Description
Analysis of Evolutionary Rates in an OU Framework.
Description
Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012).
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]