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@briochemc
Forked from mbauman/covid19.jl
Last active April 2, 2020 06:37
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using HTTP, CSV, Plots, DataFrames, Dates
# Download the data
df = CSV.read(IOBuffer(String(HTTP.get("https://covid.ourworldindata.org/data/total_cases.csv").body)), normalizenames=true)
# Plotting function
function doit(df, countries, alignment)
cp = get_color_palette(:auto, plot_color(:white), length(countries))
plot(legend=false)
for (i,country) in enumerate(countries)
c = df[:, country]
d = map(x -> x.value, df.date .- df.date[findfirst(coalesce.(c,0) .>= alignment)])
plot!(d, c, color=i, yaxis=:log, m=:circle, ms=2, msw=false, lw=2, label="")
plot!([d[end]], [c[end]], color=cp[i], yaxis=:log, m=:circle, ms=3, label="")
# annotate country next to end point instead of legend
annotate!(d[end]+1, c[end], text("$(replace(string(country), "_"=>" "))", 8, :left, :bold, color=cp[i]))
end
xlabel!("Days since $(alignment)th case")
ylabel!("Cumulative number of cases")
# pretty lims
xlims!(-1, last(xlims())+4)
ylims!(alignment*.8, last(ylims()))
yticks=vec([1,2,5] * 10 .^ (1:4)')
# pretty ticks
yticks=yticks[alignment .≤ yticks .≤ maximum(df[end,countries])]
plot!(yticks=(yticks, string.(yticks)), xticks=0:7:last(xlims())+4)
end
function addtrend(df, dailygrowth, alignment)
d = 0:last(xlims())
c = alignment * (1 + dailygrowth) .^ (d)
plot!(d, c, ls=:dot, color=:gray, lw=2, label="+$(100dailygrowth)% daily")
plot!(legend=:bottomright)
end
# Do it! (plotting the data)
doit(df, [:China, :Italy, :France, :Spain, :Australia, :United_States, :United_Kingdom, :Singapore, :South_Korea], 100)
addtrend(df, 0.25, 100)
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using HTTP, CSV, Plots, DataFrames
# Download the data
df = CSV.read(IOBuffer(String(HTTP.get("https://covid.ourworldindata.org/data/total_deaths.csv").body)), normalizenames=true)
# Plotting function
function doit(df, countries, alignment)
countries = countries[findall(map(x -> ismissing(x) ? false : x > alignment, Vector(df[end, countries])))]
cp = get_color_palette(:auto, plot_color(:white), length(countries))
plot(legend=false)
for (i, country) in enumerate(countries)
c = df[:, country]
(c[end] isa Missing || c[end] < alignment) && continue
d = map(x -> x.value, df.date .- df.date[findfirst(coalesce.(c,0) .>= alignment)])
plot!(d, c, color=cp[i], yaxis=:log, m=:circle, ms=2, msw=false, lw=2, label="")
plot!([d[end]], [c[end]], color=cp[i], yaxis=:log, m=:circle, ms=3, label="")
# annotate country next to end point instead of legend
annotate!(d[end]+1, c[end], text("$(replace(string(country), "_"=>" "))", 8, :left, :bold, color=cp[i]))
end
xlabel!("Days since $(alignment)th death")
ylabel!("Cumulative number of deaths")
# pretty lims
xlims!(-1, last(xlims())+4)
ylims!(alignment*.8, last(ylims()))
# pretty ticks
yticks=vec([1,2,5] * 10 .^ (0:4)')
yticks=yticks[alignment .≤ yticks .≤ maximum(df[end,countries])]
plot!(yticks=(yticks, string.(yticks)), xticks=0:7:last(xlims())+4)
end
function addtrend(df, dailygrowth, alignment)
d = 0:last(xlims())
c = alignment * (1 + dailygrowth) .^ (d)
plot!(d, c, ls=:dot, color=:gray, lw=2, label="+$(100dailygrowth)% daily")
plot!(legend=:bottomright)
end
# Do it! (plotting the data)
doit(df, names(df)[3:end], 10)
addtrend(df, 0.25, 10)
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using HTTP, CSV, Plots, DataFrames, Dates
file_url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
