def demand_curves(ranking_provider,
vax_policy,
phis=[25, 50, 100, 200],
phi_benchmark=25,
N_state=N_TN):
wtp_rankings = {phi: ranking_provider(phi, vax_policy) for phi in phis}
figure = plt.figure()
lines = []
# benchmark
benchmark = wtp_rankings[phi_benchmark]
x_pop = list(
chain(*zip(benchmark.loc[0]["num_vax"].shift(1).fillna(0),
benchmark.loc[0]["num_vax"])))
y_wtp = list(
chain(*zip(benchmark.loc[0]["wtp_pc_usd"], benchmark.loc[0]
["wtp_pc_usd"])))
lines.append(
plt.plot(x_pop, y_wtp, figure=figure, color="black", linewidth=2)[0])
lines.append(plt.plot(0, 0, color="white")[0])
# plot dynamic curve
for (phi, all_wtp) in wtp_rankings.items():
daily_doses = phi * percent * annually * N_state
distributed_doses = 0
x_pop = []
y_wtp = []
t_vax = []
ranking = 0
for t in range(simulation_range):
wtp = all_wtp.loc[t].reset_index()
ranking = wtp[(wtp.index >= ranking)
& (wtp.num_vax > distributed_doses)].index.min()
if np.isnan(ranking):
break
x_pop += [distributed_doses, distributed_doses + daily_doses]
t_vax += [t, t + 1]
y_wtp += [wtp.iloc[ranking].wtp_pc_usd] * 2
distributed_doses += daily_doses
lines.append(
plt.plot(x_pop,
y_wtp,
label=f"dynamic, {vax_policy}, $\phi = ${phi}%",
figure=figure)[0])
plt.legend(lines, [f"static, t = 0, $\phi = ${phi_benchmark}%", ""] +
[f"dynamic, {vax_policy}, $\phi = ${phi}%" for phi in phis],
title="allocation",
title_fontsize="24",
fontsize="20")
plt.xticks(fontsize="20")
plt.yticks(fontsize="20")
plt.PlotDevice().ylabel("WTP (USD)\n").xlabel("\nnumber vaccinated")
plt.ylim(0, 350)
plt.xlim(left=0, right=N_TN)
plt.show()
'Cumulative total per thousand': "total_per_thousand",
'Daily change in cumulative total per thousand': "delta_per_thousand",
'7-day smoothed daily change': "smoothed_delta",
'7-day smoothed daily change per thousand': "smoothed_delta_per_thousand",
'Short-term positive rate': "positivity",
'Short-term tests per case': "tests_per_case"
}
testing = pd.read_csv("data/covid-testing-all-observations.csv",
parse_dates=["Date"])
testing = testing[testing["ISO code"] == "IND"]\
.dropna()\
[schema.keys()]\
.rename(columns = schema)
testing["month"] = testing.date.dt.month
def formula(order: int) -> str:
powers = " + ".join(f"np.power(delta_per_thousand, {i + 1})"
for i in range(order))
return f"smoothed_delta ~ -1 + daily_tests + C(month)*({powers})"
model = OLS.from_formula(formula(order=3), data=testing).fit()
print(summary_col(model, regressor_order=["daily_tests"], drop_omitted=True))
plt.plot(0.2093 * df["TT"][:, "delta", "tested"], label="test-scaled")
plt.plot(df["TT"][:, "delta", "confirmed"], label="confirmed")
plt.legend()
plt.show()
outcomes_per_policy(v1_sum, reference = (25, "contact"), metric_label = "v1", fmt = "D")
proxy_sum = {}
proxy_raw = {}
for (phi, policy) in params[1:]:
pr = np.sum(np.load(src / f"proxyLLweight_BR_Gopalganj_phi{phi}_{policy}.npz")['arr_0'], axis = (0, 2))
ps = np.sum(np.load(src / f"proxyLLweight_BR_Gopalganj_phi{phi}_{policy}.npz")['arr_0'], axis = 0) @ (N_jk * years_life_remaining.loc["Bihar"])
