Package: STraTUS 1.1.2

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.

Authors:Matthew Hall [aut, cre], Caroline Colijn [ctb]

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STraTUS/json (API)

# Install 'STraTUS' in R:

install.packages('STraTUS', repos = c('https://mdhall272.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mdhall272/stratus/issues

Datasets:

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.
stratus.example.tree - An unexceptional phylogeny generated with 'rtree' from 'ape'

On CRAN:

3.30 score 4 stars 160 downloads 1 mentions 6 exports 57 dependencies

Last updated 14 days agofrom:cae43f334c. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 23 2024
R-4.5-win	NOTE	Oct 23 2024
R-4.5-linux	NOTE	Oct 23 2024
R-4.4-win	NOTE	Oct 24 2024
R-4.4-mac	NOTE	Oct 23 2024
R-4.3-win	OK	Oct 23 2024
R-4.3-mac	OK	Oct 23 2024

Exports:build.edgelist draw.fully.sampled draw.incompletely.sampled sample.partial.tt sample.tt tt.generator

Dependencies:ape aplot cli colorspace cpp11 digest dplyr fansi farver fastmatch fs generics ggfun ggplot2 ggplotify ggtree glue gmp gridGraphics gtable igraph isoband jsonlite labeling lattice lazyeval lifecycle magrittr MASS Matrix mgcv munsell nlme patchwork phangorn pillar pkgconfig purrr quadprog R6 RColorBrewer Rcpp RcppAlgos rlang scales stringi stringr tibble tidyr tidyselect tidytree treeio utf8 vctrs viridisLite withr yulab.utils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
For a sample, produce the transmission tree as a 'igraph' object	build.edgelist
For a sample with no unsampled hosts, draw the annotated phylogeny using 'ggtree'	draw.fully.sampled
For a sample with or without unsampled hosts, draw the annotated phylogeny using 'ggtree'	draw.incompletely.sampled
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.	grouping.map
Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed	sample.partial.tt
Sample one or more transmission trees uniformly	sample.tt
An unexceptional phylogeny generated with 'rtree' from 'ape'	stratus.example.tree
Enumerate transmission trees for the given pathogen phylogeny, and provide a uniform sample generator	tt.generator