Calculate Right-Truncation Correction Factors — calculate_truncation

Computes correction factors to adjust reproduction number estimates for right-truncation bias. This bias occurs because cases near the end of the observation period may have generated secondary cases that are not yet observed.

Usage

calculate_truncation_correction(dates, si_mean, si_sd, si_dist)

Arguments

dates: vector; dates corresponding to each case
si_mean: numeric; mean of the serial interval distribution in days
si_sd: numeric; standard deviation of the serial interval distribution in days
si_dist: character; distribution type, either "gamma" or "normal"

Value

numeric vector; correction factors for each case. Values > 1 indicate upward adjustment needed. Returns NA when correction would be unreliable (probability of observation <= 0.5)

Examples

# Calculate truncation correction for recent cases
case_dates <- seq(as.Date("2023-01-01"), as.Date("2023-01-20"), by = "day")
corrections <- calculate_truncation_correction(
  case_dates, si_mean = 7, si_sd = 3, si_dist = "gamma"
  )

# Show how correction increases for more recent cases
tail(corrections, 5)
#> [1] NA NA NA NA NA