proxy_raw[phi, policy] = np.percentile(pr, [50, 5, 95], axis = 0)
proxy_sum[phi, policy] = np.percentile(ps, [50, 5, 95], axis = 0)
outcomes_per_policy(proxy_raw, reference = (25, "contact"), metric_label = "sum 1-qbar * LE (no population weights)", fmt = "D")
# outcomes_per_policy(proxy_sum, reference = (25, "contact"), metric_label = "sum 1-qbar * LE", fmt = "D")
for phi, policy in params:
plt.plot(
np.median(
np.load(tev_src / f"BR_Gopalganj_phi{phi}_{policy}.npz")['dT'],
axis = 1),
label = (phi, policy)
)
plt.legend()
plt.show()
for phi, policy in params:
plt.plot(
np.median(
np.load(tev_src / f"BR_Gopalganj_phi{phi}_{policy}.npz")['dD'],
axis = 1),
label = (phi, policy)
)
plt.legend()
plt.show()
state_code, N_district, N_0, N_1, N_2, N_3, N_4, N_5, N_6 = districts_to_run.loc[state, district][population_columns]
def get_cons_decline(p1, p2 = None):
if p2:
p = src/f"{state_code}_{district}_phi{p1}_{p2}.npz"
else:
p = src/f"{state_code}_{district}_phi25_novax.npz"
with np.load(p) as policy:
dI_pc = policy['dT']/N_district
dD_pc = policy['dD']/N_district
return income_decline(state, district, dI_pc, dD_pc)
rc_vectors = {p: np.median(get_cons_decline(*p), axis = 1) for p in params}
for (k, v) in rc_vectors.items():
plt.plot(v, label = k)
plt.legend()
plt.show()
state_code = "TN"
TN_cons_predicted = {p:0 for p in params}
TN_cons2019 = consumption_2019.loc["Tamil Nadu"].sum(axis = 1)
rcs = dict()
for district in TN_cons2019.index:
N_district = districts_to_run.loc["Tamil Nadu", district].N_tot
for p in params:
if len(p) > 1:
p1, p2 = p
simfile = src/f"{state_code}_{district}_phi{p1}_{p2}.npz"
else:
simfile = src/f"{state_code}_{district}_phi25_novax.npz"
def plot_mobility(series, label, stringency = None, until = None, annotation = "Google Mobility Data; baseline mobility measured from Jan 3 - Feb 6"):
plt.plot(series.date, smoothed(series.retail_and_recreation_percent_change_from_baseline), label = "Retail/Recreation")
plt.plot(series.date, smoothed(series.grocery_and_pharmacy_percent_change_from_baseline), label = "Grocery/Pharmacy")
plt.plot(series.date, smoothed(series.parks_percent_change_from_baseline), label = "Parks")
plt.plot(series.date, smoothed(series.transit_stations_percent_change_from_baseline), label = "Transit Stations")
plt.plot(series.date, smoothed(series.workplaces_percent_change_from_baseline), label = "Workplaces")
plt.plot(series.date, smoothed(series.residential_percent_change_from_baseline), label = "Residential")
if until:
right = pd.Timestamp(until)
elif stringency is not None:
right = stringency.Date.max()
else:
right = series.date.iloc[-1]
lax = plt.gca()
if stringency is not None:
plt.sca(lax.twinx())
stringency_IN = stringency.query("CountryName == 'India'")
stringency_US = stringency.query("(CountryName == 'United States') & (RegionName.isnull())", engine = "python")
plt.plot(stringency_IN.Date, stringency_IN.StringencyIndex, 'k--', alpha = 0.6, label = "IN Measure Stringency")
plt.plot(stringency_US.Date, stringency_US.StringencyIndex, 'k.' , alpha = 0.6, label = "US Measure Stringency")
plt.PlotDevice().ylabel("lockdown stringency index", rotation = -90, labelpad = 50)
plt.legend()
plt.sca(lax)
plt.legend(loc = "lower right")
plt.fill_betweenx((-100, 60), pd.to_datetime("March 24, 2020"), pd.to_datetime("June 1, 2020"), color = "black", alpha = 0.05, zorder = -1)
plt.text(s = "national lockdown", x = pd.to_datetime("April 27, 2020"), y = -90, fontdict = plt.theme.note, ha = "center", va = "top")
plt.PlotDevice()\
.xlabel("\ndate")\
.ylabel("% change in mobility\n")
# .title(f"\n{label}: Mobility & Lockdown Trends")\
# .annotate(annotation)\
plt.ylim(-100, 60)
plt.xlim(left = series.date.iloc[0], right = right)
import flat_table
from epimargin.etl.commons import download_data
data = Path("./data")
download_data(data, 'timeseries.json', "https://api.covid19india.org/v3/")
# data prep
with (data/'timeseries.json').open("rb") as fp:
df = flat_table.normalize(pd.read_json(fp)).fillna(0)
df.columns = df.columns.str.split('.', expand = True)
dates = np.squeeze(df["index"][None].values)
df = df.drop(columns = "index").set_index(dates).stack([1, 2]).drop("UN", axis = 1)
series = mobility[mobility.sub_region_1.isna()]
plt.plot(series.date, smoothed(series.retail_and_recreation_percent_change_from_baseline), label = "Retail/Recreation")
plt.fill_betweenx((-100, 60), pd.to_datetime("March 24, 2020"), pd.to_datetime("June 1, 2020"), color = "black", alpha = 0.05, zorder = -1)
plt.text(s = "national lockdown", x = pd.to_datetime("April 27, 2020"), y = -20, fontdict = plt.note_font, ha = "center", va = "top")
plt.ylim(-100, 10)
plt.xlim(series.date.min(), series.date.max())
plt.legend(loc = 'upper right')
lax = plt.gca()
plt.sca(lax.twinx())
plt.plot(df["TT"][:, "delta", "confirmed"].index, smoothed(df["TT"][:, "delta", "confirmed"].values), label = "Daily Cases", color = plt.PRED_PURPLE)
plt.legend(loc = 'lower right')
plt.PlotDevice().ylabel("new cases", rotation = -90, labelpad = 50)
plt.sca(lax)
plt.PlotDevice().title("\nIndia Mobility and Case Count Trends")\
.annotate("Google Mobility Data + Covid19India.org")\
.xlabel("\ndate")\
.ylabel("% change in mobility\n")
all_tev_200 = pd.read_csv(
data / f"all_tev_200_{vax_policy}.csv").set_index("t")
# plot static benchmark
N_natl = districts_to_run.N_tot.sum()
figure = plt.figure()
x_pop = list(
chain(*zip(
all_tev_50.loc[0]["num_vax"].shift(1).fillna(0) * 100 /
N_natl, all_tev_50.loc[0]["num_vax"] * 100 / N_natl)))
y_tev = list(
chain(*zip(all_tev_50.loc[0]["pc_tev_usd"], all_tev_50.loc[0]
["pc_tev_usd"])))
static, = plt.plot(x_pop,
y_tev,
figure=figure,
color="grey",
linewidth=2)
lines = [static]
plt.xticks(fontsize="20")
plt.yticks(fontsize="20")
plt.PlotDevice().ylabel("TEV (USD)\n").xlabel(
"\npercentage of country vaccinated")
# plt.ylim(0, 1600)
# plt.xlim(left = 0, right = 100)
lines.append(plt.plot(0, 0, color="white")[0])
# plot dynamic curve
phis = [25, 50, 100, 200]
for (phi, all_tev) in zip(
meta_ifrs.male == 1.0)].query('age <= 70').query('age >= 10')
