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:
STraTUS_1.1.2.tar.gz
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STraTUS.pdf |STraTUS.html✨
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
- 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'
Last updated 1 months agofrom:cae43f334c. Checks:OK: 3 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 22 2024 |
R-4.5-win | NOTE | Nov 22 2024 |
R-4.5-linux | NOTE | Nov 22 2024 |
R-4.4-win | NOTE | Nov 22 2024 |
R-4.4-mac | NOTE | Nov 22 2024 |
R-4.3-win | OK | Nov 22 2024 |
R-4.3-mac | OK | Nov 22 2024 |
Exports:build.edgelistdraw.fully.sampleddraw.incompletely.sampledsample.partial.ttsample.tttt.generator
Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfastmatchfsgenericsggfunggplot2ggplotifyggtreegluegmpgridGraphicsgtableigraphisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkphangornpillarpkgconfigpurrrquadprogR6RColorBrewerRcppRcppAlgosrlangscalesstringistringrtibbletidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils