Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

Documentation for package ‘STraTUS’ version 1.1.2

build.edgelist	For a sample, produce the transmission tree as a 'igraph' object
draw.fully.sampled	For a sample with no unsampled hosts, draw the annotated phylogeny using 'ggtree'
draw.incompletely.sampled	For a sample with or without unsampled hosts, draw the annotated phylogeny using 'ggtree'
grouping.map	A vector assigning the tips of 'stratus.example.tree' to groups (in the order they appear in 'stratus.example.tree$tip.label'), as an example of multiple sampling.
sample.partial.tt	Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed
sample.tt	Sample one or more transmission trees uniformly
stratus.example.tree	An unexceptional phylogeny generated with 'rtree' from 'ape'
tt.generator	Enumerate transmission trees for the given pathogen phylogeny, and provide a uniform sample generator