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corona.py
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import sys, math, time, operator, urllib2, os, stat, csv, ctypes, random, ROOT
import numpy as np
# constants
time_to_death = 14
#mortality = 0.014
#time_to_death = 12
#mortality = 0.01
#mortality = 0.007
# settings
trends = 0
extra = 4
ndayspread = 1
fine_age_bins = 0
# Auto select worst 8 countries
# Criteria: worst fraction in 14 days, 10 mill+ pop, 1k+ current cases
worst = 0
min_pop = 1e7
case_threshold = 1e3
days_pred = 14
# Auto select best 8 countries
# Criteria: best current rate, 1 mill+ pop, 1k+ current cases
best = 0
best_min_pop = 1e6
best_case_threshold = 1e3
# set both best/worst to off to manually select countries
save = 1
# Plotting and linear projection settings
if best:
# linear project dialy ratio back to n days
ndaysback = 7
ndaysback2 = 4
# plot options
zoom = 0
ndayspread = 0 if zoom else 2
xrange = [80,110] if zoom else [0,120]
yrange = [1.01e0,1e6]
logy2 = 0
logy3 = 0
yrange2 = [1.01e-2,1e2] if logy2 else ([0,10] if zoom else [0,80])
yrange3 = [0,100]
yrange4 = [1e2,1e8]
y2leg = 0.5 if zoom else 0.95
elif worst:
# linear project dialy ratio back to n days
ndaysback = 14
ndaysback2 = 6
# plot options
xrange = [30,120]
yrange = [1.01e0,1e7]
logy2 = 0
logy3 = 0
yrange2 = [1.01e-2,1e2] if logy2 else [0,100]
yrange3 = [0,100]
yrange4 = [1e2,1e9]
y2leg = 0.95
else:
# Manually select countries
# linear project dialy ratio back to n days
ndaysback = 14
ndaysback2 = 14
# plot options
xrange = [30,180]
yrange = [1.01e0,1e7]
yrange2 = [0.01,100]
yrange3 = [0.01,100]
yrange4 = [1e2,1e8]
logy2 = 1
logy3 = 1
y2leg = 0.95
countries = [
#"WRL",
#"KOR",
#"FRA",
#"ESP",
#"AUT",
#"FIN",
#"DEU",
#"UKR",
#"SRB",
#"JPN",
#"TUR",
#"BEL",
#"NLD",
# Bad examples
#"GBR",
#"USA",
#"ITA",
#"ESP",
#"SWE",
# Good examples
#"AUT",
#"DEU",
#"NOR",
#"CHN",
#"TWN",
#"SGP",
#"KOR",
#"JPN",
# Age analysis
#"HUN",
#"AUT",
#"BEL",
#"NLD",
# Hungary and its neighbours
"HRV",
"SVK",
"AUT",
"HUN",
"SVN",
"UKR",
"ROU",
"SRB",
# RazorBoost
#"CHE",
#"TUR",
#"USA",
#"KOR",
#"HUN",
# CFR Spike
#"FRA",
#"HUN",
#"ROU",
#"BEL",
#"IRL",
]
# plot settings: marker, hollow marker, color, size
settings = [
#[20, 24, 1, 1.0],
#[21, 25, 3, 1.0],
#[22, 26, 2, 1.0],
#[23, 32, 4, 1.0],
#[33, 27, 6, 1.2],
#[34, 28, 800, 1.2],
#[29, 30, 804, 1.4],
[22, 26, 601, 1.0, 3002],
[21, 25, 632, 1.0, 3007],
[20, 24, 1, 1.0, 3020],
[23, 32, 417, 1.0, 3021],
[33, 27, 617, 1.2, 3005],
[34, 28, 433, 1.2, 3004],
[29, 30, 401, 1.4, 3006],
[20, 24, 801, 1.0, 3244],
]
# default plot style in ROOT
def set_default_style_():
ROOT.gStyle.SetPaperSize(20.,20.)
ROOT.gStyle.SetTitleFont(42,"xyz")
ROOT.gStyle.SetCanvasBorderMode(0)
ROOT.gStyle.SetCanvasColor(0)
ROOT.gStyle.SetErrorX(0)
ROOT.gStyle.SetFrameBorderMode(0)
#ROOT.gStyle.SetFrameFillColor(0)
#ROOT.gStyle.SetFrameFillStyle(0)
ROOT.gStyle.SetFrameLineWidth(2)
#ROOT.gStyle.SetLineWidth(2)
ROOT.gStyle.SetOptStat(0)
ROOT.gStyle.SetOptTitle(0)
ROOT.gStyle.SetPadBorderMode(0)
ROOT.gStyle.SetPadColor(0)
ROOT.gStyle.SetPadTickX(1)
ROOT.gStyle.SetPadTickY(1)
ROOT.gStyle.SetPalette(1)
ROOT.gStyle.SetTitleBorderSize(0)
ROOT.gStyle.SetTitleFillColor(0)
ROOT.gStyle.SetTitleStyle(0)
ROOT.gStyle.SetTitleX(1)
ROOT.gStyle.SetTitleY(1)
ROOT.gStyle.SetTitleAlign(33)
# Methods
def daily_growth(h, dh, optw=False):
count = 0
vdiff = []
growth = 0
for binx in range(1,h.GetNbinsX()+1):
if h.GetBinContent(binx)>0:
count += 1
if count>extra:
if h.GetMaximum()>20:
fit = ROOT.TF1("fit","expo",(binx-extra)*86400,(binx+extra)*86400)
h.Fit("fit","RMWQ0" if (optw or "WRL" in h.GetName()) else "RMQ0")
vdiff.append((fit.Eval(h.GetBinCenter(binx))-h.GetBinContent(binx))/fit.Eval(h.GetBinCenter(binx)))
growth = (math.exp(fit.GetParameter(1)*86400)-1)*100
#growth = (h.GetBinContent(binx)-h.GetBinContent(binx-1))/max(h.GetBinContent(binx-1),1)*100
dh. SetBinContent(binx,growth)
dh. SetBinError (binx,0)
else:
dh. SetBinContent(binx,0)
dh. SetBinError (binx,0)
return np.mean(vdiff[-extra:]) if len(vdiff) else 0
def daily_growth_and_diff(h, dh, ddh, dddh):
mean = daily_growth(h, dh)
growth = 0
for binx in range(1,h.GetNbinsX()+1):
if dh.GetBinContent(binx)>0:
prev_growth = dh.GetBinContent(binx-1)
growth = dh.GetBinContent(binx)
#prev_growth = (dh.GetBinContent(binx-2)+dh.GetBinContent(binx+1)+dh.GetBinContent(binx))/3
#growth = (dh.GetBinContent(binx-1)+dh.GetBinContent(binx)+dh.GetBinContent(binx+1))/3
growth_change = growth - prev_growth
#growth_change = (growth - prev_growth)/prev_growth*100 if prev_growth!=0 else growth - prev_growth
ddh.SetBinContent(binx,growth_change)
for binx in range(1,h.GetNbinsX()+1):
if ddh.GetBinContent(binx)>0:
prev_growth = ddh.GetBinContent(binx-1)
growth = ddh.GetBinContent(binx)
#prev_growth = (dh.GetBinContent(binx-2)+dh.GetBinContent(binx+1)+dh.GetBinContent(binx))/3
#growth = (dh.GetBinContent(binx-1)+dh.GetBinContent(binx)+dh.GetBinContent(binx+1))/3
growth_change = growth - prev_growth
#growth_change = (growth - prev_growth)/prev_growth*100 if prev_growth!=0 else growth - prev_growth
dddh.SetBinContent(binx,growth_change)
#if "ITA" in h.GetName():
# print ("bin=%d cont=%d fit=%.1f growth=%.1f change=%.1f " % (binx, h.GetBinContent(binx), fit.Eval(h.GetBinCenter(binx)),
#
return mean
def get_pred(dh, h, linear_back, c1=-9999, draw=False):
maxbin = 0
maxcont = 0
for binx in range(1,dh.GetNbinsX()+1):
if dh.GetBinContent(binx)>0:
maxbin = binx
maxcont = h.GetBinContent(binx)
if c1==-9999:
fit = ROOT.TF1(dh.GetName()+"_fit_"+str(linear_back),"pol1",(maxbin-linear_back)*86400,(maxbin+28)*86400)
name = h.GetName()+"_pred_"+str(linear_back)
dh.Fit(dh.GetName()+"_fit_"+str(linear_back),"RMWQ0")# if not "CHN" in h.GetName() else "RMW0")
if draw:
fit.SetLineColor(dh.GetMarkerColor())
fit.SetLineWidth(2)
fit.Draw("SAME")
else:
fit = ROOT.TF1(dh.GetName()+"_curfew_fit_"+str(linear_back),"pol1",(maxbin-2)*86400,(maxbin+28)*86400)
fit.FixParameter(1,c1)
name = h.GetName()+"_pred_curfew_"+str(linear_back)
dh.Fit(dh.GetName()+"_curfew_fit_"+str(linear_back),"RMQ0")
if draw:
fit.SetLineColor(dh.GetMarkerColor())
fit.SetLineStyle(7)
fit.SetLineWidth(2)
fit.Draw("SAME")
h_pred = h.Clone(name)
h_pred.SetMarkerColor(h.GetMarkerColor())
for binx in range(1,h_pred.GetNbinsX()+1):
if h_pred.GetBinContent(binx)>0:
h_pred.SetBinContent(binx,0)
elif binx>maxbin:
pred = maxcont*(1+(max(0, fit.Eval(h.GetBinCenter(binx)))/100))
maxcont = pred
h_pred.SetBinContent(binx, pred)
if c1==-9999:
return [h_pred, fit]
else:
return [h_pred, fit]
def get_pred_and_error(h, dh, diff):
h_pred_nom = h.Clone(h.GetName()+"_pred_nom")
h_pred_err = h.Clone(h.GetName()+"_err")
vhpred = []
vfpred = []
if h.GetMaximum()>20:
#for ndays in range(max(ndaysback-ndayspread*2,2),ndaysback+ndayspread*2+1):
for ndays in range(-ndayspread,ndayspread+1):
hpred,fpred = get_pred(dh,h,ndaysback+ndays*2)
vhpred.append(hpred)
vfpred.append(fpred)
for binx in range(1,hpred.GetNbinsX()+1):
if vhpred[0].GetBinContent(binx)==0:
h_pred_nom.SetBinContent(binx,0)
h_pred_nom.SetBinError (binx,0)
h_pred_err.SetBinContent(binx,0)
h_pred_err.SetBinError (binx,0)
else:
# calculate mean
logs = []
vals = []
for ifit in range(len(vhpred)):
logs.append(math.log(vhpred[ifit].GetBinContent(binx)))
vals.append(vhpred[ifit].GetBinContent(binx))
#print binx
#print logs
#print vals
#mean = math.exp(np.mean(logs))
mean = np.mean(vals)
#print "mean1="+str(mean)
#print "mean2="+str(mean2)
#print "stdev="+str(np.std(logs))
#print "stdv2="+str(np.std(vals))
h_pred_nom.SetBinContent(binx, mean)
#h_pred_nom.SetBinError (binx, np.std(vals))
h_pred_nom.SetBinError (binx,0)
# calculate error up/down separately
vup = []
vdn = []
for ifit in range(len(vals)):
if vals[ifit]>mean:
vup.append(vals[ifit])
else:
vdn.append(vals[ifit])
err_up = ((np.mean(vup) if len(vup) else 0) - mean)/mean
err_up = ((err_up**2 + diff**2)**0.5)*mean
err_dn = (mean - (np.mean(vdn) if len(vdn) else 0))/mean
err_dn = ((err_dn**2 + diff**2)**0.5)*mean
#print binx
#print mean
#print (np.mean(vup)+np.mean(vdn))/2
#print (np.mean(vup)-np.mean(vdn))/2
#h_pred_err.SetBinContent(binx, (np.mean(vup)+np.mean(vdn))/2)
#h_pred_err.SetBinError (binx, (np.mean(vup)-np.mean(vdn))/2)
#print err_up
#print err_dn
#print mean + (err_up-err_dn)/2
#print (err_up-err_dn)/2
h_pred_err.SetBinContent(binx, mean + (err_up-err_dn)/2)
h_pred_err.SetBinError (binx, (err_up+err_dn)/2)
return [h_pred_nom, h_pred_err, vfpred]
def get_date(day):
maxdiff = 9999
month = ""
months = { 1:"Jan", 2:"Feb", 3:"Mar", 4:"Apr", 5:"May", 6:"Jun", 7:"Jul", 8:"Aug", 9:"Sep", 10:"Oct", 11:"Nov", 12:"Dec" }
for key in monthtoday.keys():
diff = day - monthtoday[key]
if diff>0 and diff<maxdiff:
maxdiff = diff
month = months[key]
return month+" "+("%02d" % maxdiff)
# Coronavirus data
data = {}
data["WRL"] = [ ROOT.TH1D("WRL_dchg", ";Date;2nd derivative of growth rate (%)", 366,0,366*86400),
ROOT.TH1D("WRL_chg", ";Date;1st derivative of growth rate (%)", 366,0,366*86400),
ROOT.TH1D("WRL_gro", ";Date;Daily incrase (%)", 366,0,366*86400),
ROOT.TH1D("WRL", "World;Date;Total comfirmed cases", 366,0,366*86400)]
death = {}
death["WRL"] = [ ROOT.TH1D("WRL_death_dchg", ";Date;2nd der. of death growth rate (%)", 366,0,366*86400),
ROOT.TH1D("WRL_death_chg", ";Date;1st der. of death growth rate (%)", 366,0,366*86400),
ROOT.TH1D("WRL_death_gro", ";Date;Daily death incrase (%)", 366,0,366*86400),
ROOT.TH1D("WRL_death", "World;Date;Total comfirmed death", 366,0,366*86400) ]
monthtoday = { 1:0, 2:31, 3:60, 4:91, 5:121, 6:152, 7:182, 8:213, 9:244, 10:274, 11:305, 12:335 }
population = {"WRL":0}
total = {}
dtotal = {}
lastday = {}
lastcount = {}
lastdcount = {}
lastcountry = ""
allcountries = []
valid_day = 0
valid_count = 0
countrynames = {}
# ---------------- ECDC ----------------
# Update case data if older than an hour
update = 0
if not os.path.exists('corona_data.csv'): update = 1
elif (time.time() - os.path.getmtime('corona_data.csv')) > 3600: update = 1
if update:
print "Updating data from ECDC servers"
filedata = urllib2.urlopen('https://opendata.ecdc.europa.eu/covid19/casedistribution/csv')
datatowrite = filedata.read()
with open('corona_data.csv', 'wb') as f:
f.write(datatowrite)
print "Start reading world covid-19 data (ECDC)"
for line in reversed(open("corona_data.csv").readlines()[1:]):
info = line.rstrip().split(",")
country = info[8]
population[country] = int(info[9]) if info[9] != "" else 1
# correcting
# missing info
if country == "":
geoId = info[7]
if geoId == "FK":
country = "FLK"
population[country] = 2840
elif geoId == "CZ":
country = "CZE"
population[country] = 10650000 # 2019
elif geoId == "AI":
country = "AIA"
population[country] = 15094
else:
country = geoId
population[country] = 1
# Correcting wrong counts
if country == "HUN":
# fix deaths
if info[0] == "24/04/2020": info[5] = "11"
if info[0] == "23/04/2020": info[5] = "14"
if info[0] == "31/03/2020": info[5] = "1"
if info[0] == "25/03/2020": info[5] = "1"
if info[0] == "23/03/2020": info[5] = "2"
if info[0] == "22/03/2020": info[5] = "2"
if info[0] == "21/03/2020": info[5] = "0"
if info[0] == "20/03/2020": info[5] = "3"
if info[0] == "19/03/2020": info[5] = "0"
if info[0] == "18/03/2020": info[5] = "0"
if info[0] == "17/03/2020": info[5] = "0"
if info[0] == "16/03/2020": info[5] = "1"
# fix cases
if info[0] == "05/03/2020": info[4] = "4"
if info[0] == "07/03/2020": info[4] = "1"
if info[0] == "08/03/2020": info[4] = "2"
if info[0] == "09/03/2020": info[4] = "2"
if info[0] == "10/03/2020": info[4] = "3"
if info[0] == "11/03/2020": info[4] = "1"
if info[0] == "12/03/2020": info[4] = "3"
if info[0] == "14/03/2020": info[4] = "11"
if info[0] == "15/03/2020": info[4] = "2"
if info[0] == "16/03/2020": info[4] = "7"
if info[0] == "18/03/2020": info[4] = "8"
if info[0] == "19/03/2020": info[4] = "15"
if country != lastcountry:
if country not in allcountries:
allcountries.append(country)
population["WRL"] += (int(info[9]) if info[9] != "" else 0)
dddh = ROOT.TH1D(country+"_dchg", ";Date;2nd drivative of growth rate (%)", 366,0,366*86400)
ddh = ROOT.TH1D(country+"_chg", ";Date;1st drivative of growth rate (%)", 366,0,366*86400)
dh = ROOT.TH1D(country+"_gro", ";Date;Daily growth (%)", 366,0,366*86400)
h = ROOT.TH1D(country,info[6].replace("_"," ")+";Date;Total comfirmed cases", 366,0,366*86400)
data[country] = [dddh, ddh, dh, h]
dddd = ROOT.TH1D(country+"_death_dchg", ";Date;2nd der. of death growth rate (%)", 366,0,366*86400)
ddd = ROOT.TH1D(country+"_death_chg", ";Date;1st der. of death growth rate (%)", 366,0,366*86400)
dd = ROOT.TH1D(country+"_death_gro", ";Date;Daily death growth (%)", 366,0,366*86400)
d = ROOT.TH1D(country+"_death",info[6].replace("_"," ")+";Date;Total comfirmed death", 366,0,366*86400)
death[country] = [dddd, ddd, dd, d]
countrynames[country] = info[6].replace("_"," ")
if country not in total:
total[country] = 0
dtotal[country] = 0
lastday[country] = 0
lastcount[country] = 0
lastdcount[country] = 0
day = monthtoday[int(info[2])]+int(info[1])
# Need this temporarily, until projections are long gone
# They added later discovered deaths in one bunch
if country == "CHN" and day==108: info[5] = "0"
total[country] += int(info[4])
dtotal[country] += int(info[5])
count = total[country]
dcount = dtotal[country]
for currday in range(lastday[country]+1,day):
h.SetBinContent(currday, lastcount[country])
d.SetBinContent(currday, lastdcount[country])
#h.SetBinError (currday, 0)
h.SetBinContent(day, count)
d.SetBinContent(day, dcount)
#h.SetBinError (day, 0)
h2 = data["WRL"][3]
h2.Fill((day-1)*86400, count)
h2.SetBinError(day,0)
d2 = death["WRL"][3]
d2.Fill((day-1)*86400, dcount)
d2.SetBinError(day,0)
lastcountry = country
lastday[country] = day
lastcount[country] = count
lastdcount[country] = dcount
if country == "HUN":
valid_day = day
valid_count = count
# --------------- Testing --------------
# Update testing data if older than 4 hours
update = 0
if not os.path.exists('covid-testing-all-observations.csv'): update = 1
elif (time.time() - os.path.getmtime('covid-testing-all-observations.csv')) > 3600: update = 1
if update:
print "Updating testing data from github"
filedata = urllib2.urlopen('https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/testing/covid-testing-all-observations.csv')
datatowrite = filedata.read()
with open('covid-testing-all-observations.csv', 'wb') as f:
f.write(datatowrite)
# I need to manually add the data for Hungary
f.write("Hungary - tests performed,2020-03-04,http://abouthungary.hu/,Ministry of Interior,,230,,,\n")
f.write("Hungary - tests performed,2020-03-05,http://abouthungary.hu/,Ministry of Interior,,230,,,\n")
f.write("Hungary - tests performed,2020-03-06,http://abouthungary.hu/,Ministry of Interior,,269,,,\n")
f.write("Hungary - tests performed,2020-03-07,http://abouthungary.hu/,Ministry of Interior,,319,,,\n")
f.write("Hungary - tests performed,2020-03-08,http://abouthungary.hu/,Ministry of Interior,,362,,,\n")
f.write("Hungary - tests performed,2020-03-09,http://abouthungary.hu/,Ministry of Interior,,362,,,\n")
f.write("Hungary - tests performed,2020-03-10,http://abouthungary.hu/,Ministry of Interior,,531,,,\n")
f.write("Hungary - tests performed,2020-03-11,http://abouthungary.hu/,Ministry of Interior,,609,,,\n")
f.write("Hungary - tests performed,2020-03-12,http://abouthungary.hu/,Ministry of Interior,,730,,,\n")
f.write("Hungary - tests performed,2020-03-13,http://abouthungary.hu/,Ministry of Interior,,858,,,\n")
f.write("Hungary - tests performed,2020-03-14,http://abouthungary.hu/,Ministry of Interior,,1014,,,\n")
f.write("Hungary - tests performed,2020-03-15,http://abouthungary.hu/,Ministry of Interior,,1236,,,\n")
f.write("Hungary - tests performed,2020-03-16,http://abouthungary.hu/,Ministry of Interior,,1470,,,\n")
f.write("Hungary - tests performed,2020-03-17,http://abouthungary.hu/,Ministry of Interior,,1587,,,\n")
f.write("Hungary - tests performed,2020-03-18,http://abouthungary.hu/,Ministry of Interior,,1803,,,\n")
f.write("Hungary - tests performed,2020-03-19,http://abouthungary.hu/,Ministry of Interior,,2322,,,\n")
f.write("Hungary - tests performed,2020-03-20,http://abouthungary.hu/,Ministry of Interior,,3007,,,\n")
f.write("Hungary - tests performed,2020-03-21,http://abouthungary.hu/,Ministry of Interior,,3477,,,\n")
f.write("Hungary - tests performed,2020-03-22,http://abouthungary.hu/,Ministry of Interior,,4443,,,\n")
f.write("Hungary - tests performed,2020-03-23,http://abouthungary.hu/,Ministry of Interior,,5515,,,\n")
f.write("Hungary - tests performed,2020-03-24,http://abouthungary.hu/,Ministry of Interior,,6113,,,\n")
f.write("Hungary - tests performed,2020-03-25,http://abouthungary.hu/,Ministry of Interior,,6817,,,\n")
f.write("Hungary - tests performed,2020-03-26,http://abouthungary.hu/,Ministry of Interior,,8005,,,\n")
f.write("Hungary - tests performed,2020-03-27,http://abouthungary.hu/,Ministry of Interior,,9275,,,\n")
f.write("Hungary - tests performed,2020-03-28,http://abouthungary.hu/,Ministry of Interior,,10303,,,\n")
f.write("Hungary - tests performed,2020-03-29,http://abouthungary.hu/,Ministry of Interior,,12148,,,\n")
f.write("Hungary - tests performed,2020-03-30,http://abouthungary.hu/,Ministry of Interior,,13301,,,\n")
f.write("Hungary - tests performed,2020-03-31,http://abouthungary.hu/,Ministry of Interior,,14146,,,\n")
f.write("Hungary - tests performed,2020-04-01,http://abouthungary.hu/,Ministry of Interior,,15208,,,\n")
f.write("Hungary - tests performed,2020-04-02,http://abouthungary.hu/,Ministry of Interior,,16401,,,\n")
f.write("Hungary - tests performed,2020-04-03,http://abouthungary.hu/,Ministry of Interior,,17769,,,\n")
f.write("Hungary - tests performed,2020-04-04,http://abouthungary.hu/,Ministry of Interior,,19424,,,\n")
f.write("Hungary - tests performed,2020-04-05,http://abouthungary.hu/,Ministry of Interior,,21250,,,\n")
f.write("Hungary - tests performed,2020-04-06,http://abouthungary.hu/,Ministry of Interior,,22282,,,\n")
f.write("Hungary - tests performed,2020-04-07,http://abouthungary.hu/,Ministry of Interior,,23746,,,\n")
f.write("Hungary - tests performed,2020-04-08,http://abouthungary.hu/,Ministry of Interior,,25748,,,\n")
f.write("Hungary - tests performed,2020-04-09,http://abouthungary.hu/,Ministry of Interior,,27826,,,\n")
f.write("Hungary - tests performed,2020-04-10,http://abouthungary.hu/,Ministry of Interior,,29948,,,\n")
f.write("Hungary - tests performed,2020-04-11,http://abouthungary.hu/,Ministry of Interior,,31961,,,\n")
f.write("Hungary - tests performed,2020-04-12,http://abouthungary.hu/,Ministry of Interior,,33532,,,\n")
f.write("Hungary - tests performed,2020-04-13,http://abouthungary.hu/,Ministry of Interior,,34819,,,\n")
f.write("Hungary - tests performed,2020-04-14,http://abouthungary.hu/,Ministry of Interior,,35825,,,\n")
f.write("Hungary - tests performed,2020-04-15,http://abouthungary.hu/,Ministry of Interior,,37326,,,\n")
f.write("Hungary - tests performed,2020-04-16,http://abouthungary.hu/,Ministry of Interior,,38489,,,\n")
f.write("Hungary - tests performed,2020-04-17,http://abouthungary.hu/,Ministry of Interior,,41590,,,\n")
f.write("Hungary - tests performed,2020-04-18,http://abouthungary.hu/,Ministry of Interior,,43901,,,\n")
f.write("Hungary - tests performed,2020-04-19,http://abouthungary.hu/,Ministry of Interior,,46353,,,\n")
f.write("Hungary - tests performed,2020-04-20,http://abouthungary.hu/,Ministry of Interior,,48057,,,\n")
f.write("Hungary - tests performed,2020-04-21,http://abouthungary.hu/,Ministry of Interior,,50052,,,\n")
f.write("Hungary - tests performed,2020-04-22,http://abouthungary.hu/,Ministry of Interior,,52702,,,\n")
f.write("Hungary - tests performed,2020-04-23,http://abouthungary.hu/,Ministry of Interior,,55390,,,\n")
f.write("Hungary - tests performed,2020-04-24,http://abouthungary.hu/,Ministry of Interior,,58251,,,\n")
f.write("Hungary - tests performed,2020-04-25,http://abouthungary.hu/,Ministry of Interior,,60801,,,\n")
f.write("Hungary - tests performed,2020-04-26,http://abouthungary.hu/,Ministry of Interior,,63505,,,\n")
f.write("Hungary - tests performed,2020-04-27,http://abouthungary.hu/,Ministry of Interior,,65625,,,\n")
f.write("Hungary - tests performed,2020-04-28,http://abouthungary.hu/,Ministry of Interior,,67172,,,\n")
f.write("Hungary - tests performed,2020-04-29,http://abouthungary.hu/,Ministry of Interior,,70300,,,\n")
f.write("Hungary - tests performed,2020-04-30,http://abouthungary.hu/,Ministry of Interior,,72951,,,\n")
f.write("Hungary - tests performed,2020-05-01,http://abouthungary.hu/,Ministry of Interior,,76331,,,\n")
f.write("Hungary - tests performed,2020-05-02,http://abouthungary.hu/,Ministry of Interior,,79551,,,\n")
f.write("Hungary - tests performed,2020-05-03,http://abouthungary.hu/,Ministry of Interior,,82010,,,\n")
f.write("Hungary - tests performed,2020-05-04,http://abouthungary.hu/,Ministry of Interior,,83958,,,\n")
f.write("Hungary - tests performed,2020-05-05,http://abouthungary.hu/,Ministry of Interior,,85557,,,\n")
f.write("Hungary - tests performed,2020-05-06,http://abouthungary.hu/,Ministry of Interior,,86743,,,\n")
f.write("Hungary - tests performed,2020-05-07,http://abouthungary.hu/,Ministry of Interior,,94036,,,\n")
f.write("Hungary - tests performed,2020-05-08,http://abouthungary.hu/,Ministry of Interior,,99058,,,\n")
f.write("Hungary - tests performed,2020-05-09,http://abouthungary.hu/,Ministry of Interior,,103258,,,\n")
f.write("Hungary - tests performed,2020-05-10,http://abouthungary.hu/,Ministry of Interior,,108257,,,\n")
f.write("Hungary - tests performed,2020-05-11,http://abouthungary.hu/,Ministry of Interior,,112165,,,\n")
f.write("Hungary - tests performed,2020-05-12,http://abouthungary.hu/,Ministry of Interior,,114719,,,\n")
f.write("Hungary - tests performed,2020-05-13,http://abouthungary.hu/,Ministry of Interior,,118500,,,\n")
f.write("Hungary - tests performed,2020-05-14,http://abouthungary.hu/,Ministry of Interior,,123258,,,\n")
f.write("Hungary - tests performed,2020-05-15,http://abouthungary.hu/,Ministry of Interior,,127237,,,\n")
f.write("Hungary - tests performed,2020-05-16,http://abouthungary.hu/,Ministry of Interior,,131429,,,\n")
f.write("Hungary - tests performed,2020-05-17,http://abouthungary.hu/,Ministry of Interior,,135137,,,\n")
f.write("Hungary - tests performed,2020-05-18,http://abouthungary.hu/,Ministry of Interior,,137243,,,\n")
f.write("Hungary - tests performed,2020-05-19,http://abouthungary.hu/,Ministry of Interior,,138697,,,\n")
f.write("Hungary - tests performed,2020-05-20,http://abouthungary.hu/,Ministry of Interior,,142729,,,\n")
f.write("Hungary - tests performed,2020-05-21,http://abouthungary.hu/,Ministry of Interior,,147511,,,\n")
f.write("Hungary - tests performed,2020-05-22,http://abouthungary.hu/,Ministry of Interior,,155801,,,\n")
f.write("Hungary - tests performed,2020-05-23,http://abouthungary.hu/,Ministry of Interior,,159260,,,\n")
f.write("Hungary - tests performed,2020-05-24,http://abouthungary.hu/,Ministry of Interior,,162925,,,\n")
f.write("Hungary - tests performed,2020-05-25,http://abouthungary.hu/,Ministry of Interior,,164619,,,\n")
f.write("Hungary - tests performed,2020-05-26,http://abouthungary.hu/,Ministry of Interior,,166263,,,\n")
f.write("Hungary - tests performed,2020-05-27,http://abouthungary.hu/,Ministry of Interior,,169960,,,\n")
f.write("Hungary - tests performed,2020-05-28,http://abouthungary.hu/,Ministry of Interior,,174011,,,\n")
f.write("Hungary - tests performed,2020-05-29,http://abouthungary.hu/,Ministry of Interior,,180152,,,\n")
f.write("Hungary - tests performed,2020-05-30,http://abouthungary.hu/,Ministry of Interior,,183562,,,\n")
f.write("Hungary - tests performed,2020-05-31,http://abouthungary.hu/,Ministry of Interior,,185980,,,\n")
f.write("Hungary - tests performed,2020-06-01,http://abouthungary.hu/,Ministry of Interior,,187965,,,\n")
f.write("Hungary - tests performed,2020-06-02,http://abouthungary.hu/,Ministry of Interior,,189969,,,\n")
f.write("Hungary - tests performed,2020-06-03,http://abouthungary.hu/,Ministry of Interior,,191572,,,\n")
f.write("Hungary - tests performed,2020-06-04,http://abouthungary.hu/,Ministry of Interior,,195894,,,\n")
f.write("Hungary - tests performed,2020-06-05,http://abouthungary.hu/,Ministry of Interior,,202606,,,\n")
f.write("Hungary - tests performed,2020-06-06,http://abouthungary.hu/,Ministry of Interior,,206853,,,\n")
f.write("Hungary - tests performed,2020-06-07,http://abouthungary.hu/,Ministry of Interior,,210202,,,\n")
f.write("Hungary - tests performed,2020-06-08,http://abouthungary.hu/,Ministry of Interior,,210749,,,\n")
f.write("Hungary - tests performed,2020-06-09,http://abouthungary.hu/,Ministry of Interior,,214468,,,\n")
f.write("Hungary - tests performed,2020-06-10,http://abouthungary.hu/,Ministry of Interior,,217689,,,\n")
f.write("Hungary - tests performed,2020-06-11,http://abouthungary.hu/,Ministry of Interior,,222247,,,\n")
