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| Claddis-package | Measuring Morphological Diversity and Evolutionary Tempo |
| align_matrix_block | Aligns a phylogenetic matrix block |
| assign_taxa_to_bins | Assign taxa to time bins |
| bin_changes | Counts the changes in a series of time bins |
| bin_character_completeness | Phylogenetic character completeness in time-bins |
| bin_edge_lengths | Edge-lengths present in time-bins |
| build_cladistic_matrix | Creates a morphological data file from a matrix |
| calculate_morphological_distances | Get distance matrices from a cladistic matrix |
| Claddis | Measuring Morphological Diversity and Evolutionary Tempo |
| compactify_matrix | Collapses matrix to unique character state distributions |
| date_nodes | Returns node ages for a time-scaled tree |
| day_2016 | Character-taxon matrix from Day et al. 2016 |
| estimate_ancestral_states | Ancestral Character State Estimation |
| find_descendant_edges | Gets descendant edges of an internal node |
| find_linked_edges | Find linked edges for a tree |
| find_minimum_spanning_edges | Get edges of minimum spanning tree |
| find_mrca | Find ancestor |
| fix_root_time | Fixes root.time after taxa have been pruned from a tree |
| gauthier_1986 | Character-taxon matrix from Gauthier 1986 |
| map_dollo_changes | Stochastic Character Map For Dollo Character |
| map_stochastic_changes | Finds all state changes on a tree using stochastic character mapping |
| match_tree_edges | Edge matching function |
| michaux_1989 | Character-taxon matrix from Michaux 1989 |
| ordinate_cladistic_matrix | Principal Coordinates on a Cladistic Matrix |
| partition_time_bins | Time bin partitioner |
| plot_changes_on_tree | Plots character changes on branches |
| plot_chronophylomorphospace | Chronophylomorphospace Plot |
| plot_morphospace | Plot Morphopace |
| plot_morphospace_stack | Plot stacked ordination spaces |
| plot_multi_morphospace | Plot Multiple Morphopaces |
| plot_rates_character | Visualize a rate test time series |
| plot_rates_time | Visualize a rate test time series |
| plot_rates_tree | Visualize a rate test time series |
| print.cladisticMatrix | Compact display of a cladistic matrix |
| prune_cladistic_matrix | Prunes a character matrix of characters or taxa |
| read_nexus_matrix | Reads in a morphological #NEXUS data file |
| safe_taxonomic_reduction | Safe Taxonomic Reduction |
| safe_taxonomic_reinsertion | Reinsert Safely Removed Taxa Into A Tree |
| test_rates | Discrete character rates across trees, time, and character types |
| trim_marginal_whitespace | Trims marginal whitespace |
| trim_matrix | Trims a morphological distance matrix |
| write_nexus_matrix | Writes out a morphological #NEXUS data file |
| write_tnt_matrix | Writes out a morphological TNT data file |