cai_bihar_male = all_location_comparison[
(all_location_comparison.location == "Bihar")
& (all_location_comparison.male == 1.0)].query('ifr > 0')
cai_mumbai_male = all_location_comparison[
(all_location_comparison.location == "Mumbai")
& (all_location_comparison.male == 1.0)].sort_values("age_bin_pooled")
cai_karnataka_male = all_location_comparison[
(all_location_comparison.location == "Karnataka")
& (all_location_comparison.male == 1.0)]
cai_tamilnadu_male = all_location_comparison[
(all_location_comparison.location == "tamil_nadu")
& (all_location_comparison.male == 1.0)]
plt.plot(levin_male.age, (levin_male.ifr),
color="gray",
linestyle="dotted",
label="meta (Levin et al. 2020; slope = 0.123)")
plt.plot(od_male.age, (od_male.ifr),
color="black",
label="meta (O'Driscoll et al. 2020; slope = 0.114) ")
plt.plot(cai_bihar_male.age_bin_pooled, (100 * cai_bihar_male.ifr),
color="#007CD4",
label="Bihar (Cai et al. 2021; slope = 0.047)")
plt.plot(cai_mumbai_male.age_bin_pooled, (100 * cai_mumbai_male.ifr),
color="#FF0000",
label="Mumbai (Cai et al. 2021; slope = 0.100)")
plt.plot(cai_karnataka_male.age_bin_pooled, (100 * cai_karnataka_male.ifr),
color="#55A423",
label="Karnataka (Cai et al. 2021; slope = 0.103)")
plt.plot(cai_tamilnadu_male.age_bin_pooled, (100 * cai_tamilnadu_male.ifr),
color="#FFB700",
one_day = pd.Timedelta(days=1)
# fig 1
infections = ts[
ts.date >= "May 01, 2020"].Hospitalized #.sum(level = 2).sort_index()
smoothed = convolution("uniform")
scatter = plt.scatter(infections.index[:-7],
infections.values[:-7],
color="#CC4C75",
marker="s",
s=5,
alpha=0.5)
lineplot, = plt.plot(infections.index[:-7],
smoothed(infections.values[:-7]),
color="#CC4C75",
linewidth=2)
plt.PlotDevice()\
.l_title("daily confirmed cases in India")\
.r_title("source:\nCOVID19India")\
.axis_labels(x = "date", y = "cases", enforce_spacing = True)\
.adjust(left = 0.10, bottom = 0.15, right = 0.98, top = 0.90)
plt.xlim(infections.index[0] - one_day, infections.index[-1] + one_day)
plt.legend([scatter, lineplot],
["reported infection counts", "7-day moving average"],
handlelength=0.5,
framealpha=0,
prop={'size': 16})
plt.show()
# fig 2
plt.figure()
plt.Rt(dates, Rt_pred, RR_CI_lower, RR_CI_upper, CI)\
.ylabel("Estimated $R_t$")\
.xlabel("Date")\
.title(district)\
.size(11, 8)\
.save(figs/f"Rt_est_MP{district}.png", dpi=600, bbox_inches="tight")#\
#.show()
plt.close()
from matplotlib.dates import DateFormatter
formatter = DateFormatter("%b\n%Y")
f = notched_smoothing(window=smoothing)
plt.plot(ts.loc["Maharashtra"].index,
ts.loc["Maharashtra"].Hospitalized,
color="black",
label="raw case counts from API")
plt.plot(ts.loc["Maharashtra"].index,
f(ts.loc["Maharashtra"].Hospitalized),
color="black",
linestyle="dashed",
alpha=0.5,
label="smoothed, seasonality-adjusted case counts")
plt.PlotDevice()\
.l_title("daily case counts in Maharashtra")\
.axis_labels(x = "date", y = "daily cases")
plt.gca().xaxis.set_major_formatter(formatter)
