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![Build Status](https://travis-ci.org/thej022214/OUwie.svg)
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]
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.