f.write("Hungary - tests performed,2020-06-12,http://abouthungary.hu/,Ministry of Interior,,226669,,,\n")
f.write("Hungary - tests performed,2020-06-13,http://abouthungary.hu/,Ministry of Interior,,230169,,,\n")
f.write("Hungary - tests performed,2020-06-14,http://abouthungary.hu/,Ministry of Interior,,233742,,,\n")
f.write("Hungary - tests performed,2020-06-15,http://abouthungary.hu/,Ministry of Interior,,235377,,,\n")
f.write("Hungary - tests performed,2020-06-16,http://abouthungary.hu/,Ministry of Interior,,236828,,,\n")
f.write("Hungary - tests performed,2020-06-17,http://abouthungary.hu/,Ministry of Interior,,242139,,,\n")
f.write("Hungary - tests performed,2020-06-18,http://abouthungary.hu/,Ministry of Interior,,245598,,,\n")
print "Start reading world testing data (github)"
testcountries = []
testdata = {}
testdata["WRL"] = [ ROOT.TH1D("WRL_test_gro", ";Date;Daily growth in tests (%)", 366,0,366*86400),
ROOT.TH1D("WRL_test", "World;Date;Total tests done", 366,0,366*86400),
"sample"]
lasttestday = {}
lasttestcount = {}
lasttestcountry = ""
testtotal = {}
nline = 0
with open('covid-testing-all-observations.csv') as csvfile:
csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
for info in csvreader:
if nline != 0 and info[0] != '' and info[2] != '' and info[6] != '':
countryname = info[0].split(" - ")[0]
if countryname == "Czech Republic": countryname = "Czechia"
testinginfo = info[0].split(" - ")[1]
datatype = "sample"
norm = 1
if "people" in testinginfo or "cases" in testinginfo:
datatype = "case"
norm = 1.5
country = ""
for short, name in countrynames.items():
if name == countryname:
country = short
elif countryname in name:
country = short
if countryname == "Hong Kong": country = "HKG"
# corrections
if country != lasttestcountry:
#if lasttestcountry != '': print countrynames[lasttestcountry]+" "+str(lasttestcount[lasttestcountry])
if country not in testcountries:
#print "TESTINFO: "+country+" "+testinginfo
testcountries.append(country)
dtest = ROOT.TH1D(country+"_test_gro", ";Date;Daily growth in tests (%)", 366,0,366*86400)
test = ROOT.TH1D(country+"_test",countryname+";Date;Total tests done", 366,0,366*86400)
testdata[country] = [dtest, test, datatype]
if country not in testtotal:
testtotal[country] = 0
lasttestday[country] = 0
lasttestcount[country] = 0
testtotal[country] = int(info[6]) * norm
testcount = testtotal[country]
day = monthtoday[int(info[2].split("-")[1])]+int(info[2].split("-")[2])
for currday in range(lasttestday[country]+1,day):
test.SetBinContent(currday, lasttestcount[country])
test.SetBinContent(day, testcount)
t2 = data["WRL"][1]
t2.Fill((day-1)*86400, testcount)
t2.SetBinError(day,0)
lasttestcountry = country
lasttestday[country] = day
lasttestcount[country] = testcount
nline += 1
#if lasttestcountry != '': print countrynames[lasttestcountry]+" "+str(lasttestcount[lasttestcountry])
print "Reading world data done"
print
# Estimating Chinese population age for Lancet bins
print "Performing fit to the observed fatalities (Lancet)"
age_bins = {}
age_avgs = {}
age_bins["Lancet"] = [0, 10, 20, 30, 40, 50, 60, 70, 80, 100]
age_avgs["Lancet"] = [0]*(len(age_bins["Lancet"])-1)
with open('WPP2019_INT_F03_1_POPULATION_BY_AGE_ANNUAL_BOTH_SEXES.csv') as csvfile:
csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
for info in csvreader:
if info[2] == 'China' and info[7] == '2020' and info[8] != '...':
for i in range(len(age_bins["Lancet"])-1):
binpop = 0
bin_age = 0
for age in range(100):
npop = int(info[8+age].replace(" ",""))*1000
if age >= age_bins["Lancet"][i] and age<age_bins["Lancet"][i+1]:
binpop += npop
bin_age += npop * (age+0.5)
bin_age = bin_age / binpop
age_avgs["Lancet"][i] = bin_age
fatalities = {}
fatalities["Lancet"] = [0.0000161, 0.0000695, 0.000309, 0.000844, 0.00161, 0.00595, 0.0193, 0.0428, 0.078]
fat_ylow = [0.00000185, 0.0000149, 0.000138, 0.000408, 0.000764, 0.00344, 0.0111, 0.0245, 0.0380]
fat_yhigh = [0.000249, 0.000502, 0.000923, 0.00185, 0.00323, 0.0128, 0.0389, 0.0844, 0.133]
gfat = ROOT.TGraphAsymmErrors(len(fatalities["Lancet"]))
for i in range(len(fatalities["Lancet"])):
#x = (age_bins["Lancet"][i+1]+age_bins["Lancet"][i])/2
x = age_avgs["Lancet"][i]
y = fatalities["Lancet"][i]
gfat.SetPoint(i, x, y)
gfat.SetPointError(i, x-age_bins["Lancet"][i],age_bins["Lancet"][i+1]-x, y-fat_ylow[i], fat_yhigh[i]-y)
set_default_style_()
can = ROOT.TCanvas("Fatality", "", 600,600)
can.SetTopMargin (0.04)
can.SetLeftMargin (0.13)
can.SetRightMargin(0.04)
can.SetGrid(1,1)
can.SetLogy(1)
gfat.GetXaxis().SetTitleSize(0.05)
gfat.GetYaxis().SetTitleSize(0.05)
gfat.GetXaxis().SetTitle("Age (years)")
gfat.GetYaxis().SetTitle("Infection fatality rate")
gfat.GetXaxis().SetRangeUser(0,100)
#gfat.GetYaxis().SetRangeUser(0,0.3)
gfat.GetYaxis().SetRangeUser(1e-6,1e2)
gfat.Draw("AP")
ffat = ROOT.TF1("ffit", "expo")
ffat.SetLineColor(2)
gfat.Fit("ffit","MQ")
can.SaveAs("www/Fatality_fit.png")
#ft = ROOT.TFile.Open("test.root","recreate")
