STraTUS
Uniform sampling of transmission trees for a fixed pathogen phylogeny
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 3 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.3%) to scientific vocabulary
Repository
Uniform sampling of transmission trees for a fixed pathogen phylogeny
Basic Info
- Host: GitHub
- Owner: mdhall272
- Language: R
- Default Branch: master
- Size: 599 KB
Statistics
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
STraTUS (Software for Transmission Tree Uniform Sampling)
This utility takes as input a phylogenetic tree and, interpreting it as a pathogen phylogeny, uses it to sample uniformly from the set of compatible transmission trees. The procedure is described here.
It is primarily intended for those interested in exploring the structure of transmission tree space, or in developing algorithms to do this.
The code is provided as an R package, with is also available through CRAN. Documentation is here.
Owner
- Name: Matthew Hall
- Login: mdhall272
- Kind: user
- Repositories: 5
- Profile: https://github.com/mdhall272
GitHub Events
Total
- Issues event: 1
- Issue comment event: 2
Last Year
- Issues event: 1
- Issue comment event: 2
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| twoseventwo | m****l@b****k | 75 |
| Matthew Hall | m****l@w****k | 22 |
| Matthew Hall | m****l@i****k | 2 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- cran 214 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
cran.r-project.org: STraTUS
Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny
- Homepage: http://github.com/mdhall272/STraTUS/
- Documentation: http://cran.r-project.org/web/packages/STraTUS/STraTUS.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL]
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Latest release: 1.1.2
published over 6 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4 depends
- RcppAlgos * imports
- ape * imports
- ggplot2 * imports
- ggtree >= 2.0.0 imports
- gmp * imports
- igraph * imports
- phangorn * imports
- stats * imports