Man pages for graemetlloyd/Claddis
Measuring Morphological Diversity and Evolutionary Tempo
| 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_g | Calculate the maximum tree length, g, under parsimony |
| calculate_gmax | Calculate the maximum possible tree length, gmax, under... |
| calculate_kardashian_index | Calculates a researcher's Kardashian Index |
| calculate_morphological_distances | Get distance matrices from a cladistic matrix |
| calculate_MPD | Calculate mean pairwise distances |
| calculate_tree_length | Calculates the parsimony length of a set of phylogenetic... |
| calculate_WMPD | Calculate weighted mean pairwise distances |
| 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 |
| Claddis-package | Measuring Morphological Diversity and Evolutionary Tempo... |
| 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_stategraph_to_costmatrix | Convert a minimal state graph to a costmatrix |
| convert_state_tree_to_adjacency_matrix | Converts a character state tree to an adjacency matrix |
| 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 |
| 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_graph_connected | Is a graph connected? |
| is.stateGraph | Stategraph class |
| is.taxonGroups | Taxon groups class |
| is.timeBins | Time bins class |
| locate_bracket_positions | Locates matching positions for sets of brackets in a text... |
| 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... |
| 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 |
