STraTUS (1.1.1)

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) for methodology.

Maintainer: Matthew Hall
Author(s): Matthew Hall [aut, cre], Caroline Colijn [ctb]

License: GPL

Uses: ape, ggplot2, gmp, igraph, phangorn, RcppAlgos

Released 4 months ago.