Man pages for xavierdidelot/TransPhylo
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 |
