Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny
For a sample, produce the transmission tree as a igraph object
For a sample with no unsampled hosts, draw the annotated phylogeny usi...
For a sample with or without unsampled hosts, draw the annotated phylo...
Resample the subtree rooted at any tree node, keeping the annotations ...
Sample one or more transmission trees uniformly
An unexceptional phylogeny generated with rtree from ape
Enumerate transmission trees for the given pathogen phylogeny, and pro...
For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.