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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 |
| 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 |
| Reference manual: | STraTUS.pdf |
| Package source: | STraTUS_1.1.2.tar.gz |
| Windows binaries: | r-devel: STraTUS_1.1.2.zip, r-release: STraTUS_1.1.2.zip, r-oldrel: STraTUS_1.1.2.zip |
| macOS binaries: | r-release (arm64): STraTUS_1.1.2.tgz, r-oldrel (arm64): STraTUS_1.1.2.tgz, r-release (x86_64): STraTUS_1.1.2.tgz, r-oldrel (x86_64): STraTUS_1.1.2.tgz |
| Old sources: | STraTUS archive |
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