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map_covid19_animate.jl
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map_covid19_animate.jl
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#module map_covid19
using Dates, DataFrames, ColorSchemes, PlotlyJS
#include("load_covid19_data.jl")
reasonable_resolution() = (1440, 900)
# time index
#for ti = 8:length(covid19us[1].confirmed)
#for ti = length(covid19us[1].confirmed)-length(covid19us[1].confirmed)+8 : length(covid19us[1].confirmed)
for ti = length(covid19us[1].confirmed)-200 : length(covid19us[1].confirmed)
#ti = 200
#ti = length(covid19us[1].confirmed)
display(covid19us[1].time[ti])
local cconfirmed = [covid19us[i].confirmed[ti] for i in 1:length(covid19us)];
local dcconfirmed = [mean(covid19us[i].confirmed[ti-7+1:ti] - covid19us[i].confirmed[ti-8+1:ti-1]) for i in 1:length(covid19us)];
local dcconfirmedinst = [mean(covid19us[i].confirmed[ti] - covid19us[i].confirmed[ti-1]) for i in 1:length(covid19us)];
local cdeath = [covid19us[i].death[ti] for i in 1:length(covid19us)];
local dcdeath = [mean(covid19us[i].death[ti-7+1:ti] - covid19us[i].death[ti-8+1:ti-1]) for i in 1:length(covid19us)];
local dcdeathinst = [mean(covid19us[i].death[ti] - covid19us[i].death[ti-1]) for i in 1:length(covid19us)];
# extracting county indices with land area and population
local cind = findall((countyarea .> 0) .& (cpop .> 0));
local tind = 1:length(covid19us[1].confirmed);
local t = covid19us[1].time[tind];
# plot a map of confirmed cases
#cval = cconfirmed[cind] ./ (countyarea[cind] .* cpop[cind]);
local cval = cconfirmed[cind] ./ cpop[cind];
local log10cval = log10.(cval);
#sval = countyarea[cind] .* cpop[cind];
local sval = cpop[cind];
local log10sval = log10.(sval);
# daily confirmed cases per 100k averaged over 7 days
local dCONFIRMEDpc = dcconfirmed[cind] ./ cpop[cind] .* 1e5;
local bind = findall(dCONFIRMEDpc .<= 0);
local dCONFIRMEDpc[bind] .= NaN;
# daily instant confirmed cases per 100k
local dCONFIRMEDpcinst = dcconfirmedinst[cind] ./ cpop[cind] .* 1e5;
local bind = findall(dCONFIRMEDpcinst .<= 0);
local dCONFIRMEDpcinst[bind] .= NaN;
# daily death per 100k averaged over 7 days
local dDEATHpc = dcdeath[cind] ./ cpop[cind] .* 1e5;
local bind = findall(dDEATHpc .<= 0);
local dDEATHpc[bind] .= NaN;
# daily instant death per 100k
local dDEATHpcinst = dcdeathinst[cind] ./ cpop[cind] .* 1e5;
local bind = findall(dDEATHpcinst .<= 0);
local dDEATHpcinst[bind] .= NaN;
local df = DataFrame(LON = clon[cind],
LAT = clat[cind],
POPULATION = cpop[cind],
log10POPULATION = log10.(cpop[cind]),
logPOPULATION = log.(cpop[cind]),
nrootPOPULATION = (cpop[cind]) .^ (1.0/3)/5,
CONFIRMEDpc = cconfirmed[cind] ./ cpop[cind] .* 1e5,
CONFIRMED = cconfirmed[cind],
log10CONFIRMEDpc = log10.(cconfirmed[cind] ./ cpop[cind] .* 1e5),
dCONFIRMEDpc = dCONFIRMEDpc,
dCONFIRMED = dcconfirmed[cind],
log10dCONFIRMEDpc = log10.(dCONFIRMEDpc),
dCONFIRMEDpcinst = dCONFIRMEDpcinst,
dCONFIRMEDinst = dcconfirmedinst[cind],
log10dCONFIRMEDpcinst = log10.(dCONFIRMEDpcinst),
DEATHpc = cdeath[cind] ./ cpop[cind] .* 1e5,
DEATH = cdeath[cind],
log10DEATHpc = log10.(cdeath[cind] ./ cpop[cind] .* 1e5),
dDEATHpc = dDEATHpc,
dDEATH = dcdeath[cind],
log10dDEATHpc = log10.(dDEATHpc),
dDEATHpcinst = dDEATHpcinst,
dDEATHinst = dcdeathinst[cind],
log10dDEATHpcinst = log10.(dDEATHpcinst),
);
function pmapconfirmed()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
