README.md
In OUwie: Analysis of Evolutionary Rates in an OU Framework

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]