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| carex | Carex section Ovales tree, chromosome data, and nodes |
| informationCriterion | Information criterion and weights for a set of models |
| informationCriterion.hansenBatch | Information criterion and weights for a set of models |
| isMonophyletic | Test whether a set of taxa is monophyletic on an ouch-style tree |
| mrcaOUCH | Test whether a set of taxa is monophyletic on an ouch-style tree |
| multiModel | Test multiple models of character transition at a single node |
| nodeDescendents | Test whether a set of taxa is monophyletic on an ouch-style tree |
| ouSim | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.browntree | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.hansenBatch | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.hansenSummary | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.hansentree | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.ouchtree | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| ouSim.phylo | Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree. |
| paintBranches | Paint branches for Ornstein-Uhlenbeck analysis |
| plot.ouSim | Visualizing discrete-time simulation of Ornstein-Uhlenbeck models. |
| print.hansenSummary | Summarize output from runBatchHansen |
| print.informationCriterion | Information criterion and weights for a set of models |
| regimeMaker | Paint ouch-style regimes over a set of trees based on a user-defined matrix |
| regimeMatrix | Create a matrix that defines models for batch analysis |
| regimeVectors | Paint all possible regimes |
| runBatchHansen | Analyze Ornstein-Uhlenbeck models over a set of trees |
| summary.hansenBatch | Summarize output from runBatchHansen |