covid19.jl

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)

covid19.svg

covid19_CSSEdata.svg

covid19_deaths.jl

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)

covid19_deaths.svg

covid19_logΔc_vs_logc.jl

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 $Δdays days")
    α = log(2) / τ
    c = cstart * exp.(α*Δdays*[0,1])
    plot!(Δx, Δc_vs_c(Δx, τ, Δdays), ls=ls, color=:gray, lw=1, label="$τ 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)

covid19_logΔc_vs_logc.svg

covid19_othersource.jl

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)

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

Second output: All death cases above 10