Man pages for donkeyshot/phybreak
Analysis of Outbreaks with Sequence Data
| AvianFluH7N7_2003 | Avian influenza (H7N7) epidemic |
| burnin_phybreak | MCMC updating of a phybreak-object. |
| c.phybreak | Combine mcmc-chains of phybreak-objects. |
| ESS | Effective sample size |
| FMD_2001 | Foot-and-Mouth Disease outbreak (2001) |
| FMD_2007 | Foot-and-Mouth Disease outbreak (2007) |
| get_phybreak | Extracting from a phybreak object |
| infectorsets | Sampled infectors for each host in a phybreak-object. |
| logLik.phybreak | Log-likelihood of a phybreak-object. |
| M_tuberculosis_2013 | Mycobacterium tuberculosis outbreak |
| phybreak | Create a phybreak-object from data and prior distributions. |
| phybreakdata | Create a phybreakdata-object from raw data. |
| phylotree | Maximum clade credibility tree. |
| plot.phybreak | Plotting a phybreak object. |
| plot.phybreakdata | Plotting a phybreakdata object. |
| plotPhylo | Plotting a phybreak object phylogenetic tree. |
| plotPhyloTrans | Plotting a phybreak object transmission and phylogenetic... |
| plotTrans | Plotting a phybreak or phybreakdata transmission tree. |
| print.phybreak | Description of phybreak object. |
| quantile.phybreak | Quantiles of sampled parameter values. |
| 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. |
