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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev libgmp3-dev make libicu-dev
        libpng-dev libuv1-dev libxml2-dev
Repository: https://mdhall272.r-universe.dev
Date/Publication: 2024-10-23 13:36:45 UTC
RemoteUrl: https://github.com/mdhall272/stratus
RemoteRef: HEAD
RemoteSha: cae43f334cc4b08ad95bcb4483cad05d1e5eaba5
RemoteSubdir: STraTUS
NeedsCompilation: no
Packaged: 2026-06-20 08:05:30 UTC; root