Measuring Morphological Diversity and Evolutionary Tempo

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Documentation for package ‘Claddis’ version 0.6.3

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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