Files in graemetlloyd/Claddis
Measuring Morphological Diversity and Evolutionary Tempo
.Rbuildignore
.github/.gitignore
.github/workflows/r.yml
.github/workflows/test-coverage.yml
.gitignore
CHANGELOG
DESCRIPTION
NAMESPACE
R/Claddis-package.R
R/add_polymorphisms_to_costmatrix.R
R/add_uncertainties_to_costmatrix.R
R/align_matrix_block.R
R/assign_taxa_to_bins.R
R/bin_changes.R
R/bin_character_completeness.R
R/bin_edge_lengths.R
R/build_cladistic_matrix.R
R/calculate_MPD.R
R/calculate_WMPD.R
R/calculate_g.r
R/calculate_gmax.r
R/calculate_kardashian_index.R
R/calculate_morphological_distances.R
R/calculate_tree_length.r
R/check_cladisticMatrix.R
R/check_costMatrix.R
R/check_stateGraph.R
R/check_taxonGroups.R
R/check_timeBins.R
R/classify_costmatrix.R
R/compactify_cladistic_matrix.R
R/convert_adjacency_matrix_to_costmatrix.r
R/convert_costmatrix_to_stategraph.r
R/convert_state_tree_to_adjacency_matrix.r
R/convert_stategraph_to_costmatrix.r
R/count_cherries.R
R/date_nodes.R
R/drop_time_tip.R
R/estimate_ancestral_states.R
R/find_costmatrix_minimum_span.r
R/find_descendant_edges.R
R/find_linked_edges.R
R/find_minimum_spanning_edges.R
R/find_mrca.R
R/find_shortest_costmatrix_path.r
R/find_stategraph_minimum_span.r
R/find_time_bin_midpoints.R
R/find_unique_trees.r
R/fix_costmatrix.R
R/fix_root_time.R
R/is.cladisticMatrix.R
R/is.costMatrix.R
R/is.stateGraph.R
R/is.taxonGroups.R
R/is.timeBins.R
R/is_graph_connected.R
R/locate_bracket_positions.r
R/make_costmatrix.r
R/make_labels.r
R/map_dollo_changes.R
R/match_tree_edges.R
R/ordinate_cladistic_matrix.R
R/partition_time_bins.R
R/permute_all_polymorphisms.r
R/permute_all_treeshape_labellings.r
R/permute_all_uncertainties.r
R/permute_connected_graphs.r
R/permute_costmatrices.r
R/permute_graph_splits.r
R/permute_restricted_compositions.r
R/permute_tipstates.r
R/permute_treeshapes.r
R/plot_changes_on_tree.R
R/plot_chronophylomorphospace.R
R/plot_morphospace.R
R/plot_morphospace_stack.R
R/plot_multi_morphospace.R
R/plot_rates_character.R
R/plot_rates_time.R
R/plot_rates_tree.R
R/print.cladisticMatrix.r
R/print.costMatrix.r
R/print.stateGraph.r
R/print.taxonGroups.r
R/print.timeBins.r
R/prune_cladistic_matrix.R
R/read_nexus_matrix.R
R/reconstruct_ancestral_states.r
R/safe_taxonomic_reduction.R
R/safe_taxonomic_reinsertion.R
R/split_out_subgraphs.R
R/test_rates.R
R/trim_marginal_whitespace.r
R/trim_matrix.R
R/write_nexus_matrix.R
R/write_tnt_matrix.R
README.md
data/.Rhistory
data/day_2016.RData
data/gauthier_1986.RData
data/michaux_1989.RData
inst/CITATION
man/.Rhistory
man/Claddis-package.Rd
man/add_polymorphisms_to_costmatrix.Rd
man/add_uncertainties_to_costmatrix.Rd
man/align_matrix_block.Rd
man/assign_taxa_to_bins.Rd
man/bin_changes.Rd
man/bin_character_completeness.Rd
man/bin_edge_lengths.Rd
man/build_cladistic_matrix.Rd
man/calculate_MPD.Rd
man/calculate_WMPD.Rd
man/calculate_g.Rd
man/calculate_gmax.Rd
man/calculate_kardashian_index.Rd
man/calculate_morphological_distances.Rd
man/calculate_tree_length.Rd
man/check_cladisticMatrix.Rd
man/check_costMatrix.Rd
man/check_stateGraph.Rd
man/check_taxonGroups.Rd
man/check_timeBins.Rd
man/classify_costmatrix.Rd
man/compactify_cladistic_matrix.Rd
man/convert_adjacency_matrix_to_costmatrix.Rd
man/convert_costmatrix_to_stategraph.Rd
man/convert_state_tree_to_adjacency_matrix.Rd
man/convert_stategraph_to_costmatrix.Rd
man/count_cherries.Rd
man/date_nodes.Rd
man/day_2016.Rd
man/drop_time_tip.Rd
man/estimate_ancestral_states.Rd
man/figures/logo.png
man/find_costmatrix_minimum_span.Rd
man/find_descendant_edges.Rd
man/find_linked_edges.Rd
man/find_minimum_spanning_edges.Rd
man/find_mrca.Rd
man/find_shortest_costmatrix_path.Rd
man/find_stategraph_minimum_span.Rd
man/find_time_bin_midpoints.Rd
man/find_unique_trees.Rd
man/fix_costmatrix.Rd
man/fix_root_time.Rd
man/gauthier_1986.Rd
man/is.cladisticMatrix.Rd
man/is.costMatrix.Rd
man/is.stateGraph.Rd
man/is.taxonGroups.Rd
man/is.timeBins.Rd
man/is_graph_connected.Rd
man/locate_bracket_positions.Rd
man/make_costmatrix.Rd
man/make_labels.Rd
man/map_dollo_changes.Rd
man/match_tree_edges.Rd
man/michaux_1989.Rd
man/ordinate_cladistic_matrix.Rd
man/partition_time_bins.Rd
man/permute_all_polymorphisms.Rd
man/permute_all_treeshape_labellings.Rd
man/permute_all_uncertainties.Rd
man/permute_connected_graphs.Rd
man/permute_costmatrices.Rd
man/permute_graph_splits.Rd
man/permute_restricted_compositions.Rd
man/permute_tipstates.Rd
man/permute_treeshapes.Rd
man/plot_changes_on_tree.Rd
man/plot_chronophylomorphospace.Rd
man/plot_morphospace.Rd
man/plot_morphospace_stack.Rd
man/plot_multi_morphospace.Rd
man/plot_rates_character.Rd
man/plot_rates_time.Rd
man/plot_rates_tree.Rd
man/print.cladisticMatrix.Rd
man/print.costMatrix.Rd
man/print.stateGraph.Rd
man/print.taxonGroups.Rd
man/print.timeBins.Rd
man/prune_cladistic_matrix.Rd
man/read_nexus_matrix.Rd
man/reconstruct_ancestral_states.Rd
man/safe_taxonomic_reduction.Rd
man/safe_taxonomic_reinsertion.Rd
man/split_out_subgraphs.Rd
man/test_rates.Rd
man/trim_marginal_whitespace.Rd
man/trim_matrix.Rd
man/write_nexus_matrix.Rd
man/write_tnt_matrix.Rd
tests/testthat/test_bin_changes.R
tests/testthat/test_find_linked_edges.R
tests/testthat/test_find_mrca.R
