Serial Interval and Case Reproduction Number Estimation

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Documentation for package ‘mitey’ version 0.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
flower	Calculate flower for Different Components
fupper	Calculate fupper 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
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