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.

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>
License: GPL-2 | GPL-3 [expanded from: GPL]
NeedsCompilation: no
CRAN checks: STraTUS results


Reference manual: STraTUS.pdf


Package source: STraTUS_1.1.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
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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