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| ancRECON | Ancestral state reconstruction |
| ConvertPhangornReconstructions | Convert phangorn reconstruction to a vector |
| corDISC | Correlated evolution binary traits |
| corHMM | Hidden Rates Model |
| corPAINT | Binary character evolution with tree painting |
| dev.raydisc | Evolution of categorical traits |
| lewisMkv | Phylogenetic inference of morphology using mkv model |
| plotRECON | Plot ancestral state reconstructions |
| primates | Example datasets |
| primates.paint | Example datasets |
| rate.mat.maker | Rate matrix maker |
| rate.par.drop | Rate matrix maker |
| rate.par.eq | Rate matrix maker |
| rayDISC | Evolution of categorical traits |
| rayDISC.example | Example datasets |
| readNexusMorph | Reads morphological character data In NEXUS Format |