marker_size=df[!, :nrootPOPULATION],
marker_color=df[!, :log10CONFIRMEDpc],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = 2,
marker_cmax = 4,
hoverinfo="text",
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :CONFIRMED]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :CONFIRMEDpc], digits=2)) .* "<br>" .*
"Cumulative Deaths (actual): " .* string.(df[!, :DEATH]) .* "<br>" .*
"Cumulative Deaths per 100k: " .* string.(round.(df[!, :DEATHpc], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Cumulative Confirmed Cases per 100k " * string(t[ti])[1:10] * " (log10) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
function pmapdconfirmed()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
#marker_size=df[!, :logPOPULATION]/1.3,
marker_size=df[!, :nrootPOPULATION],
marker_color=df[!, :log10dCONFIRMEDpc],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = -0.5,
marker_cmax = 2.5,
hoverinfo="text",
#hovertext=string.(df[!, :dCONFIRMED]) .* " " .* county[cind],
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :CONFIRMED]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :CONFIRMEDpc], digits=2)) .* "<br>" .*
"Daily New Cases (actual): " .* string.(df[!, :dCONFIRMED]) .* "<br>" .*
"Daily New Cases per 100k: " .* string.(round.(df[!, :dCONFIRMEDpc], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Daily New Cases per 100k " * string(t[ti])[1:10] * " (log10, 7 day avg.) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
function pmapdconfirmedinst()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
marker_size=df[!, :nrootPOPULATION],
#marker_size=df[!, :logPOPULATION]/1.3,
marker_color=df[!, :log10dCONFIRMEDpcinst],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = -0.5,
marker_cmax = 2.5,
hoverinfo="text",
#hovertext=string.(df[!, :dCONFIRMED]) .* " " .* county[cind],
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :CONFIRMED]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :CONFIRMEDpc], digits=2)) .* "<br>" .*
"Daily New Cases (actual): " .* string.(df[!, :dCONFIRMEDinst]) .* "<br>" .*
"Daily New Cases per 100k: " .* string.(round.(df[!, :dCONFIRMEDpcinst], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Daily New Cases per 100k " * string(t[ti])[1:10] * " (log10) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
function pmapdeath()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
marker_size=df[!, :nrootPOPULATION],
#marker_size=df[!, :logPOPULATION]/1.3,
marker_color=df[!, :log10DEATHpc],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = 0,
marker_cmax = 2.5,
hoverinfo="text",
#hovertext=string.(df[!, :DEATH]) .* " " .* county[cind],
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :CONFIRMED]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :CONFIRMEDpc], digits=2)) .* "<br>" .*
"Cumulative Deaths (actual): " .* string.(df[!, :DEATH]) .* "<br>" .*
"Cumulative Deaths per 100k: " .* string.(round.(df[!, :DEATHpc], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Cumulative Death per 100k " * string(t[ti])[1:10] * " (log10) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
function pmapddeath()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
#marker_size=df[!, :logPOPULATION]/1.3,
marker_size=df[!, :nrootPOPULATION],
marker_color=df[!, :log10dDEATHpc],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = -1.5,
marker_cmax = 1,
hoverinfo="text",
#hovertext=string.(df[!, :dDEATH]) .* " " .* county[cind],
