Package: STraTUS
Title: Enumeration and Uniform Sampling of Transmission Trees for a
        Known Phylogeny
Version: 1.1.2
Authors@R: c(person("Matthew", "Hall", email = "matthew.hall@bdi.ox.ac.uk", role = c("aut", "cre")), person("Caroline", "Colijn", role = c("ctb")))
Author: Matthew Hall [aut, cre],
  Caroline Colijn [ctb]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Description: 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.
Depends: R (>= 3.4)
Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 2.0.0),
        RcppAlgos, stats
License: GPL
URL: http://github.com/mdhall272/STraTUS/
Encoding: UTF-8
RoxygenNote: 7.1.0
LazyData: TRUE
NeedsCompilation: no
Packaged: 2020-04-04 11:40:46 UTC; mdhall
Repository: CRAN
Date/Publication: 2020-04-04 12:20:06 UTC
Built: R 4.6.0; ; 2026-04-26 10:39:20 UTC; unix
