highly specialized function to demonstrate how to produce an estimated Rt based on JHU confirmed case time-series

gistfile1.R

library(sars2pack)
easyRt = function(alpha3="ITA", src = (suppressWarnings(enriched_jhu_data())),
         init = "2020-03-01",  ...) {
  cur = cumulative_events_ejhu(src, eventtype="confirmed",
           alpha3=alpha3)
  inc = form_incident_events( trim_from (cur, init ) )
  newd = data.frame(I=inc$count, dates=inc$dates)
  EpiEstim::estimate_R(newd, ...)
}
rtBya3 = function(a3="ITA") {
  data("Flu2009", package="EpiEstim")
  easyRt(alpha3=a3, method = "non_parametric_si", 
        config = EpiEstim::make_config(list(si_distr = Flu2009$si_distr)))
}
chk = rtBya3()
plot(chk)