Cori et al. (2013) instantaneous reproduction number

Usage

RtSi(incidence, serial_interval, window = 7L, a_prior = 1, b_prior = 5)

Arguments

incidence: daily incidence I_0 ... I_{T-1}
serial_interval: discrete serial-interval distribution w_0, w_1, ...
window: sliding window length tau, in days
a_prior, b_prior: gamma prior shape and SCALE (EpiEstim default prior mean 5, sd 5 is a = 1, b = 5)

Value

list(r_mean, r_std, a_posterior, b_posterior, lambda, t_start, t_end, n_windows, n)

Examples

V <- c(1, 2, 3, 4, 5, 6, 7, 8)
RtSi(V, V)
#> $r_mean
#> [1] 0.109356
#> 
#> $r_std
#> [1] 0.018226
#> 
#> $a_posterior
#> [1] 36
#> 
#> $b_posterior
#> [1] 0.003037667
#> 
#> $lambda
#> [1]   0   4  10  20  35  56  84 120
#> 
#> $t_start
#> [1] 1
#> 
#> $t_end
#> [1] 7
#> 
#> $window
#> [1] 7
#> 
#> $a_prior
#> [1] 1
#> 
#> $b_prior
#> [1] 5
#> 
#> $n_windows
#> [1] 1
#> 
#> $n
#> [1] 8
#> 
#> $method
#> [1] "Cori et al. (2013) instantaneous R, gamma-Poisson conjugate posterior"
#>