#gfat.Write("gfat")
#ft.Close()
print "Start reading world age data (WPP)"
agedata = {}
avg_fatality = {}
avg_fatality_fit = {}
pop = {}
age_bins["BEL"] = [0, 25, 45, 65, 75, 85, 100] if fine_age_bins else [0, 65, 75, 85, 100]
age_bins["HUN"] = [0, 20, 40, 60, 70, 80, 100] if fine_age_bins else [0, 60, 70, 80, 100]
age_bins["AUT"] = [0, 25, 45, 65, 75, 85, 100]# if fine_age_bins else [0, 65, 75, 85, 100]
age_bins["USA"] = [0, 20, 40, 60, 70, 80, 100]
default_age_bins = [0, 65, 75, 85, 100]
with open('WPP2019_INT_F03_1_POPULATION_BY_AGE_ANNUAL_BOTH_SEXES.csv') as csvfile:
csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
for info in csvreader:
if info[2] != '' and info[7] == '2020' and info[8] != '...':
countryname = info[2]
if countryname == "Republic of Korea":
countryname = "South Korea"
country = ""
for short, name in countrynames.items():
if name == countryname:
country = short
elif countryname in name:
country = short
elif name in countryname:
country = short
popdata = [0]*(len(default_age_bins)-1)
ifr_fit = 0
for age in range(100):
npop = int(info[8+age].replace(" ",""))*1000
ifr_fit += npop * ffat.Eval(age+0.5)
for i in range(len(default_age_bins)-1):
if age >= default_age_bins[i] and age<default_age_bins[i+1]:
popdata[i] += npop
ifr_fit = ifr_fit / sum(popdata)
for short, name in countrynames.items():
if countryname == name:
if not short in age_bins:
age_bins[short] = default_age_bins
pop[short] = [0] * (len(age_bins[short])-1)
fatalities[short] = [0] * (len(age_bins[short])-1)
for i in range(len(age_bins[short])-1):
binpop = 0
bin_ifr = 0
for age in range(100):
npop = int(info[8+age].replace(" ",""))*1000
if age >= age_bins[short][i] and age<age_bins[short][i+1]:
binpop += npop
bin_ifr += npop * ffat.Eval(age+0.5)
bin_ifr = bin_ifr / binpop if binpop>0 else 0
pop[short][i] = binpop
fatalities[short][i] = bin_ifr
ifr = 0
for i in range(len(default_age_bins)-1):
ifr += popdata[i] * fatalities["Lancet"][i] / sum(popdata)
if country in countrynames.keys():
agedata[country] = popdata
avg_fatality[country] = ifr
avg_fatality_fit[country] = ifr_fit
#print ("%.3f%% %.3f%% - %s" % (ifr*100, ifr_fit*100, countryname))
print "Reading world age data done"
print
def print_fatality_infos(short):
print "Binned IFRs for "+data[short][3].GetTitle()+":"
for i in range(len(age_bins[short])-1):
if i<len(age_bins[short])-2:
print ("%d-%d: %.3f%%" % (age_bins[short][i], age_bins[short][i+1]-1, fatalities[short][i]*100))
else:
print ("%d+: %.3f%%" % (age_bins[short][i], fatalities[short][i]*100))
print ("AVG: %.3f%%" % (avg_fatality_fit[short]*100))
print "and population:"
for i in range(len(age_bins[short])-1):
if i<len(age_bins[short])-2:
print ("%d-%d: %d" % (age_bins[short][i], age_bins[short][i+1]-1, pop[short][i]))
else:
print ("%d+: %d" % (age_bins[short][i], pop[short][i]))
print ("SUM: %d" % (sum(pop[short])))
for short in countries:
if short in fatalities:
print_fatality_infos(short)
#sys.exit()
def clone_harray(vh, repl1, repl2, axistitle):
newvh = []
for h in vh:
newh = h.Clone(h.GetName().replace(repl1,repl2))
newh.GetYaxis().SetTitle(axistitle)
newvh.append(newh)
return newvh
print "Start reading Belgian mortality data (Sciensano)"
if fine_age_bins:
vd_BEL = [ ROOT.TH1D("BEL_death_12", "0-24;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_35", "25-44;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_55", "45-64;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_70", "65-74;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_80", "75-84;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_90", "85+;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400) ]
else:
vd_BEL = [ ROOT.TH1D("BEL_death_49", "0-64;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_70", "65-74;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_80", "75-84;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400),
ROOT.TH1D("BEL_death_90", "85+;Date;Comfirmed deaths (Sciensano)", 366,0,366*86400) ]
vt_BEL = clone_harray(vd_BEL, "death", "est_true", "Est. total infected")
vdt_BEL = clone_harray(vd_BEL, "death", "est_true_gro", "Daily growth of estimated true cases (%)")
total_NA = 0
with open('www/COVID19BE_MORT.csv') as csvfile:
csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
for info in csvreader:
if "2020" in info[0]:
day = monthtoday[int(info[0].replace('"','').split("-")[1])]+int(info[0].replace('"','').split("-")[2])
age_group = info[2].replace('"','')
age = 80 # most likely default age for NA
dtd = 20
deaths = int(info[4])
i = (4 if fine_age_bins else 2) + (1 if random.random()>0.13 else 0) # update from values in Excel fit
if fine_age_bins:
if age_group == "0-24":
age = 12.5
i = 0
elif age_group == "25-44":
age = 35
i = 1
elif age_group == "45-64":
age = 55
i = 2
elif age_group == "65-74":
age = 70
i = 3
elif age_group == "75-84":
age = 80
i = 4
elif age_group == "85+":
age = 90
i = 5
else:
age = 80
i = 6
total_NA += deaths
else:
if age_group == "45-64" or age_group == "25-44" or age_group == "0-24":
