In ku-awdc/Covid19RR: Estimation of Reproduction Rates for the COVID-19 Pandemic in Denmark based on Publicly Available Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

COVID-19 in Denmark

library("Covid19RR")
cv19dat <- download_data()
Tref <- 70000  # Reference tests
mod <- estimate_cv19rr(cv19dat,RefTests=Tref,logtau=log(7))
plot(mod)

With Epiestim

library("EpiEstim")
cv19dat$dates <- cv19dat$Date
cv19dat$I <- cv19dat$NewPositive
res_epiestim_cv19 <- estimate_R(cv19dat,
                           method="parametric_si",
                           config = make_config(list(
                                  mean_si = 2.6, 
                                  std_si = 1.5))
)
plot(res_epiestim_cv19)                           

Flu2009

library("Covid19RR")
library("EpiEstim")
data(Flu2009)

Flu2009_cv19rr <- Flu2009$incidence
names(Flu2009_cv19rr) <- c("Date", "NewPositive")
# Make up a constant:
Flu2009_cv19rr$NotPrevPos <- 100

res_cv19rr_flu <- estimate_cv19rr(Flu2009_cv19rr,beta=0)
plot(res_cv19rr_flu)

Estimation using EpiEstim:

library("EpiEstim")
data(Flu2009)
head(Flu2009$incidence)
res_epiestim_flu <- estimate_R(Flu2009$incidence, 
                                method="parametric_si",
                                config = make_config(list(
                                  mean_si = 2.6, 
                                  std_si = 1.5))
)
plot(res_epiestim_flu)

ku-awdc/Covid19RR documentation built on Feb. 2, 2021, 12:49 p.m.