legacy ====== .. currentmodule:: ~phyloframe .. automodule:: phyloframe.legacy :undoc-members: :members: :imported-members: :special-members: __call__, __repr__, __str__ .. rubric:: Functions .. autosummary:: :toctree: ~alifestd_add_global_root ~alifestd_add_global_root_polars ~alifestd_add_inner_knuckles_asexual ~alifestd_add_inner_knuckles_polars ~alifestd_add_inner_leaves ~alifestd_add_inner_niblings_asexual ~alifestd_add_inner_niblings_polars ~alifestd_aggregate_phylogenies ~alifestd_aggregate_phylogenies_polars ~alifestd_as_newick_asexual ~alifestd_as_newick_polars ~alifestd_assign_contiguous_ids ~alifestd_assign_contiguous_ids_polars ~alifestd_assign_root_ancestor_token ~alifestd_calc_clade_lookback_n_asexual ~alifestd_calc_clade_lookback_origin_time_delta_asexual ~alifestd_calc_clade_trait_count_asexual ~alifestd_calc_clade_trait_frequency_asexual ~alifestd_calc_distance_matrix_asexual ~alifestd_calc_distance_matrix_polars ~alifestd_calc_mrca_id_matrix_asexual ~alifestd_calc_mrca_id_matrix_asexual_polars ~alifestd_calc_mrca_id_vector_asexual ~alifestd_calc_mrca_id_vector_asexual_polars ~alifestd_calc_polytomic_index ~alifestd_calc_polytomic_index_polars ~alifestd_categorize_triplet_asexual ~alifestd_check_topological_sensitivity ~alifestd_check_topological_sensitivity_polars ~alifestd_chronological_sort ~alifestd_chronological_sort_polars ~alifestd_coarsen_dilate_asexual ~alifestd_coarsen_dilate_polars ~alifestd_coarsen_mask ~alifestd_coarsen_taxa_asexual ~alifestd_coarsen_taxa_asexual_make_agg ~alifestd_coerce_chronological_consistency ~alifestd_collapse_trunk_asexual ~alifestd_collapse_trunk_polars ~alifestd_collapse_unifurcations ~alifestd_collapse_unifurcations_polars ~alifestd_convert_root_ancestor_token ~alifestd_count_children_of_asexual ~alifestd_count_children_of_polars ~alifestd_count_inner_nodes ~alifestd_count_inner_nodes_polars ~alifestd_count_leaf_nodes ~alifestd_count_leaf_nodes_polars ~alifestd_count_polytomies ~alifestd_count_polytomies_polars ~alifestd_count_root_nodes ~alifestd_count_root_nodes_polars ~alifestd_count_unifurcating_roots_asexual ~alifestd_count_unifurcating_roots_polars ~alifestd_count_unifurcations ~alifestd_count_unifurcations_polars ~alifestd_delete_trunk_asexual ~alifestd_delete_trunk_asexual_polars ~alifestd_delete_unifurcating_roots_asexual ~alifestd_delete_unifurcating_roots_polars ~alifestd_downsample_tips_asexual ~alifestd_downsample_tips_canopy_asexual ~alifestd_downsample_tips_canopy_polars ~alifestd_downsample_tips_clade_asexual ~alifestd_downsample_tips_clade_polars ~alifestd_downsample_tips_lineage_asexual ~alifestd_downsample_tips_lineage_polars ~alifestd_downsample_tips_lineage_stratified_asexual ~alifestd_downsample_tips_lineage_stratified_polars ~alifestd_downsample_tips_polars ~alifestd_downsample_tips_uniform_asexual ~alifestd_downsample_tips_uniform_polars ~alifestd_drop_topological_sensitivity ~alifestd_drop_topological_sensitivity_polars ~alifestd_estimate_triplet_distance_asexual ~alifestd_find_chronological_inconsistency ~alifestd_find_chronological_inconsistency_polars ~alifestd_find_leaf_ids ~alifestd_find_leaf_ids_polars ~alifestd_find_mrca_id_asexual ~alifestd_find_pair_distance_asexual ~alifestd_find_pair_distance_polars ~alifestd_find_pair_mrca_id_asexual ~alifestd_find_pair_mrca_id_polars ~alifestd_find_root_ids ~alifestd_find_root_ids_polars ~alifestd_from_avida_spop ~alifestd_from_avida_spop_polars ~alifestd_from_newick ~alifestd_from_newick_polars ~alifestd_has_compact_ids ~alifestd_has_compact_ids_polars ~alifestd_has_contiguous_ids ~alifestd_has_contiguous_ids_polars ~alifestd_has_increasing_ids ~alifestd_has_increasing_ids_polars ~alifestd_has_multiple_roots ~alifestd_has_multiple_roots_polars ~alifestd_is_asexual ~alifestd_is_asexual_polars ~alifestd_is_chronologically_ordered ~alifestd_is_chronologically_ordered_polars ~alifestd_is_chronologically_sorted ~alifestd_is_chronologically_sorted_polars ~alifestd_is_sexual ~alifestd_is_sexual_polars ~alifestd_is_strictly_bifurcating_asexual ~alifestd_is_strictly_bifurcating_polars ~alifestd_is_topologically_sorted ~alifestd_is_topologically_sorted_polars ~alifestd_is_ultrametric ~alifestd_is_ultrametric_polars ~alifestd_is_working_format_asexual ~alifestd_is_working_format_polars ~alifestd_join_roots ~alifestd_join_roots_polars ~alifestd_ladderize_asexual ~alifestd_ladderize_polars ~alifestd_make_ancestor_id_col ~alifestd_make_ancestor_id_col_polars ~alifestd_make_ancestor_list_col ~alifestd_make_ancestor_list_col_polars ~alifestd_make_balanced_bifurcating ~alifestd_make_balanced_bifurcating_polars ~alifestd_make_comb ~alifestd_make_comb_polars ~alifestd_make_edge_split ~alifestd_make_edge_split_polars ~alifestd_make_empty ~alifestd_make_empty_polars ~alifestd_make_leaf_split ~alifestd_make_leaf_split_polars ~alifestd_make_star ~alifestd_make_star_polars ~alifestd_mark_ancestor_origin_time_asexual ~alifestd_mark_ancestor_origin_time_polars ~alifestd_mark_clade_duration_asexual ~alifestd_mark_clade_duration_polars ~alifestd_mark_clade_duration_ratio_sister_asexual ~alifestd_mark_clade_duration_ratio_sister_polars ~alifestd_mark_clade_faithpd_asexual ~alifestd_mark_clade_faithpd_polars ~alifestd_mark_clade_fblr_growth_children_asexual ~alifestd_mark_clade_fblr_growth_sister_asexual ~alifestd_mark_clade_leafcount_ratio_sister_asexual ~alifestd_mark_clade_leafcount_ratio_sister_polars ~alifestd_mark_clade_logistic_growth_children_asexual ~alifestd_mark_clade_logistic_growth_sister_asexual ~alifestd_mark_clade_nodecount_ratio_sister_asexual ~alifestd_mark_clade_nodecount_ratio_sister_polars ~alifestd_mark_clade_subtended_duration_asexual ~alifestd_mark_clade_subtended_duration_polars ~alifestd_mark_clade_subtended_duration_ratio_sister_asexual ~alifestd_mark_clade_subtended_duration_ratio_sister_polars ~alifestd_mark_colless_index_asexual ~alifestd_mark_colless_index_corrected_asexual ~alifestd_mark_colless_index_corrected_polars ~alifestd_mark_colless_index_polars ~alifestd_mark_colless_like_index_mdm_asexual ~alifestd_mark_colless_like_index_mdm_polars ~alifestd_mark_colless_like_index_sd_asexual ~alifestd_mark_colless_like_index_sd_polars ~alifestd_mark_colless_like_index_var_asexual ~alifestd_mark_colless_like_index_var_polars ~alifestd_mark_csr_children_asexual ~alifestd_mark_csr_children_polars ~alifestd_mark_csr_offsets_asexual ~alifestd_mark_csr_offsets_polars ~alifestd_mark_first_child_id_asexual ~alifestd_mark_first_child_id_polars ~alifestd_mark_is_left_child_asexual ~alifestd_mark_is_left_child_polars ~alifestd_mark_is_right_child_asexual ~alifestd_mark_is_right_child_polars ~alifestd_mark_leaves ~alifestd_mark_leaves_polars ~alifestd_mark_left_child_asexual ~alifestd_mark_left_child_polars ~alifestd_mark_lineage_cummax_asexual ~alifestd_mark_lineage_cummax_polars ~alifestd_mark_lineage_cummin_asexual ~alifestd_mark_lineage_cummin_polars ~alifestd_mark_lineage_cumprod_asexual ~alifestd_mark_lineage_cumprod_polars ~alifestd_mark_lineage_cumsum_asexual ~alifestd_mark_lineage_cumsum_polars ~alifestd_mark_max_descendant_origin_time_asexual ~alifestd_mark_max_descendant_origin_time_polars ~alifestd_mark_next_sibling_id_asexual ~alifestd_mark_next_sibling_id_polars ~alifestd_mark_node_depth_asexual ~alifestd_mark_node_depth_polars ~alifestd_mark_num_children_asexual ~alifestd_mark_num_children_polars ~alifestd_mark_num_descendants_asexual ~alifestd_mark_num_descendants_polars ~alifestd_mark_num_leaves_asexual ~alifestd_mark_num_leaves_polars ~alifestd_mark_num_leaves_sibling_asexual ~alifestd_mark_num_leaves_sibling_polars ~alifestd_mark_num_preceding_leaves_asexual ~alifestd_mark_num_preceding_leaves_polars ~alifestd_mark_oldest_root ~alifestd_mark_oldest_root_polars ~alifestd_mark_origin_time_delta_asexual ~alifestd_mark_origin_time_delta_polars ~alifestd_mark_ot_mrca_asexual ~alifestd_mark_ot_mrca_polars ~alifestd_mark_prev_sibling_id_asexual ~alifestd_mark_prev_sibling_id_polars ~alifestd_mark_right_child_asexual ~alifestd_mark_right_child_polars ~alifestd_mark_root_id ~alifestd_mark_root_id_polars ~alifestd_mark_roots ~alifestd_mark_roots_polars ~alifestd_mark_sackin_index_asexual ~alifestd_mark_sackin_index_polars ~alifestd_mark_sample_tips_asexual ~alifestd_mark_sample_tips_canopy_asexual ~alifestd_mark_sample_tips_canopy_polars ~alifestd_mark_sample_tips_clade_asexual ~alifestd_mark_sample_tips_clade_polars ~alifestd_mark_sample_tips_lineage_asexual ~alifestd_mark_sample_tips_lineage_polars ~alifestd_mark_sample_tips_lineage_stratified_asexual ~alifestd_mark_sample_tips_lineage_stratified_polars ~alifestd_mark_sample_tips_polars ~alifestd_mark_sample_tips_uniform_asexual ~alifestd_mark_sample_tips_uniform_polars ~alifestd_mark_sister_asexual ~alifestd_mark_sister_polars ~alifestd_mask_descendants_asexual ~alifestd_mask_descendants_polars ~alifestd_mask_monomorphic_clades_asexual ~alifestd_parse_ancestor_id ~alifestd_parse_ancestor_ids ~alifestd_pipe_unary_ops ~alifestd_pipe_unary_ops_polars ~alifestd_prefix_roots ~alifestd_prefix_roots_polars ~alifestd_prune_extinct_lineages_asexual ~alifestd_prune_extinct_lineages_polars ~alifestd_reroot_at_id_asexual ~alifestd_reroot_at_id_polars ~alifestd_sample_triplet_comparisons_asexual ~alifestd_screen_trait_defined_clades_fisher_asexual ~alifestd_screen_trait_defined_clades_fitch_asexual ~alifestd_screen_trait_defined_clades_naive_asexual ~alifestd_sort_children_asexual ~alifestd_sort_children_polars ~alifestd_splay_polytomies ~alifestd_splay_polytomies_polars ~alifestd_sum_origin_time_deltas_asexual ~alifestd_sum_origin_time_deltas_polars ~alifestd_test_leaves_isomorphic_asexual ~alifestd_test_leaves_isomorphic_polars ~alifestd_to_iplotx_pandas ~alifestd_to_iplotx_polars ~alifestd_to_working_format ~alifestd_to_working_format_polars ~alifestd_topological_sensitivity_warned ~alifestd_topological_sensitivity_warned_polars ~alifestd_topological_sort ~alifestd_topological_sort_polars ~alifestd_try_add_ancestor_id_col ~alifestd_try_add_ancestor_id_col_polars ~alifestd_try_add_ancestor_list_col ~alifestd_try_add_ancestor_list_col_polars ~alifestd_ultrametricize ~alifestd_ultrametricize_polars ~alifestd_unfurl_lineage_asexual ~alifestd_unfurl_traversal_inorder_asexual ~alifestd_unfurl_traversal_inorder_polars ~alifestd_unfurl_traversal_levelorder_asexual ~alifestd_unfurl_traversal_levelorder_polars ~alifestd_unfurl_traversal_postorder_asexual ~alifestd_unfurl_traversal_postorder_contiguous_asexual ~alifestd_unfurl_traversal_postorder_contiguous_polars ~alifestd_unfurl_traversal_postorder_polars ~alifestd_unfurl_traversal_preorder_asexual ~alifestd_unfurl_traversal_preorder_polars ~alifestd_unfurl_traversal_semiorder_asexual ~alifestd_unfurl_traversal_semiorder_polars ~alifestd_unfurl_traversal_topological_asexual ~alifestd_unfurl_traversal_topological_polars ~alifestd_validate ~alifestd_warn_topological_sensitivity ~alifestd_warn_topological_sensitivity_polars .. rubric:: Classes .. autosummary:: :toctree: ~AlifestdIplotxShimNumpy ~AlifestdIplotxShimPandas ~AlifestdIplotxShimPolars