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| burnin.phybreak | MCMC updating of a phybreak-object. |
| get.mcmc | Accessing a phybreak object |
| get.parameters | Accessing a phybreak object |
| get.phybreak | Accessing a phybreak object |
| get.phylo | Accessing a phybreak object |
| get.seqdata | Accessing a phybreak object |
| get.tree | Accessing a phybreak object |
| infectorsets | Sampled infectors for each host in a phybreak-object. |
| logLik.phybreak | Log-likelihood of a phybreak-object. |
| phybreak | Create a phybreak-object from data and prior distributions. |
| phylotree | Maximum clade credibility tree. |
| plot.phybreak | Plotting a phybreak object. |
| sample.phybreak | Sampling from a phybreak MCMC-chain. |
| sim.phybreak | Outbreak simulation. |
| thin.phybreak | Remove posterior samples from a phybreak-object. |
| transtree | Create a consensus transmission tree. |