R: Hidden Markov Models of Character Evolution

# Hidden Markov Models of Character Evolution

## Documentation for package ‘corHMM’ version 2.8

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

ancRECON | Ancestral state reconstruction
ConvertPhangornReconstructions | Convert phangorn reconstruction to a vector
corDISC | Correlated evolution binary traits
corHMM | Hidden Rates Model
dev.raydisc | Evolution of categorical traits
dropStateMatPars | Combines several rate class index matrices
equateStateMatPars | Combines several rate class index matrices
fitCorrelationTest | Test for correlation
getFullMat | Combines several rate class index matrices
getRateCatMat | Combines several rate class index matrices
getStateMat4Dat | Produce an index matrix and legend from a dataset
makeSimmap | Simulate a character history
plotMKmodel | Plot a Markov model
plotRECON | Plot ancestral state reconstructions
primates | Example datasets
primates.paint | Example datasets
rayDISC | Evolution of categorical traits
rayDISC.example | Example datasets