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| bitrugs | Bayesian Inference of Transmission Routes Using Genome Sequences |
| hospitaldata | Example hospital data |
| mcmcoutput | Example MCMC output |
| plot_transnetwork | Plot transmission networks |
| simulate_data | Nosocomial transmission data simulation |
| simulate_data_dates | Nosocomial transmission data simulation with fixed dates. |
| traceplots | Create MCMC trace plots |
| translinks | Calculate tree distance |
| transmission_analysis | Estimate transmission dynamics and parameters |