Claddis-package         Measuring Morphological Diversity and
                        Evolutionary Tempo Measures morphological
                        diversity from discrete character data and
                        estimates evolutionary tempo on phylogenetic
                        trees.
add_polymorphisms_to_costmatrix
                        Adds polymorphisms to a costmatrix
add_uncertainties_to_costmatrix
                        Adds uncertainties to a costmatrix
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_MPD           Calculate mean pairwise distances
calculate_WMPD          Calculate weighted mean pairwise distances
calculate_g             Calculate the maximum tree length, g, under
                        parsimony
calculate_gmax          Calculate the maximum possible tree length,
                        gmax, under parsimony
calculate_kardashian_index
                        Calculates a researcher's Kardashian Index
calculate_morphological_distances
                        Get distance matrices from a cladistic matrix
calculate_tree_length   Calculates the parsimony length of a set of
                        phylogenetic tree(s)
check_cladisticMatrix   Check cladisticMatrix object for errors
check_costMatrix        Check a costMatrix object for errors
check_stateGraph        Check a stateGraph object for errors
check_taxonGroups       Check taxonGroups object for errors
check_timeBins          Check timeBins object for errors
classify_costmatrix     Classify a costmatrix character
compactify_cladistic_matrix
                        Collapses matrix to unique character state
                        distributions
convert_adjacency_matrix_to_costmatrix
                        Converts an adjacency matrix to a costmatrix
convert_costmatrix_to_stategraph
                        Convert a costmatrix to a minimal state graph
convert_state_tree_to_adjacency_matrix
                        Converts a character state tree to an adjacency
                        matrix
convert_stategraph_to_costmatrix
                        Convert a minimal state graph to a costmatrix
count_cherries          Counts the number of cherries in a tree
date_nodes              Returns node ages for a time-scaled tree
day_2016                Character-taxon matrix from Day et al. 2016
drop_time_tip           Drop tips from a time-scaled tree
estimate_ancestral_states
                        Ancestral Character State Estimation
estimate_squared_change_ancestors
                        Estimate ancestral states for a continuous
                        character under squared-change parsimony
find_costmatrix_minimum_span
                        Finds a minimum spanning tree of a costmatrix
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
find_shortest_costmatrix_path
                        Finds the shortest path between two states in a
                        costmatrix
find_stategraph_minimum_span
                        Finds a minimum spanning tree of a stategraph
find_time_bin_midpoints
                        Find time bin midpoints
find_unique_trees       Finds only the unique topologies amongst a set
fix_costmatrix          Fixes a costmatrix that has inconsistent costs
fix_root_time           Fixes root.time after taxa have been pruned
                        from a tree
gauthier_1986           Character-taxon matrix from Gauthier 1986
is.cladisticMatrix      Cladistic matrix class
is.costMatrix           Costmatrix class
is.stateGraph           Stategraph class
is.taxonGroups          Taxon groups class
is.timeBins             Time bins class
is_graph_connected      Is a graph connected?
locate_bracket_positions
                        Locates matching positions for sets of brackets
                        in a text string
make_costmatrix         Make a costmatrix for a given set of states
make_labels             Make unique text labels
map_dollo_changes       Stochastic Character Map For Dollo Character
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
permute_all_polymorphisms
                        Permute all possible polymorphisms for a given
                        set of states
permute_all_treeshape_labellings
                        Label treeshapes
permute_all_uncertainties
                        Permute all possible uncertainties for a given
                        set of states
permute_connected_graphs
                        Permute all connected graphs
permute_costmatrices    Permute costmatrices
permute_graph_splits    Permute all ways to split a graph
permute_restricted_compositions
                        Permute all ways to place n items into m bins
permute_tipstates       Permute all tip states on a tree
permute_treeshapes      Permute all treeshapes of N tips
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
print.costMatrix        Compact display of a costmatrix
print.stateGraph        Compact display of a stategraph
print.taxonGroups       Compact display of taxon groups
print.timeBins          Compact display of time bins
prune_cladistic_matrix
                        Prunes a character matrix of characters or taxa
read_nexus_matrix       Reads in a morphological #NEXUS data file
reconstruct_ancestral_states
                        Determine maximum parsimony ancestral state
                        reconstruction(s)
safe_taxonomic_reduction
                        Safe Taxonomic Reduction
safe_taxonomic_reinsertion
                        Reinsert Safely Removed Taxa Into A Tree
split_out_subgraphs     Split adjacency matrix into subgraphs
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