plt.legend(prop=plt.theme.note, handlelength=1, framealpha=0)
plt.show()
.dropna(how = 'all')
parse_datetimes(cases.loc[:, "confirmed"])
cases.regency = cases.regency.str.title().map(
lambda s: regency_names.get(s, s))
# generation_interval = cases[~cases.symptom_onset.isna() & ~cases.confirmed.isna()]\
# .apply(get_generation_interval, axis = 1)\
# .dropna()\
# .value_counts()\
# .sort_index()
# generation_interval = generation_interval[(generation_interval.index >= 0) & (generation_interval.index <= 60)]
# generation_interval /= generation_interval.sum()
new_cases = cases.confirmed.value_counts().sort_index()
new_cases_smoothed = smoothing(new_cases)
plt.plot(new_cases, '.', color="blue")
plt.plot(new_cases.index, new_cases_smoothed, '-', color="black")
plt.show()
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")
dayfirst=False)
valid.loc[(~monthfirst_idx)] = pd.to_datetime(valid[(~monthfirst_idx)],
errors='coerce',
format="%d/%m/%Y",
dayfirst=True)
# assert df.max() <= pd.to_datetime("October 03, 2020"), "date parsing resulted in future dates"
df.loc[valid_idx] = valid.apply(pd.Timestamp)
sulsel = pd.read_csv("data/3 OCT 2020 Data collection template update South Sulawesi_CASE.csv", usecols = schema.keys())\
.rename(columns = schema)\
.dropna(how = 'all')
parse_datetimes(sulsel.loc[:, "confirmed"])
sulsel = sulsel.confirmed.value_counts().sort_index()
plt.plot(dkij.index, dkij.values, color="royalblue", label="private")
plt.plot(dkij_public.diff(), color="firebrick", label="public")
plt.legend()
plt.PlotDevice()\
.title("\nJakarta: public vs private case counts")\
.xlabel("date")\
.ylabel("cases")
plt.xlim(right=dkij.index.max())
plt.ylim(top=800)
plt.show()
plt.plot(sulsel, color="royalblue", label="private", linewidth=3)
plt.plot(sulsel_public.diff(), color="firebrick", label="public")
plt.legend()
plt.PlotDevice()\
.title("\nSouth Sulawesi: public vs private case counts")\
smoothed_cases = pd.Series(data=smoother(daily_cases), index=daily_cases.index)
# plot raw and cleaned data
beg = "December 15, 2020"
end = "March 1, 2021"
training_cases = smoothed_cases[beg:end]
plt.scatter(daily_cases[beg:end].index,
daily_cases[beg:end].values,
color="black",
s=5,
alpha=0.5,
label="raw case count data")
plt.plot(training_cases.index,
training_cases.values,
color="black",
linewidth=2,
label="notch-filtered, smoothed case count data")
plt.PlotDevice()\
.l_title("case timeseries for Mumbai")\
.axis_labels(x = "date", y = "daily cases")\
.legend()\
.adjust(bottom = 0.15, left = 0.15)\
.format_xaxis()\
.size(9.5, 6)\
.save(figs / "fig_1.svg")\
.show()
# estimate Rt
from epimargin.estimators import analytical_MPVS
policy_labels=["contact rate", "random", "mortality"])
plt.gca().ticklabel_format(axis="y", useOffset=False)
plt.gcf().set_size_inches((16.8, 9.92))
plt.PlotDevice().l_title(f"{state_code}: tev")
plt.savefig(dst / f"{state_code}_{district}_tev.png")
plt.close("all")
for (state, code) in [("Bihar", "BR")]:
dst = dst0 / code
dst.mkdir(exist_ok=True)
