Package: STraTUS
Title: Enumeration and Uniform Sampling of Transmission Trees for a
        Known Phylogeny
Version: 1.1
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 <doi:10.1101/160812> for methodology.
Depends: R (>= 3.4)
Imports: ape, phangorn, igraph, gmp, gtools, ggplot2, ggtree (>=
        1.14.6), RcppAlgos, stats
License: GPL
URL: http://github.com/mdhall272/STraTUS/
Encoding: UTF-8
RoxygenNote: 6.1.1
LazyData: TRUE
NeedsCompilation: no
Packaged: 2019-03-13 17:25:13 UTC; mdhall
Repository: CRAN
Date/Publication: 2019-03-18 16:23:22 UTC
