Measuring Morphological Diversity and Evolutionary Tempo

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Documentation for package ‘Claddis’ version 0.7.0

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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