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

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.

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Package details

AuthorMatthew Hall [aut, cre], Caroline Colijn [ctb]
MaintainerMatthew Hall <[email protected]>
Package repositoryView on CRAN
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STraTUS documentation built on May 21, 2019, 5:03 p.m.