# Bayesian Household Transmission Modeling with 'Stan'

## Documentation for package ‘HHBayes’ version 0.1.1

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

## Help Pages

calculate_sar_quick | Quick Secondary Attack Rate (SAR) Calculator
calculate_sar_robust | Calculate Secondary Attack Rate (SAR)
fill_missing_viral_data | Fill Missing Viral Data (Cycle Threshold or Log10) Based on Episode Start
fit_household_model | Fit Household Transmission Model
plot_covariate_effects | Plot Covariate Coefficients (Forest Plot)
plot_epidemic_curve | Plot Dual-Axis Epidemic Curve (Binned)
plot_household_timeline | Plot Household Timeline with Person-Centric Reinfections
plot_posterior_distributions | Plot Posterior Distributions (Phi and Kappa)
prepare_stan_data | Prepare Data for Stan Model
reconstruct_transmission_chains | Reconstruct Transmission Chains
simulate_multiple_households_comm | Simulate Household Transmission
summarize_attack_rates | Summarize Attack Rates and Reinfections