Inference of Transmission Tree from a Dated Phylogeny

as.mcmc.resTransPhylo | Convert to coda mcmc format |

computeMatTDist | Build a matrix indicating for each pairs of individuals how... |

computeMatWIW | Build a matrix of probability of who infected whom from a... |

consTTree | Build a consensus transmission tree from a MCMC output |

convertToCoda | Convert to coda mcmc format |

dateLastSample | Return the date of last sample from a ttree or ctree or ptree |

extractCTree | Return the combined tree corresponding to a given iteration... |

extractPTree | Extracts phylogenetic tree from a combined... |

extractTTree | Extracts transmission tree from a combined... |

getGenerationTimeDist | Extract and return realised generation time distribution |

getIncidentCases | Returns and/or plot numbers of sampled and unsampled cases... |

getInfectionTimeDist | Extract and return distribution of infection time of given... |

getOffspringDist | Extract and return offspring distribution of given sampled... |

getSamplingTimeDist | Extract and return realised sampling time distribution |

infer_multittree_share_param | Simultaneously infer transmission trees given phylogenetic... |

inferTTree | Infer transmission tree given a phylogenetic tree |

makeCTreeFromPTree | Create a transmission tree compatible with the provided... |

makeTTree | Simulate a transmission tree |

medTTree | Return the medoid from a MCMC output |

phyloFromPTree | Converts a phylogenetic tree into an ape phylo object |

plot.ctree | Plotting for ctree |

plotCTree | Plot both phylogenetic and transmission trees using colors on... |

plot.ptree | Plotting for ptree |

plot.resTransPhylo | Plotting for resTransPhylo |

plotTraces | Plot MCMC traces |

plot.ttree | Plotting for ttree |

plotTTree | Plot a transmission tree in a detailed format |

plotTTree2 | Plot a transmission tree in an economic format |

print.ctree | Print function for ctree objects |

print.ptree | Print function for ptree objects |

print.resTransPhylo | Print function for resTransPhylo objects |

print.ttree | Print function for ttree objects |

probPTreeGivenTTree | Calculate the probability of a phylogenetic tree given a... |

probPTreeGivenTTreeR | Calculate the probability of a phylogenetic tree given a... |

probTTree | Calculates the log-probability of a transmission tree |

probTTreeR | Calculates the log-probability of a transmission tree |

ptreeFromPhylo | Converts an ape phylo object into a phylogenetic tree |

selectTTree | Select the most representative transmission tree from a MCMC... |

simulateOutbreak | Simulate an outbreak |

summary.resTransPhylo | Summary function for resTransPhylo objects |

TransPhylo-package | Inference of Transmission Tree from a Dated Phylogeny |

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