age = 49
i = 0
elif age_group == "65-74":
age = 70
i = 1
elif age_group == "75-84":
age = 80
i = 2
elif age_group == "85+":
age = 90
i = 3
if i!= 6:
#est_cases = deaths / ffat.Eval(age)
est_cases = deaths / fatalities["BEL"][i]
vd_BEL[i].SetBinContent(day, vd_BEL[i].GetBinContent(day)+deaths)
vd_BEL[i].SetBinError (day, 0)
vt_BEL[i].SetBinContent(day-dtd, vd_BEL[i].GetBinContent(day-dtd)+est_cases)
vt_BEL[i].SetBinError (day-dtd, 0)
print "Reading Belgian mortality data (Sciensano) done"
print
print "Start reading Hungarian mortality data"
if fine_age_bins:
vd_HUN = [ ROOT.TH1D("HUN_death_10", "0-19;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_30", "20-39;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_50", "40-59;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_65", "60-69;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_75", "70-79;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_90", "80+;Date;Comfirmed deaths", 366,0,366*86400) ]
else:
vd_HUN = [ ROOT.TH1D("HUN_death_50", "0-59;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_65", "60-69;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_75", "70-79;Date;Comfirmed deaths", 366,0,366*86400),
ROOT.TH1D("HUN_death_90", "80+;Date;Comfirmed deaths", 366,0,366*86400) ]
vt_HUN = clone_harray(vd_HUN, "death", "est_true", "Est. total infected")
vdt_HUN = clone_harray(vd_HUN, "death", "est_true_gro", "Daily growth of estimated true cases (%)")
with open('www/Mortality_data_Hungary.csv') as csvfile:
csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
for info in csvreader:
if info[0] != '':
n = int(info[0])
day = 0
prev = 0
for binx in range(1,death["HUN"][3].GetNbinsX()+1):
cont = death["HUN"][3].GetBinContent(binx)
if n>prev and n<=cont:
day = binx
prev = cont
#print "n="+str(n)+" --> day="+str(day) #"date="+get_date(day)
age = int(info[2])
dtd = 20
if fine_age_bins:
if age>=0 and age<20:
i = 0
elif age>=20 and age<40:
i = 1
elif age>=40 and age<60:
i = 2
elif age>=60 and age<70:
i = 3
elif age>=70 and age<80:
i = 4
elif age>=80:
i = 5
else:
if age>=0 and age<60:
i = 0
elif age>=60 and age<70:
i = 1
elif age>=70 and age<80:
i = 2
elif age>=80:
i = 3
if i!= 6:
deaths = 1
est_cases = deaths / fatalities["HUN"][i]
vd_HUN[i].SetBinContent(day, vd_HUN[i].GetBinContent(day)+deaths)
vd_HUN[i].SetBinError (day, 0)
#vt_HUN[i].SetBinContent(day-dtd, vd_HUN[i].GetBinContent(day-dtd)+est_cases)
#vt_HUN[i].SetBinError (day-dtd, 0)
#print str(n)+" "+get_date(day)
print "Reading Hungarian mortality data done"
print
# Belgian Mortality plots
# Make cumulative plot
for i in range(len(vt_BEL)):
total = 0
for binx in range(1, valid_day-20+1):
count = vt_BEL[i].GetBinContent(binx)
total += count
vt_BEL[i].SetBinContent(binx, total)
# Print some values for age analysis
deaths = [0] * len(vd_BEL)
for day in range(1, valid_day+1):
for i in range(len(vd_BEL)):
deaths[i] += vd_BEL[i].GetBinContent(day)
if sum(deaths)>0:
if fine_age_bins:
print ("%s - DEAD: %3d %3d %3d %3d %3d %3d" % (get_date(day), deaths[0], deaths[1], deaths[2], deaths[3], deaths[4], deaths[5]))
print ("%s - COMF: %3d" % (get_date(day-14), data["BEL"][3].GetBinContent(day-14)))
#else:
# print ("%s - DEAD: %3d %3d %3d %3d" % (get_date(day), deaths[0], deaths[1], deaths[2], deaths[3]))
# print ("%s - COMF: %3d" % (get_date(day-14), data["BEL"][3].GetBinContent(day-14)))
if fine_age_bins:
print ("NA: %3d" % (total_NA))
#sys.exit()
# Hungarian Mortality plots
# Make cumulative plot
for i in range(len(vt_HUN)):
total = 0
for binx in range(1, valid_day-20+1):
count = vt_HUN[i].GetBinContent(binx)
total += count
vt_HUN[i].SetBinContent(binx, total)
# Print some values for age analysis
deaths = [0] * len(vd_HUN)
for day in range(1, valid_day+1):
for i in range(len(vd_HUN)):
deaths[i] += vd_HUN[i].GetBinContent(day)
if sum(deaths)>0:
if fine_age_bins>0:
print ("%s - DEAD: %3d %3d %3d %3d %3d %3d" % (get_date(day), deaths[0], deaths[1], deaths[2], deaths[3], deaths[4], deaths[5]))
print ("%s - COMF: %3d" % (get_date(day-14), data["HUN"][3].GetBinContent(day-14)))
#else:
# print ("%s - DEAD: %3d %3d %3d %3d" % (get_date(day), deaths[0], deaths[1], deaths[2], deaths[3]))
# print ("%s - COMF: %3d" % (get_date(day-14), data["HUN"][3].GetBinContent(day-14)))
if fine_age_bins:
sys.exit()
def est_true_cases(h, ht, vd, vt, short, monotonous=True):
deaths14 = [0] * len(vd)
prev_est = 0
prev_ests = [0] * len(vd)
prev_detection = 0
for day in range(1, h.GetNbinsX()+1):
case0 = h.GetBinContent(day)
deathtot = 0
for i in range(len(vd)):
deaths14[i] += vd[i].GetBinContent(day+time_to_death)
deathtot += vd[i].GetBinContent(day+time_to_death)
#print get_date(day)+" "+str(case0)+" "+str(deathtot)
if case0>0 and deathtot>0:
avg_fat = 0
for i in range(len(vd)):
avg_fat += pop[short][i]*fatalities[short][i]
avg_fat /= sum(pop[short])
crude_est = sum(deaths14)/avg_fat
crude_inf = crude_est / sum(pop[short])
obs_fat_low = 0
pred_fat_low = 0
for i in range(len(vd)):