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using CovidSEIR,  Plots, DataFrames, JLD2, StatsPlots, MCMCChains
Plots.pyplot()
jmddir = normpath(joinpath(dirname(Base.find_package("CovidSEIR")),"..","docs","jmd"))
covdf = covidjhudata();

Italy¶

italy = CountryData(covdf, "Italy");

itmod = CovidSEIR.TimeVarying.countrymodel(italy)
cc = Turing.psample(itmod, NUTS(0.65), 5000, 4)
import JLD2
JLD2.@save "$jmddir/italy_tv_$(Dates.today()).jld2" cc

JLD2.@load "$jmddir/italy_dhmc_2020-04-13.jld2" cc;

Error: SystemError: opening file "/home/paul/.julia/dev/CovidSEIR/docs/jmd/
italy_dhmc_2020-04-13.jld2": No such file or directory

cc = MCMCChains.Chains(collect(cc.value.data), replace.(cc.name_map.parameters, r"([^\[])([1-9])" => s"\1[\2]"))

Error: UndefVarError: cc not defined

Estimates¶

plot(cc)

Error: UndefVarError: cc not defined

describe(cc)

Error: UndefVarError: cc not defined

Fit¶

sdf = simtrajectories(cc, italy, 1:200)

Error: UndefVarError: cc not defined

f = plotvars(sdf, italy)

Error: UndefVarError: sdf not defined

f.fit

Error: UndefVarError: f not defined

As with Canada, the fit is very good, and the posterior distribution of observables is very precise.

Implications¶

for fig in f.trajectories
  display(fig)
end

Error: UndefVarError: f not defined