# Download the data
df = CSV.read(IOBuffer(String(HTTP.get(file_url).body)), normalizenames=true, header=2, transpose=true, datarow=5)
const allcountries = unique(replace.(string.(names(df)), r"_\d*$"=>""))[2:end]
# Plotting function
function doit(df, countries, lockdowndict=Dict(); Δdays=1)
cp = get_color_palette(:auto, plot_color(:white), length(countries))
plot(xaxis=:log, yaxis=:log)
for country in allcountries
country == "Cruise_Ship" && continue
country == "Diamond_Princess" && continue
i = findfirst(Symbol(country) .== countries)
if i isa Nothing
color, m, ms, α, mα, lw, fs = RGBA{Float64}(0,0,0,0.1), 0, 0, 0.1, 0, 1, 4
elseif country == "Australia"
color, m, ms, α, mα, lw, fs = cp[i], :star, 4, 1, 0, 4, 12
else
color, m, ms, α, mα, lw, fs = cp[i], :circle, 2, 0.5, 0, 2, 8
end
cases = Float64.(sum(eachcol(select(df, occursin.(string(country), string.(names(df)))))))
Δcases = cases[1+Δdays:end] - cases[1:end-Δdays]
cases = cases[1+Δdays:end]
ikeep = findall((cases .> 0) .& (Δcases .> 0))
cases = cases[ikeep]
Δcases = Δcases[ikeep]
(any(Δcases .≤ 0) || length(ikeep) == 0) && continue
plot!(cases, Δcases, color=color, m=m, ms=ms, msw=0, lw=lw, α=α, mα=mα, label="")
plot!([cases[end]], [Δcases[end]], color=color, m=m, α=1, ms=ms+1, msw=0, label="")
# annotate country next to end point instead of legend
cases[end] > 30 && Δcases[end] > 10 && annotate!(cases[end] * 1.1, Δcases[end], text("$(replace(string(country), "_"=>" "))", fs, :left, :bold, color=color))
end
# axis labels
xlabel!("Total confirmed cases")
ylabel!("Δcases over $Δdays days")
# pretty lims
ticks=vec([1,3] * 10 .^ (0:5)')
plot!(xlims=(30,last(xlims())))
plot!(ylims=(10,last(ylims())))
xticks = ticks[first(xlims()) .≤ ticks .≤ last(xlims())]
yticks = ticks[first(ylims()) .≤ ticks .≤ last(ylims())]
# pretty ticks
plot!(xticks=(xticks, addprefix.(string.(xticks))), yticks=(yticks, addprefix.(string.(yticks))))
Δx, cstart = collect(xlims()), 300
growth(Δx, cstart, 1, Δdays, :solid)
growth(Δx, cstart, 3, Δdays, :dash, "")
growth(Δx, cstart, 7, Δdays, :dashdot, "")
growth(Δx, cstart, 21, Δdays, :dot, "")
plot!(legend=:topleft, legendtitle="Doubling time")
end
Δc_vs_c(c, τ, Δdays) = (1 - 0.5^(Δdays/τ)) .* c
function growth(Δx, cstart, τ, Δdays, ls, str=" in $Δdays days")
α = log(2) / τ
c = cstart * exp.(α*Δdays*[0,1])
plot!(Δx, Δc_vs_c(Δx, τ, Δdays), ls=ls, color=:gray, lw=1, label=" days")
plot!(c, Δc_vs_c(c, τ, Δdays), m=[:circle, :dtriangle], ms=2, ls=:solid, color=:black, lw=1, label="")
str = "×$(round(c[end]/c[1], digits=1))$str"
if length(str) > 10
annotate!(c[end] * 0.8, Δc_vs_c(c, τ, Δdays)[end], text(str, 8, :right, color=:black))
else
annotate!(c[end] * 1.1, Δc_vs_c(c, τ, Δdays)[end], text(str, 8, :left, color=:black))
end
end
function addprefix(s)
s = replace(s, r"(.*)000000000$"=>s"\1G")
s = replace(s, r"(.*)000000$"=>s"\1M")
s = replace(s, r"(.*)000$"=>s"\1k")
return s
end
function addtrend(xlims, trend, Δdays)
plot!(collect(xlims), trend * Δdays * collect(xlims), ls=:dot, color=:gray, lw=2, label="+$(100trend)%", legend=:topleft)
end
function adddoublingtime(Δx, τ, Δdays)
plot!(Δx, Δx * 1 ./ τ' * Δdays, ls=:dot, color=:gray, lw=2, label=string.(τ, " days"), legend=:topleft)
end
lockdowndict = Dict(
:Australia => nothing,
:Italy => Date("9 March 2020", dateformat"d U Y"),
:France => Date("16 March 2020", dateformat"d U Y"),
:China => Date("23 January 2020", dateformat"d U Y"),
)
