Overview | Input data | Fitting the model | Viewing results | Visualization | MCMC diagnostics | Antibody trajectories | Boosting and waning | Infection probabilities | Tables | Subgroup analysis | Joint model with shared parameters | Simulation | Citation

Model overview | Notation | Antibody dynamics model | Measurement error model | Infection risk model | Prior distributions | MCMC implementation | Convergence diagnostics | Recommendations for production analyses | Parameter layout | Shared parameter models | References

Overview | Data format | Serial interval | Fitting the model | Inspecting results | Quick overview | Parameter estimates | Posterior means | Accessing MCMC output | Visualization | MCMC diagnostics | Transmission probability over time | Covariate effects (forest plot) | Secondary attack rates | Household timeline | Summary tables | Covariate effects | Input validation | Missing data handling | Missing onset times | Missing covariates | Estimating the serial interval | Simulation

Overview | Model | Study design | Infection hazard | Covariates | Likelihood | Individual likelihood | Full likelihood | Prior distributions | MCMC algorithm | Metropolis-Hastings sampler | Adaptive proposal tuning | Data augmentation | Serial interval estimation | Convergence diagnostics | Recommended MCMC settings | Interpretation of parameters | Base parameters | Covariate effects | Serial interval parameters | Computational details | References