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :DEATH]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :DEATHpc], digits=2)) .* "<br>" .*
"Daily New Deaths (actual): " .* string.(df[!, :dDEATH]) .* "<br>" .*
"Daily New Deaths per 100k: " .* string.(round.(df[!, :dDEATHpc], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Daily New Deaths per 100k " * string(t[ti])[1:10] * " (log10, 7 day avg.) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
function pmapddeathinst()
pmapsg = PlotlyJS.scattergeo(; locationmode="USA-states",
lat = df[!, :LAT],
lon = df[!, :LON],
#marker_size=df[!, :logPOPULATION]/1.3,
marker_size=df[!, :nrootPOPULATION],
marker_color=df[!, :log10dDEATHpcinst],
marker_colorscale="Jet",
marker_showscale = true,
marker_cmin = -1.5,
marker_cmax = 1,
hoverinfo="text",
#hovertext=string.(df[!, :dDEATH]) .* " " .* county[cind],
hovertext=
"County: " .* county[cind] .* ", " .* state[cind] .* "<br>" .*
"Population: " .* string.(df[!, :POPULATION]) .* "<br>" .*
"Confirmed Cases (actual): " .* string.(df[!, :DEATH]) .* "<br>" .*
"Confirmed Cases per 100k: " .* string.(round.(df[!, :DEATHpc], digits=2)) .* "<br>" .*
"Daily New Deaths (actual): " .* string.(df[!, :dDEATHinst]) .* "<br>" .*
"Daily New Deaths per 100k: " .* string.(round.(df[!, :dDEATHpcinst], digits=2)) .* "<br>" .*
"% infected with COVID19: " .* string.(round.(df[!, :CONFIRMED] ./ df[!, :POPULATION] .* 100, digits=2)) .* "<br>" .*
"% death rate: " .* string.(round.(df[!, :DEATH] ./ df[!, :CONFIRMED] .*100, digits=2))
);
geo = attr(scope="usa",
projection_type="ablbers usa",
showland=true,
landcolor="rgb(220, 220, 220)",
subunitwidth=1,
countrywidth=1,
subunitcolor="rgb(255,255,255)",
countrycolor="rgb(255,255,255)",
);
title = attr(text = "Daily New Deaths per 100k " * string(t[ti])[1:10] * " (log10) <br><sub><a href=\"https://truedichotomy.github.io/covid19_public/\">https://truedichotomy.github.io/covid19_public/</a></sub></br>", yref = "paper", y=1.0)
layout = Layout(; title=title, showlegend=false, geo=geo)
PlotlyJS.plot(pmapsg, layout)
end
#figoutdir = "/Volumes/GoogleDrive/My Drive/COVID19/";
local figoutdir = "../covid19_public/ts_maps/";
#PlotlyJS._js_path = "https://cdn.plot.ly/plotly-latest.min.js";
#PlotlyJS.savehtml(pmapconfirmed(), figoutdir * "covid19map_confirmed.html", :remote);
#PlotlyJS.savehtml(pmapdconfirmed(), figoutdir * "covid19map_delta_confirmed_7days.html", :remote);
#PlotlyJS.savehtml(pmapdconfirmedinst(), figoutdir * "covid19map_delta_confirmed_latest.html", :remote);
#PlotlyJS.savehtml(pmapdeath(), figoutdir * "covid19map_death.html", :remote);
#PlotlyJS.savehtml(pmapddeath(), figoutdir * "covid19map_delta_death_7days.html", :remote);
#PlotlyJS.savehtml(pmapddeathinst(), figoutdir * "covid19map_delta_death_latest.html", :remote);
#end
#p = pmapdconfirmed()
local mio = open(figoutdir * "covid19map_delta_confirmed_7days_" * string(t[ti]) * ".jpg", "w")
PlotlyJS.savefig(mio, pmapdconfirmed(); format="jpeg", width=1280, height=720, scale = 3);
close(mio)
local mio = open(figoutdir * "covid19map_confirmed_7days_" * string(t[ti]) * ".jpg", "w")
PlotlyJS.savefig(mio, pmapconfirmed(); format="jpeg", width=1280, height=720, scale = 3);
close(mio)
local mio = open(figoutdir * "covid19map_death_7days_" * string(t[ti]) * ".jpg", "w")
PlotlyJS.savefig(mio, pmapdeath(); format="jpeg", width=1280, height=720, scale = 3);
close(mio)
end