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]