calculate_bootstrap_ci

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

Provides methods to estimate serial intervals and time-varying case
reproduction numbers from infectious disease outbreak data. Serial intervals measure
the time between symptom onset in linked transmission pairs, while case reproduction
numbers quantify how many secondary cases each infected individual generates
over time. These parameters are essential for understanding transmission
dynamics, evaluating control measures, and informing public health responses.
The package implements the maximum likelihood framework from Vink et al. (2014)
<doi:10.1093/aje/kwu209> for serial interval estimation and the retrospective
method from Wallinga & Lipsitch (2007) <doi:10.1098/rspb.2006.3754> for
reproduction number estimation. Originally developed for scabies transmission
analysis but applicable to other infectious diseases including influenza,
COVID-19, and emerging pathogens. Designed for epidemiologists, public health
researchers, and infectious disease modelers working with outbreak surveillance
data.

Kylie Ainslie

mitey

Serial Interval and Case Reproduction Number Estimation

calculate_bootstrap_ci function

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

Arguments

Calculate Bootstrap Confidence Intervals for R Estimates — calculate_bootstrap_ci

<dl>

<dt>incidence</dt>
<dd>numeric vector; daily case counts</dd>


<dt>si_prob</dt>
<dd>numeric matrix; serial interval probability matrix</dd>


<dt>dates</dt>
<dd>vector; dates corresponding to incidence data</dd>


<dt>si_mean</dt>
<dd>numeric; mean of the serial interval distribution</dd>


<dt>si_sd</dt>
<dd>numeric; standard deviation of the serial interval distribution</dd>


<dt>si_dist</dt>
<dd>character; distribution type, either "gamma" or "normal"</dd>


<dt>smoothing</dt>
<dd>integer; window size for temporal smoothing</dd>


<dt>n_bootstrap</dt>
<dd>integer; number of bootstrap samples to generate</dd>


<dt>conf_level</dt>
<dd>numeric; confidence level (between 0 and 1)</dd>

</dl>

calculate_bootstrap_ci: Calculate Bootstrap Confidence Intervals for R Estimates

Description

Usage

Value

Arguments