Other packages > Find by keyword >

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]
All associated links for this package
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 25 Jun. 2026.
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
sitmo  
Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel enviro ...
Download / Learn more Package Citations See dependency  
foster  
Forest Structure Extrapolation with R
Set of tools to streamline the modeling of the relationship betweensatellite imagery time series or ...
Download / Learn more Package Citations See dependency  
airGRiwrm  
'airGR' Integrated Water Resource Management
Semi-distributed Precipitation-Runoff Modelling based on 'airGR' package models integrating human i ...
Download / Learn more Package Citations See dependency  
edeaR  
Exploratory and Descriptive Event-Based Data Analysis
Exploratory and descriptive analysis of event based data. Provides methods for describing and select ...
Download / Learn more Package Citations See dependency  

27,535

R Packages

236,180

Dependencies

73,223

Author Associations

27,536

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA