OUwie
Estimates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to vary across selective regimes.
Science Score: 36.0%
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4 of 11 committers (36.4%) from academic institutions -
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Low similarity (9.4%) to scientific vocabulary
Repository
Estimates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to vary across selective regimes.
Basic Info
- Host: GitHub
- Owner: thej022214
- Language: HTML
- Default Branch: master
- Size: 6.13 MB
Statistics
- Stars: 9
- Watchers: 4
- Forks: 5
- Open Issues: 6
- Releases: 0
Metadata Files
README.md
OUwie is an R package for using Brownian motion and Ornstein-Uhlenbeck models for trait evolution. Its friendly webpage is at http://thej022214.github.io/OUwie/; its source code is at https://github.com/thej022214/OUwie/.
Some of the features:
- Brownian motion models that allow the rate (sigma-squared) to vary over the tree
- Ornstein-Uhlenbeck models that allow the rate, optima (theta), and/or strength of pull (alpha) to vary over the tree
- Uncertainty estimation using contour plots to find potential ridges
- Simulation functions
- Automatic testing of some identifiability issues using methods from Ho and Ané (2014)
- Ancestral state estimation under all these models (though use substantial caution)
- Use of measurement error at the tips
Some of its caveats:
- It is univariate (a single trait) only
- For multiple rate models, it requires some mapping of regimes (stochastic character mapping of a discrete state, using node labels for regimes on trees, etc.).
- It warns you about models that are very complex for what your data may allow, but it will let you run them
- Optimization can be a difficult problem -- it tries its best, and will announce failures when it notices them, but still be careful
This is the bleeding edge version: you can install it with remotes::install_github("thej022214/OUwie") [install the remotes package from CRAN first]
Owner
- Name: Jeremy Beaulieu
- Login: thej022214
- Kind: user
- Location: University of Arkansas
- Website: www.jeremybeaulieu.org
- Repositories: 3
- Profile: https://github.com/thej022214
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Push event: 7
- Pull request event: 1
- Pull request review event: 1
- Fork event: 2
Last Year
- Issues event: 1
- Watch event: 1
- Push event: 7
- Pull request event: 1
- Pull request review event: 1
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| jboyko | j****1@g****m | 74 |
| Jeremy Beaulieu | j****i@A****t | 50 |
| Brian O'Meara | o****n@g****m | 41 |
| Jeremy Beaulieu | j****u@o****u | 26 |
| Jeremy Beaulieu | j****i@A****l | 24 |
| Jeremy Beaulieu | j****u@J****l | 11 |
| Jeremy Beaulieu | j****i@u****u | 10 |
| Jeremy Beaulieu | j****u@J****t | 7 |
| Jeremy Beaulieu | j****u@o****u | 6 |
| Jeremy Beaulieu | j****u@n****g | 2 |
| Jeremy Beaulieu | j****i@a****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 17
- Total pull requests: 4
- Average time to close issues: 11 months
- Average time to close pull requests: about 1 month
- Total issue authors: 12
- Total pull request authors: 2
- Average comments per issue: 1.41
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 4 months
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bomeara (5)
- mpnelsen (2)
- jamie-thompson (1)
- Caetanods (1)
- dwbapst (1)
- ghost (1)
- coyotree (1)
- soungalo (1)
- ltaylor2 (1)
- C-G-L (1)
- jonnations (1)
- jakeberv (1)
Pull Request Authors
- irmoodie (2)
- jboyko (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 676 last-month
- Total docker downloads: 43,390
- Total dependent packages: 0
- Total dependent repositories: 4
- Total versions: 39
- Total maintainers: 1
cran.r-project.org: OUwie
Analysis of Evolutionary Rates in an OU Framework
- Homepage: https://github.com/thej022214/OUwie
- Documentation: http://cran.r-project.org/web/packages/OUwie/OUwie.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
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Latest release: 2.10
published about 4 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.2.0 depends
- RColorBrewer * depends
- ape * depends
- corpcor * depends
- geiger * depends
- nloptr * depends
- GenSA * imports
- MASS * imports
- corHMM * imports
- data.table * imports
- expm * imports
- grDevices * imports
- igraph * imports
- interp * imports
- lhs * imports
- numDeriv * imports
- paleotree * imports
- parallel * imports
- phangorn * imports
- phylolm * imports
- phytools * imports
- stats * imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests