STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny (original) (raw)
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.
| Version: | 1.1.2 |
|---|---|
| Depends: | R (≥ 3.4) |
| Imports: | ape, phangorn, igraph, gmp, ggplot2, ggtree (≥ 2.0.0), RcppAlgos, stats |
| Published: | 2020-04-04 |
| DOI: | 10.32614/CRAN.package.STraTUS |
| Author: | Matthew Hall [aut, cre], Caroline Colijn [ctb] |
| Maintainer: | Matthew Hall <matthew.hall at bdi.ox.ac.uk> |
| License: | GPL-2 | GPL-3 [expanded from: GPL] |
| URL: | http://github.com/mdhall272/STraTUS/ |
| NeedsCompilation: | no |
| CRAN checks: | STraTUS results |
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