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| computeMatTDist | Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chain |
| computeMatWIW | Build a matrix of probability of who infected whom from a MCMC output |
| consTTree | Build a consensus transmission tree from a MCMC output |
| convertToCoda | Convert to coda mcmc format |
| extractPTree | Extracts phylogenetic tree from a combined phylogenetic/transmission tree |
| extractTTree | Extracts transmission tree from a combined phylogenetic/transmission tree |
| getGenerationTimeDist | Extract and return realised generation time distribution |
| getIncidentCases | Returns and/or plot numbers of sampled and unsampled cases over time |
| getInfectionTimeDist | Extract and return distribution of infection time of a given sampled case |
| getSamplingTimeDist | Extract and return realised sampling time distribution |
| inferTTree | Infer transmission tree given a phylogenetic tree |
| infer_multittree_share_param | Simultaneously infer transmission trees given phylogenetic trees User can specify any subset of parameters that will be shared by providing a character vector of parameter names to the argument "share". |
| makeCtreeFromPTree | Create a transmission tree compatible with the provided phylogenetic tree |
| makeTTree | Simulate a transmission tree |
| phyloFromPTree | Converts a phylogenetic tree into an ape phylo object |
| plotCTree | Plot both phylogenetic and transmission trees using colors on the phylogeny |
| plotTraces | Plot MCMC traces |
| plotTTree | Plot a transmission tree |
| plotTTree2 | Plot a transmission tree in an economic format |
| probPTreeGivenTTree | Calculate the probability of a phylogenetic tree given a transmission tree |
| 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 output |
| simulateOutbreak | Simulate an outbreak |
| TransPhylo | Inference of Transmission Tree under a Within-Host Evolution Model |