computeMatWIW | Build a matrix of probability of who infected whom from a... |
consTTree | Build a consensus transmission tree from a MCMC output |
extractPTree | Extracts phylogenetic tree from a combined... |
extractTTree | Extracts transmission tree from a combined... |
inferTTree | Infer transmission tree given a phylogenetic tree |
makeCtreeFromPTree | Create a transmission tree compatible with the provided... |
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... |
plotTTree | Plot a transmission tree |
plotTTree2 | Plot a transmission tree in an economic format |
probPTreeGivenTTree | Calculate the probability of a phylogenetic tree given a... |
probTTree | Calculates the log-probability of a transmission tree |
ptreeFromPhylo | Converts an ape phylo object into a phylogenetic tree |
simulateOutbreak | Simulate an outbreak |
TransPhylo-package | Inference of transmission tree under a within-host evolution... |
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