R: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

# Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

## Documentation for package ‘STraTUS’ version 1.1.2

- DESCRIPTION file

## Help Pages

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