# The R codes for calculating the basic reproductive number (R0)

# The estimated exponential rate (per year)
rate_mean_y <- 61.5
rate_lower_y <- 1.66
rate_upper_y <- 143.5

# Days in 2020
days <- 366

# The average duration of infectiousness (day)
dur_inf_d <- 9.3 

# The average duration of infectiousness (year)
dur_inf_y <- dur_inf_d / days 

# R0 = rD + 1 (Pybus et al., 2001; Wallinga and Lipsitch, 2007)
# where r is the exponential growth rate and D is the average duration of infectiousness.
R0 <- rate_mean_y * dur_inf_y + 1
R0_lower <- rate_lower_y * dur_inf_y + 1
R0_upper <- rate_upper_y * dur_inf_y + 1

print(round(R0,2))
print(round(R0_lower,2))
print(round(R0_upper,2))