Package index

All functions

calculate_bootstrap_ci()

Calculate Bootstrap Confidence Intervals for R Estimates

calculate_r_estimates()

Calculate Reproduction Number Estimates

calculate_si_probability_matrix()

Calculate Serial Interval Probability Matrix

calculate_truncation_correction()

Calculate Right-Truncation Correction Factors

conv_tri_dist()

Convolution of the triangular distribution with the mixture component density (continuous case)

create_day_diff_matrix()

Create Day Difference Matrix

f0()

Calculate f0 for Different Components

f_gam()

Calculate serial interval mixture density assuming underlying gamma distribution

f_norm()

Calculate serial interval mixture density assuming underlying normal distribution

flower()

Calculate flower for Different Components

fupper()

Calculate fupper for Different Components

generate_case_bootstrap()

Generate Bootstrap Sample of Case Incidence

generate_synthetic_epidemic()

Generate Synthetic Epidemic Data Using the Renewal Equation

integrate_component()

Integrate Serial Interval Component Functions for Likelihood Calculation

integrate_components_wrapper()

Compute Serial Interval Component Integrals for All Transmission Routes

plot_si_fit()

Visualize Serial Interval Distribution Fit to Outbreak Data

si_estim()

Estimate Serial Interval Distribution Using the Vink Method

smooth_estimates()

Apply Moving Average Smoothing to R Estimates

wallinga_lipsitch()

Estimate Time-Varying Case Reproduction Number Using Wallinga-Lipsitch Method

weighted_var()

Calculate Sample Weighted Variance

wt_loglik()

Calculate Weighted Negative Log-Likelihood for Gamma Distribution Parameters