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STraTUS  

Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny
View on CRAN: Click here


Download and install STraTUS package within the R console
Install from CRAN:
install.packages("STraTUS")

Install from Github:
library("remotes")
install_github("cran/STraTUS")

Install by package version:
library("remotes")
install_version("STraTUS", "1.1.2")



Attach the package and use:
library("STraTUS")
Maintained by
Matthew Hall
[Scholar Profile | Author Map]
First Published: 2019-03-18
Latest Update: 2020-04-04
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) <doi:10.1093/molbev/msz058> for methodology.
How to cite:
Matthew Hall (2019). STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny. R package version 1.1.2, https://cran.r-project.org/web/packages/STraTUS. Accessed 29 Mar. 2025.
Previous versions and publish date:
1.1.1 (2019-05-21 12:10), 1.1 (2019-03-18 17:23)
Other packages that cited STraTUS R package
View STraTUS citation profile
Other R packages that STraTUS depends, imports, suggests or enhances
Complete documentation for STraTUS
Functions, R codes and Examples using the STraTUS R package
Some associated functions: build.edgelist . draw.fully.sampled . draw.incompletely.sampled . grouping.map . sample.partial.tt . sample.tt . stratus.example.tree . tt.generator . 
Some associated R codes: data_for_docs.R . enumeration.R . sampling.R . utility_functions.R .  Full STraTUS package functions and examples
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