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| Claddis-package | Measuring Morphological Diversity and Evolutionary Tempo |
| AncStateEstMatrix | Ancestral Character State Estimation |
| BlockAligner | Align a phylogenetic matrix block |
| ChangesInBins | Counts the changes in a series of time bins |
| ChronoPhyloMorphospacePlot | Chronophylomorphospace Plot |
| Claddis | Measuring Morphological Diversity and Evolutionary Tempo |
| CompactifyMatrix | Collapses matrix to unique character state distributions |
| CorrectRootTime | Corrects root.time after taxa have been pruned from a tree |
| Day2016 | Character-taxon matrix from Day et al. 2016 |
| DiscreteCharacterRate | Discrete character rates across trees, time, and character types |
| DolloSCM | Stochastic Character Map For Dollo Character |
| 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 |
| MakeMorphMatrix | Creates a morphological data file from a matrix |
| MatrixPruner | Prunes a character matrix of characters or taxa |
| Michaux1989 | Character-taxon matrix from Michaux 1989 |
| MinSpanTreeEdges | Get edges of minimum spanning tree |
| MorphDistMatrix | Get distance matrices from a cladistic matrix |
| MorphMatrix2PCoA | Principal Coordinates on a Cladistic Matrix |
| MorphospacePlot | Plot Morphopace |
| MultiMorphospacePlot | Plot Multiple Morphopaces |
| PhyloCharCompletenessInBins | Phylogenetic character completeness in time-bins |
| PlotCharacterChanges | Plots character changes on branches |
| ReadMorphNexus | Reads in a morphological #NEXUS data file |
| SafeTaxonomicReduction | Safe Taxonomic Reduction |
| SafeTaxonomicReinsertion | Reinsert Safely Removed Taxa Into A Tree |
| StackPlot | Plot Stacked Ordination Spaces |
| TrimMorphDistMatrix | Trims a morphological distance matrix |
| WriteMorphNexus | Writes out a morphological #NEXUS data file |
| WriteMorphTNT | Writes out a morphological TNT data file |