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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.
Getting started
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Package details |
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| Author | Matthew Hall [aut, cre], Caroline Colijn [ctb] |
| Maintainer | Matthew Hall <matthew.hall@bdi.ox.ac.uk> |
| License | GPL |
| Version | 1.1.2 |
| URL | http://github.com/mdhall272/STraTUS/ |
| Package repository | View on CRAN |
| Installation |
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