Calculate Bootstrap Confidence Intervals for R Estimates

Generates bootstrap confidence intervals for reproduction number estimates by resampling the incidence data multiple times and calculating quantiles of the resulting R distributions.

Usage

calculate_bootstrap_ci(
  incidence,
  si_prob,
  dates,
  si_mean,
  si_sd,
  si_dist,
  smoothing,
  n_bootstrap,
  conf_level
)

Arguments

incidence: numeric vector; daily case counts
si_prob: numeric matrix; serial interval probability matrix
dates: vector; dates corresponding to incidence data
si_mean: numeric; mean of the serial interval distribution
si_sd: numeric; standard deviation of the serial interval distribution
si_dist: character; distribution type, either "gamma" or "normal"
smoothing: integer; window size for temporal smoothing
n_bootstrap: integer; number of bootstrap samples to generate
conf_level: numeric; confidence level (between 0 and 1)

Value

named list with confidence interval bounds:

r_lower, r_upper: Confidence intervals for raw R estimates
r_corrected_lower, r_corrected_upper: Confidence intervals for corrected R estimates