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.

Getting started

Package details

AuthorMatthew Hall [aut, cre], Caroline Colijn [ctb]
MaintainerMatthew Hall <[email protected]>
LicenseGPL
Version1.1.1
URL http://github.com/mdhall272/STraTUS/
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("STraTUS")

Try the STraTUS package in your browser

Any scripts or data that you put into this service are public.

STraTUS documentation built on May 21, 2019, 5:03 p.m.