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

Peer review:

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 179 downloads 1 mentions 6 exports 57 dependencies

Last updated 1 months agofrom:cae43f334c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winNOTENov 22 2024
R-4.5-linuxNOTENov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winOKNov 22 2024
R-4.3-macOKNov 22 2024

Exports:build.edgelistdraw.fully.sampleddraw.incompletely.sampledsample.partial.ttsample.tttt.generator

Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfastmatchfsgenericsggfunggplot2ggplotifyggtreegluegmpgridGraphicsgtableigraphisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkphangornpillarpkgconfigpurrrquadprogR6RColorBrewerRcppRcppAlgosrlangscalesstringistringrtibbletidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils