Renewal-equation reproduction number with reporting delay

Formula: I_t = R_t sum_{tau=1}^{gmax} g(tau) I_{t-tau}, so R_t = I_t / sum_tau g(tau) I_{t-tau}

Usage

Rtrenew(incidence, gen_int, delays = NULL)

Arguments

incidence

See Usage.

gen_int

See Usage.

delays

See Usage.

Value

List with rt, time, infections, shift, mean_rt, n.

References

Abbott, Hellewell, Sherratt et al (2020), EpiNow2. Model definition verified against the package's own estimate_infections() vignette, which states I_t = R_t sum_tau g(tau) I_{t-tau} and the delay convolution D_t = xi sum_tau xi(tau) I_{t-tau}.

Examples

V <- c(1, 2, 3, 4, 5, 6, 7, 8)
Rtrenew(V, V)
#> $rt
#> numeric(0)
#> 
#> $time
#> integer(0)
#> 
#> $infections
#> [1] 1 2 3 4 5 6 7 8
#> 
#> $shift
#> [1] 0
#> 
#> $mean_rt
#> [1] NaN
#> 
#> $n
#> [1] 8
#> 
#> $method
#> [1] "Renewal-equation Rt with reporting delay"
#> 
#> attr(,"class")
#> [1] "morie_rich_result" "list"