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 bdi.ox.ac.uk>
License:	GPL-2 | GPL-3 [expanded from: GPL]
URL:	http://github.com/mdhall272/STraTUS/
NeedsCompilation:	no
CRAN checks:	STraTUS results

Documentation:

Reference manual:

STraTUS.pdf

Downloads:

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