Claddis-package	Claddis-package
add_polymorphisms_to_costmatrix	add_polymorphisms_to_costmatrix
add_uncertainties_to_costmatrix	add_uncertainties_to_costmatrix
align_matrix_block	align_matrix_block
assign_taxa_to_bins	assign_taxa_to_bins
bin_changes	bin_changes
bin_character_completeness	bin_character_completeness
bin_edge_lengths	bin_edge_lengths
build_cladistic_matrix	build_cladistic_matrix
calculate_g	calculate_g
calculate_gmax	calculate_gmax
calculate_kardashian_index	calculate_kardashian_index
calculate_morphological_distances	calculate_morphological_distances
calculate_MPD	calculate_MPD
calculate_tree_length	calculate_tree_length
calculate_WMPD	calculate_WMPD
check_cladisticMatrix	check_cladisticMatrix
check_costMatrix	check_costMatrix
check_stateGraph	check_stateGraph
check_taxonGroups	check_taxonGroups
check_timeBins	check_timeBins
Claddis	Claddis-package
classify_costmatrix	classify_costmatrix
compactify_cladistic_matrix	compactify_cladistic_matrix
convert_adjacency_matrix_to_costmatrix	convert_adjacency_matrix_to_costmatrix
convert_costmatrix_to_stategraph	convert_costmatrix_to_stategraph
convert_stategraph_to_costmatrix	convert_stategraph_to_costmatrix
convert_state_tree_to_adjacency_matrix	convert_state_tree_to_adjacency_matrix
count_cherries	count_cherries
date_nodes	date_nodes
day_2016	day_2016
drop_time_tip	drop_time_tip
estimate_ancestral_states	estimate_ancestral_states
estimate_squared_change_ancestors	estimate_squared_change_ancestors
find_costmatrix_minimum_span	find_costmatrix_minimum_span
find_descendant_edges	find_descendant_edges
find_linked_edges	find_linked_edges
find_minimum_spanning_edges	find_minimum_spanning_edges
find_mrca	find_mrca
find_shortest_costmatrix_path	find_shortest_costmatrix_path
find_stategraph_minimum_span	find_stategraph_minimum_span
find_time_bin_midpoints	find_time_bin_midpoints
find_unique_trees	find_unique_trees
fix_costmatrix	fix_costmatrix
fix_root_time	fix_root_time
gauthier_1986	gauthier_1986
is.cladisticMatrix	is.cladisticMatrix
is.costMatrix	is.costMatrix
is.stateGraph	is.stateGraph
is.taxonGroups	is.taxonGroups
is.timeBins	is.timeBins
is_graph_connected	is_graph_connected
locate_bracket_positions	locate_bracket_positions
make_costmatrix	make_costmatrix
make_labels	make_labels
map_dollo_changes	map_dollo_changes
match_tree_edges	match_tree_edges
michaux_1989	michaux_1989
ordinate_cladistic_matrix	ordinate_cladistic_matrix
partition_time_bins	partition_time_bins
permute_all_polymorphisms	permute_all_polymorphisms
permute_all_treeshape_labellings	permute_all_treeshape_labellings
permute_all_uncertainties	permute_all_uncertainties
permute_connected_graphs	permute_connected_graphs
permute_costmatrices	permute_costmatrices
permute_graph_splits	permute_graph_splits
permute_restricted_compositions	permute_restricted_compositions
permute_tipstates	permute_tipstates
permute_treeshapes	permute_treeshapes
plot_changes_on_tree	plot_changes_on_tree
plot_chronophylomorphospace	plot_chronophylomorphospace
plot_morphospace	plot_morphospace
plot_morphospace_stack	plot_morphospace_stack
plot_multi_morphospace	plot_multi_morphospace
plot_rates_character	plot_rates_character
plot_rates_time	plot_rates_time
plot_rates_tree	plot_rates_tree
print.cladisticMatrix	print.cladisticMatrix
print.costMatrix	print.costMatrix
print.stateGraph	print.stateGraph
print.taxonGroups	print.taxonGroups
print.timeBins	print.timeBins
prune_cladistic_matrix	prune_cladistic_matrix
read_nexus_matrix	read_nexus_matrix
reconstruct_ancestral_states	reconstruct_ancestral_states
safe_taxonomic_reduction	safe_taxonomic_reduction
safe_taxonomic_reinsertion	safe_taxonomic_reinsertion
split_out_subgraphs	split_out_subgraphs
test_rates	test_rates
trim_marginal_whitespace	trim_marginal_whitespace
trim_matrix	trim_matrix
write_nexus_matrix	write_nexus_matrix
write_tnt_matrix	write_tnt_matrix
