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: 1.1.1
Depends: R (≥ 3.4)
Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (≥ 1.14.6), RcppAlgos, stats
Published: 2019-05-21
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_1.1.1.tar.gz
Windows binaries: r-devel:, r-devel-gcc8:, r-release:, r-oldrel:
OS X binaries: r-release: STraTUS_1.1.1.tgz, r-oldrel: not available
Old sources: STraTUS archive


Please use the canonical form to link to this page.