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STraTUS (version 1.1.2)

Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

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) for methodology.

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Install

install.packages('STraTUS')

Monthly Downloads

161

Version

1.1.2

License

GPL

Issues

0

Pull Requests

0

Stars

4

Forks

2

Maintainer

Matthew Hall

Last Published

April 4th, 2020

Functions in STraTUS (1.1.2)

draw.fully.sampled

For a sample with no unsampled hosts, draw the annotated phylogeny using ggtree
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.
sample.partial.tt

Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed
sample.tt

Sample one or more transmission trees uniformly
tt.generator

Enumerate transmission trees for the given pathogen phylogeny, and provide a uniform sample generator
build.edgelist

For a sample, produce the transmission tree as a igraph object
draw.incompletely.sampled

For a sample with or without unsampled hosts, draw the annotated phylogeny using ggtree
stratus.example.tree

An unexceptional phylogeny generated with rtree from ape