Bayesian Household Transmission Modeling with 'Stan'
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Documentation for package ‘HHBayes’ version 0.1.1
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 |