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 |