# Do it! (plotting the data)
#countries = [:China, :Canada, :Turkey, :India, :Iraq, :Bahrain, :Iran, :Germany, :Switzerland, :Netherlands, :Belgium, :Italy, :France, :Spain, :Australia, :US, :United_Kingdom, :Singapore, :Korea_South, :Japan, :Norway, :Finland, :Sweden]
countries = [:China, :Canada, :Italy, :France, :Spain, :Australia, :US, :United_Kingdom, :Singapore, :Korea_South, :Japan]
doit(df, countries, lockdowndict; Δdays=3)
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using HTTP, CSV, Plots, DataFrames, Dates
file_url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
# Download the data
df = CSV.read(IOBuffer(String(HTTP.get(file_url).body)), normalizenames=true, header=2, transpose=true, datarow=5)
const allcountries = unique(replace.(string.(names(df)), r"_\d*$"=>""))[2:end]
# Plotting function
function doit(df, countries, alignment, lockdowndict=Dict())
cp = get_color_palette(:auto, plot_color(:white), length(countries))
plot(legend=false, yaxis=:log)
dates = Date.(df.Country_Region, dateformat"mm/dd/yy") .+ Year(2000)
days = [d.value for d in (dates .- dates[1])]
n = length(days)
for country in allcountries
country == "Cruise_Ship" && continue
i = findfirst(Symbol(country) .== countries)
if i isa Nothing
color, m, ms, α, ma, lw, fs = RGBA{Float64}(0,0,0,0.1), 0, 0, 0.1, 0, 1, 4
elseif country == "Australia"
color, m, ms, α, ma, lw, fs = cp[i], :star, 4, 1, 0, 4, 12
else
color, m, ms, α, ma, lw, fs = cp[i], :circle, 2, 0.5, 0, 2, 8
end
cases = Float64.(sum(eachcol(select(df, occursin.(string(country), string.(names(df)))))))
# alignment by interpolating
if cases[1] > alignment
baseline = -cases[1] / (cases[2] - cases[1])
elseif cases[end] < alignment
continue
else
ialign = findlast(cases .< alignment)
baseline = ialign + (alignment - cases[ialign]) / (cases[ialign+1] - cases[ialign]) - 1
end
# don't plot 0 values
cases[cases .== 0] .= NaN
plot!(days .- baseline, cases, color=color, m=m, ms=ms, msw=0, lw=lw, alpha=α, ma=ma, label="")
plot!([days[end] - baseline], [cases[end]], color=color, m=m, alpha=1, ms=ms+1, msw=0, label="")
# annotate country next to end point instead of legend
annotate!(days[end] - baseline + 0.5, cases[end], text("$(replace(string(country), "_"=>" "))", fs, :left, :bold, color=color))
end
# axis labels
xlabel!("Days since $(alignment)th case")
ylabel!("Cumulative number of cases")
# pretty lims
xlims!(0, last(xlims())+4)
ylims!(alignment, last(ylims()))
yticks=vec([1,2,5] * 10 .^ (1:4)')
# pretty ticks
yticks=yticks[first(ylims()) .≤ yticks .≤ last(ylims())]
plot!(yticks=(yticks, string.(yticks)), xticks=0:7:last(xlims())+4)
end
lockdowndict = Dict(
:Australia => nothing,
:Italy => Date("9 March 2020", dateformat"d U Y"),
:France => Date("16 March 2020", dateformat"d U Y"),
:China => Date("23 January 2020", dateformat"d U Y"),
)
function addtrend(dailygrowth, alignment)
d = 0:last(xlims())
c = alignment * (1 + dailygrowth) .^ (d)
plot!(d, c, ls=:dot, color=:gray, lw=2, label="+$(100dailygrowth)% daily")
plot!(legend=:bottomright)
end
# Do it! (plotting the data)
countries = [:China, :Turkey, :India, :Iraq, :Bahrain, :Iran, :Germany, :Switzerland, :Netherlands, :Belgium, :Italy, :France, :Spain, :Australia, :US, :United_Kingdom, :Singapore, :Korea_South, :Japan, :Norway, :Finland, :Sweden]
doit(df, countries, 100, lockdowndict)
addtrend(0.25, 100)
@briochemc
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briochemc commented Mar 18, 2020

First output "Will Australia be like current Italy in ~3 weeks?"

covid19.jl output

Second output: All death cases above 10

covid19_deaths.jl output

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