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.


Reference manual

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1.1.2 by Matthew Hall, a year ago


Browse source code at https://github.com/cran/STraTUS

Authors: Matthew Hall [aut, cre] , Caroline Colijn [ctb]

Documentation:   PDF Manual  

GPL license

Imports ape, phangorn, igraph, gmp, ggplot2, ggtree, RcppAlgos, stats

See at CRAN