sample_posterior_R(R, n = 1000, window = 1L)

## load data on pandemic flu in a school in 2009
data("Flu2009")

## estimate the reproduction number (method "non_parametric_si")
## when not specifying t_start and t_end in config, they are set to estimate
## the reproduction number on sliding weekly windows                          
res <- estimate_R(incid = Flu2009$incidence, 
                  method = "non_parametric_si",
                  config = make_config(list(si_distr = Flu2009$si_distr)))

## Sample R from the first weekly window
win <- 1L
R_median <- res$R$`Median(R)`[win]
R_CrI <- c(res$R$`Quantile.0.025(R)`[win], res$R$`Quantile.0.975(R)`[win])

set.seed(2019-06-06) # fixing the random seed for reproducibility
R_sample <- sample_posterior_R(res, n = 1000, window = win)
hist(R_sample, col = "grey", main = "R sampled from the first weekly window")
abline(v = R_median, col = "red")       # show the median estimated R
abline(v = R_CrI, col = "red", lty = 2) # show the 95%CrI of R