Package: STraTUS 1.1.2

Matthew Hall

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]

STraTUS_1.1.2.tar.gz
STraTUS_1.1.2.zip(r-4.7)STraTUS_1.1.2.zip(r-4.6)STraTUS_1.1.2.zip(r-4.5)
STraTUS_1.1.2.tgz(r-4.6-any)STraTUS_1.1.2.tgz(r-4.5-any)
STraTUS_1.1.2.tar.gz(r-4.7-any)STraTUS_1.1.2.tar.gz(r-4.6-any)
STraTUS_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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 216 downloads 1 mentions 6 exports 79 dependencies

Last updated from:cae43f334c. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	192
source / vignettes	OK	195
linux-release-x86_64	NOTE	217
macos-release-arm64	NOTE	125
macos-oldrel-arm64	NOTE	117
windows-devel	NOTE	143
windows-release	NOTE	932
windows-oldrel	NOTE	121
wasm-release	OK	117

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

Dependencies:ape aplot base64enc bslib cachem cli cpp11 digest dplyr evaluate farver fastmap fastmatch fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggfun ggiraph ggplot2 ggplotify ggtree glue gmp gridGraphics gtable highr htmltools htmlwidgets igraph isoband jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme patchwork phangorn pillar pkgconfig purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppAlgos rlang rmarkdown S7 sass scales stringi stringr systemfonts tibble tidyr tidyselect tidytree tinytex treeio utf8 vctrs viridisLite withr xfun yaml 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