# This file no longer generated by roxygen as that cannot handle the S3 methods properly

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

# Imports:
import(ape)
import(phytools)
import(strap)

# Import from:
importFrom(clipr,write_clip)
importFrom(geoscale,geoscalePlot)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,chull)
importFrom(grDevices,hcl.colors)
importFrom(grDevices,rgb)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,text)
importFrom(methods,hasArg)
importFrom(multicool,allPerm)
importFrom(multicool,initMC)
importFrom(partitions,restrictedparts)
importFrom(stats,as.dist)
importFrom(stats,dist)
importFrom(stats,dpois)
importFrom(stats,optim)
importFrom(stats,pchisq)
importFrom(stats,runif)
importFrom(stats,var)
importFrom(utils,combn)
importFrom(utils,stack)

# S3:
S3method(print, cladisticMatrix)
S3method(print, costMatrix)
S3method(print, stateGraph)
S3method(print, taxonGroups)
S3method(print, timeBins)
