stratus.example.tree

<p>An unexceptional phylogeny generated with <code>rtree</code> from <code>ape</code></p>

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.

Matthew Hall

STraTUS

Enumeration and Uniform Sampling of Transmission Trees for a
Known Phylogeny

Caroline Colijn

stratus.example.tree function

<p>A phylogenetic tree (<code>phylo</code> format) with 20 tips and 19 internal nodes</p>

stratus.example.tree: An unexceptional phylogeny generated with `rtree` from `ape`

Description

Arguments

Format