-1], Rt0 = Rt_pred[-1], mobility = 0, I0 = I0, upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1], random_seed = 0).run(10)
empirical = state_ts_full[(state_ts_full.index >= "Oct 14, 2020") & (state_ts_full.index < "Oct 25, 2020")]
plt.daily_cases(dates, T_pred, T_CI_upper, T_CI_lower, new_cases_ts, anomaly_dates, anomalies, CI,
prediction_ts=[
(state_model.dT, state_model.lower_CI, state_model.upper_CI, plt.PRED_PURPLE, "predicted cases"),
] + [(empirical, empirical, empirical, "black", "empirical post-prediction cases")] if state != "Maharashtra" else [])\
.ylabel("cases")\
.xlabel("date")\
.title(f"\n{state}: Daily Cases")\
.annotate("\nBayesian training process on empirical data, with anomalies identified")
_, r = plt.xlim()
plt.xlim(left = pd.Timestamp("August 01, 2020"), right = r)
plt.show()
