Impute unobserved generations of infection

This function imputes incidence prior the first date of reported cases to address early bias in R_t estimates. A simple linear model is fitted on shifted, logged-incidence cases, based on an initial observation window. Log-incidence is computed as log(local + 0.5) to avoid -infinite logs. Currently, no cases are assumed to be imported.

backimpute_I(incid, window_b)

Arguments

incid

the raw, reported incidence cases.

window_b

length of the observation window to fit the exponential growth model for back-imputation

Value

an incidence data.frame, combining back-imputed cases for a maximum of 100 time points (with rows indexed by a negative integer rowname) and cases (with rows #' indexed by a non-negative integer)

Examples

incid_all <- ceiling(exp(.3 * 0:20))
incid_trunc <- tail(incid_all, 10)
x <- backimpute_I(incid=incid_trunc, window_b=6)
idx <- as.integer(rownames(x)) > -10
x[idx, ]$local
#>  [1]   1.005090   1.517613   2.204664   3.125674   4.360311   6.015376
#>  [7]   8.234033  11.208202  15.195154  20.539768  28.000000  37.000000
#> [13]  50.000000  67.000000  91.000000 122.000000 165.000000 222.000000
#> [19] 299.000000 404.000000
incid_all
#>  [1]   1   2   2   3   4   5   7   9  12  15  21  28  37  50  67  91 122 165 222
#> [20] 299 404