grouping.map

<p>A vector assigning the tips of <code>stratus.example.tree</code> to groups (in the order they appear in <code>stratus.example.tree$tip.label</code>), as an example of multiple sampling.</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

grouping.map function

Format

A vector assigning the tips of <code>stratus.example.tree</code> to groups (in the order they appear in <code>stratus.example.tree$tip.label</code>), as an example of multiple sampling. — grouping.map

A vector assigning the tips of <code>stratus.example.tree</code> to groups (in the order they appear in <code>stratus.example.tree$tip.label</code>), as an example of multiple sampling.

grouping.map: A vector assigning the tips of `stratus.example.tree` to groups (in the order they appear in `stratus.example.tree$tip.label`), as an example of multiple sampling.

Description

Arguments

Format