Mapping Transitions in Continuous Character Evolution


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Documentation for package ‘maticce’ version 0.9-2

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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