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| as.igraph.simOutbreak | Simulation of pathogen genotypes during disease outbreaks |
| as.igraph.tTree | Simple transmission tree from outreaber's output |
| disperse | Simulation of pathogen genotypes during disease outbreaks |
| fakeOutbreak | Toy outbreak dataset used to illustrate outbreaker |
| findMutations.tTree | Simple transmission tree from outreaber's output |
| get.incid | Derive reproduction numbers from outbreak's outputs |
| get.mu | Derive mutation rate estimation from outbreak's outputs |
| get.R | Derive reproduction numbers from outbreak's outputs |
| get.Rt | Derive reproduction numbers from outbreak's outputs |
| get.tTree | Simple transmission tree from outreaber's output |
| labels.simOutbreak | Simulation of pathogen genotypes during disease outbreaks |
| outbreaker | Outbreaker: disease outbreak reconstruction using genetic data |
| outbreaker.package | outbreaker: disease outbreak reconstruction using epidemiological and genetic data |
| outbreaker.parallel | Outbreaker: disease outbreak reconstruction using genetic data |
| plot.simOutbreak | Simulation of pathogen genotypes during disease outbreaks |
| plot.tTree | Simple transmission tree from outreaber's output |
| plotChains | Plot outbreaker's results |
| plotOutbreak | Plot outbreaker's results |
| print.simOutbreak | Simulation of pathogen genotypes during disease outbreaks |
| selectChains | Select 'good' runs from independent MCMC chains |
| simOutbreak | Simulation of pathogen genotypes during disease outbreaks |
| simOutbreak-class | Simulation of pathogen genotypes during disease outbreaks |
| simulated outbreak dataset | Toy outbreak dataset used to illustrate outbreaker |
| transGraph | Plot outbreaker's results |
| tTree | Simple transmission tree from outreaber's output |
| [.simOutbreak | Simulation of pathogen genotypes during disease outbreaks |