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| Claddis-package | Cladistic disparity |
| AncStateEstMatrix | Ancestral State Estimation |
| ChangesInBins | Counts the changes in a series of time bins |
| Claddis | Cladistic disparity |
| CorrectRootTime | Corrects root.time after taxa have been pruned from a tree |
| DiscreteCharacterRate | A function for examining discrete character rates |
| EdgeLengthsInBins | Edge-lengths present in time-bins |
| EdgeMatch | Edge matching function |
| FindAncestor | Find ancestor |
| FindLinkedEdges | Find linked edges for a tree |
| Gauthier1986 | Character-taxon matrix from Gauthier 1986 |
| GetAllStateChanges | Finds all state changes on a tree using stochastic character mapping |
| GetDescendantEdges | Gets descendant edges of an internal node |
| GetNodeAges | Returns node ages for a time-scaled tree |
| Michaux1989 | Character-taxon matrix from Michaux 1989 |
| MinSpanTreeEdges | Get edges of minimum spanning tree |
| MorphDistMatrix | Get distance matrices from a cladistic matrix |
| ReadMorphNexus | Reads in a morphological #NEXUS data file |
| SafeTaxonomicReduction | Safe Taxonomic Reduction |
| TrimMorphDistMatrix | Trims a morphological distance matrix |