# for district in simulation_initial_conditions.query(f"state == '{state}'").index.get_level_values(1).unique():
for district in simulation_initial_conditions.loc[state].index[:16]:
cf_consumption = np.load(
src / f"c_p0v0{code}_{district}_phi25_novax.npz")['arr_0']
cons_mean = np.mean(cf_consumption, axis=1)
plt.plot(cons_mean)
plt.PlotDevice().l_title(f"{code} {district}: mean consumption")
plt.savefig(dst / f"c_p0v0_{district}.png")
plt.close("all")
for (phi, pol) in product(phis,
["contact", "random", "mortality"]):
p_consumption = np.load(
src /
f"c_p1v1_{code}_{district}_phi{phi}_{pol}.npz")['arr_0']
cons_mean = np.mean(p_consumption, axis=1)
plt.plot(cons_mean)
plt.PlotDevice().l_title(
f"{code} {district}: mean consumption")
plt.savefig(dst / f"c_p1v1{district}_phi{phi}_{pol}.png")
plt.close("all")
idx = dT_conf_scaled_TT.index[("March 1, 2020" <= dT_conf_scaled_TT.index)
& (dT_conf_scaled_TT.index <= simulation_start)]
fig = plt.figure()
scatter_TN = plt.scatter(idx,
dT_conf_scaled_TN[idx] / N_TN,
color=TN_color,
label="Tamil Nadu (raw)",
figure=fig,
alpha=0.5,
marker="o",
s=10,
zorder=5)
plot_TN, = plt.plot(idx,
dT_conf_scaled_smooth_TN[idx] / N_TN,
color=TN_color,
label="Tamil Nadu (smoothed)",
figure=fig,
zorder=5,
linewidth=2)
scatter_TT = plt.scatter(idx,
dT_conf_scaled_TT[idx] / N_TT,
color=IN_color,
label="India (raw)",
figure=fig,
alpha=0.5,
marker="o",
s=10,
zorder=10)
plot_TT, = plt.plot(idx,
dT_conf_scaled_smooth_TT[idx] / N_TT,
color=IN_color,
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,
right=0.99,
top=0.99)
plt.ylim(0.5, 1.5)
plt.show()
# 1: parametric scheme:
dates, Rt, Rt_lb, Rt_ub, *_, anomalies, anomaly_dates = analytical_MPVS(
pd.DataFrame(sir_model.dT),
smoothing=convolution("uniform", 2),
.xlabel("\nDate")\
.ylabel("Probability\n")
plt.subplots_adjust(left=0.12, bottom=0.12, right=0.94, top=0.96)
plt.gca().xaxis.set_minor_locator(mpl.ticker.NullLocator())
plt.gca().xaxis.set_minor_formatter(mpl.ticker.NullFormatter())
plt.gca().xaxis.set_major_locator(mdates.AutoDateLocator())
plt.gca().xaxis.set_major_formatter(mdates.DateFormatter('%b %d'))
plt.xticks(fontsize="16")
plt.yticks(fontsize="16")
plt.gca().xaxis.grid(True, which="major")
plt.semilogy()
plt.ylim(bottom=1e-7)
plt.show()
PrD = pd.DataFrame(prob_death).set_index(
pd.date_range(start=simulation_start, freq="D", periods=len(prob_death)))
plt.plot(PrD, color=TN_color, linewidth=2, label="probability of death")
plt.xlim(left=pd.Timestamp("Jan 01, 2021"), right=pd.Timestamp("Jan 01, 2022"))
plt.PlotDevice().ylabel("log-probability\n")
# plt.subplots_adjust(left = 0.12, bottom = 0.12, right = 0.94, top = 0.96)
plt.gca().xaxis.set_minor_locator(mpl.ticker.NullLocator())
plt.gca().xaxis.set_minor_formatter(mpl.ticker.NullFormatter())
plt.gca().xaxis.set_major_locator(mdates.AutoDateLocator())
plt.gca().xaxis.set_major_formatter(mdates.DateFormatter('%b %y'))
plt.xticks(fontsize="20", rotation=45)
plt.yticks(fontsize="20")
plt.gca().xaxis.grid(True, which="major")
plt.semilogy()
plt.ylim(bottom=1e-7)
plt.show()
