# Measuring Morphological Diversity and Evolutionary Tempo

## Documentation for package ‘Claddis’ version 0.7.0

- DESCRIPTION file
- Package README

## Help Pages

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_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_MPD | Calculate mean pairwise distances
calculate_tree_length | Calculates the parsimony length of a set of phylogenetic tree(s)
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 | Measuring Morphological Diversity and Evolutionary Tempo Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.
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
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