Compute Daily Incident Cases from Cumulative Simulation Output

This function takes a data frame or matrix containing irregularly spaced simulation time points and cumulative case counts (C), and returns the number of new cases per day using linear interpolation.

Usage

get_daily_cases(r)

Arguments

r

A data frame or matrix with columns "time" and "C", representing time (in continuous units) and cumulative number of cases, respectively.

Value

A tibble() with two columns:

day

Integer day values from the floor of the minimum time to the ceiling of the maximum time

daily_incidence

Number of new cases per day, computed as the difference in interpolated cumulative cases

Details

Since simulation outputs may record cumulative cases at non-integer time points, this function performs linear interpolation to estimate cumulative cases at each whole-number day. It then computes the number of incident cases as the first difference of the interpolated values. The first day is assigned 0 new cases by default.

Examples

sim_data <- as.matrix(dplyr::tibble(
  time = c(0, 0.1, 0.9, 1.4, 2.3, 3.8),
  C = c(0, 1, 5, 7, 10, 15)
))
get_daily_cases(sim_data)
#> # A tibble: 5 × 2
#>     day daily_incidence
#>   <int>           <dbl>
#> 1     0            0   
#> 2     1            5.4 
#> 3     2            3.6 
#> 4     3            3.33
#> 5     4           NA