Man pages for yuanwxu/TransPhyloC
Inference of Transmission Tree under a Within-Host Evolution Model
| 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... |
