API for mailund/admixture_graph
Admixture Graph Manipulation and Fitting
| Global functions | |
|---|---|
| add_a_leaf | Man page Source code |
| add_an_admixture | Man page Source code |
| add_an_admixture2 | Man page Source code |
| add_graph_f4 | Man page Source code |
| add_graph_f4_sign | Man page Source code |
| admix_props | Man page Source code |
| admixture_edge | Man page Source code |
| admixture_proportions | Man page Source code |
| admixturegraph-package | Man page |
| agraph | Man page Source code |
| agraph_children | Man page Source code |
| agraph_parents | Man page Source code |
| agraph_weights | Man page Source code |
| all_graphs | Man page Source code |
| all_path_overlaps | Man page Source code |
| all_paths | Man page Source code |
| all_paths_to_leaves | Source code |
| all_paths_to_root | Source code |
| arrange_graph | Source code |
| bears | Man page |
| branch_count | Source code |
| break_graph | Source code |
| build_edge_optimisation_matrix | Man page Source code |
| burn_in | Man page Source code |
| calculate_concentration | Man page Source code |
| canonise_expression | Man page Source code |
| canonise_graph | Man page Source code |
| clear_node | Source code |
| coef.agraph_fit | Man page Source code |
| cost_function | Man page Source code |
| drawing_cost | Source code |
| edge | Man page Source code |
| edge_optimisation_function | Man page Source code |
| eight_leaves_trees | Man page |
| evaluate_f4 | Man page Source code |
| examine_edge_optimisation_matrix | Man page Source code |
| exceptional_behavior | Source code |
| export_to_qpGraph | Man page Source code |
| extract_admixture_proportion_parameters | Man page Source code |
| extract_graph_parameters | Man page Source code |
| extract_trees | Man page Source code |
| f2 | Man page Source code |
| f3 | Man page Source code |
| f4 | Man page Source code |
| f4stats | Man page Source code |
| fast_fit | Man page Source code |
| fast_plot | Man page Source code |
| filter_on_leaves | Man page Source code |
| first_collision | Source code |
| fit_graph | Man page Source code |
| fit_graph_list | Man page Source code |
| fit_permutations_and_graphs | Man page Source code |
| fitted.agraph_fit | Man page Source code |
| five_leaves_graphs | Man page |
| flow | Source code |
| format_edge | Source code |
| format_overlaps | Source code |
| format_path | Man page Source code |
| format_path_overlap | Source code |
| four_leaves_graphs | Man page |
| get_admixtures | Source code |
| get_edges | Source code |
| get_graph_f4_sign | Man page Source code |
| get_labels | Source code |
| get_root | Source code |
| graph_environment | Man page Source code |
| graph_to_vector | Man page Source code |
| graphs_2_0 | Man page |
| graphs_3_0 | Man page |
| graphs_3_1 | Man page |
| graphs_4_0 | Man page |
| graphs_4_1 | Man page |
| graphs_4_2 | Man page |
| graphs_5_0 | Man page |
| graphs_5_1 | Man page |
| graphs_5_2 | Man page |
| graphs_6_0 | Man page |
| graphs_6_1 | Man page |
| graphs_6_2 | Man page |
| graphs_7_0 | Man page |
| graphs_7_1 | Man page |
| graphs_8_0 | Man page |
| inner_fast_fit | Source code |
| inner_fit_graph | Source code |
| invent_name | Source code |
| is_descendant_of | Man page Source code |
| is_negative | Man page Source code |
| is_positive | Man page Source code |
| is_unknown | Man page Source code |
| is_zero | Man page Source code |
| leaf_order | Source code |
| load_admixture_information | Source code |
| log_likelihood | Man page Source code |
| log_sum_of_logs | Man page Source code |
| make_an_outgroup | Man page Source code |
| make_mcmc_model | Man page Source code |
| make_permutations | Man page Source code |
| make_predict_function | Source code |
| mk_edge_label | Source code |
| model_bayes_factor_n | Man page Source code |
| model_likelihood | Man page Source code |
| model_likelihood_n | Man page Source code |
| mynonneg | Man page Source code |
| no_admixture_events | Man page Source code |
| no_admixture_events.agraph | Man page Source code |
| no_admixture_events.agraph_fit | Man page Source code |
| no_admixture_events.agraph_fit_list | Man page Source code |
| no_parents | Source code |
| no_poor_fits | Man page Source code |
| no_poor_fits.agraph_fit | Man page Source code |
| no_poor_fits.agraph_fit_list | Man page Source code |
| overlaps_sign | Man page Source code |
| parent_edges | Man page Source code |
| path_negative | Source code |
| path_non_negative | Source code |
| path_non_positive | Source code |
| path_overlap | Man page Source code |
| path_positive | Source code |
| path_probability | Source code |
| path_zero | Source code |
| plot.agraph | Man page Source code |
| plot.agraph_fit | Man page Source code |
| plot.f4stats | Man page Source code |
| plot_fit_1 | Man page Source code |
| plot_fit_2 | Man page Source code |
| poor_fits | Man page Source code |
| poor_fits.agraph_fit | Man page Source code |
| poor_fits.agraph_fit_list | Man page Source code |
| print.agraph_fit | Man page Source code |
| project_to_population | Man page Source code |
| recognize_forbidden_parellelness | Source code |
| refined_graph | Source code |
| remove_duplicates | Man page Source code |
| remove_eightness | Source code |
| remove_false_leaves | Source code |
| remove_joints_from_a_tree | Source code |
| rename_nodes | Man page Source code |
| residuals.agraph_fit | Man page Source code |
| root_graph | Source code |
| run_metropolis_hasting | Man page Source code |
| save_admixture_information | Source code |
| seven_leaves_graphs | Man page |
| seven_leaves_trees | Man page |
| sf2 | Man page Source code |
| sf3 | Man page Source code |
| sf4 | Man page Source code |
| six_leaves_graphs | Man page |
| split_first_admixture | Source code |
| split_population | Man page Source code |
| split_population.agraph_fit | Man page Source code |
| split_population.data.frame | Man page Source code |
| sum_of_squared_errors | Man page Source code |
| sum_of_squared_errors.agraph_fit | Man page Source code |
| sum_of_squared_errors.agraph_fit_list | Man page Source code |
| summary.agraph_fit | Man page Source code |
| symmetry_4_I | Source code |
| symmetry_4_II | Source code |
| symmetry_4_III | Source code |
| symmetry_4_IV | Source code |
| symmetry_4_IX | Source code |
| symmetry_4_V | Source code |
| symmetry_4_VI | Source code |
| symmetry_4_VII | Source code |
| symmetry_4_VIII | Source code |
| symmetry_5_I | Source code |
| symmetry_5_II | Source code |
| symmetry_5_III | Source code |
| symmetry_5_IV | Source code |
| symmetry_5_V | Source code |
| symmetry_5_VI | Source code |
| symmetry_5_VII | Source code |
| symmetry_6_I | Source code |
| symmetry_6_II | Source code |
| symmetry_6_III | Source code |
| symmetry_6_IV | Source code |
| symmetry_6_IX | Source code |
| symmetry_6_V | Source code |
| symmetry_6_VI | Source code |
| symmetry_6_VII | Source code |
| symmetry_6_VIII | Source code |
| symmetry_6_X | Source code |
| symmetry_6_XI | Source code |
| symmetry_6_XII | Source code |
| symmetry_6_XIII | Source code |
| symmetry_6_XIV | Source code |
| symmetry_6_XV | Source code |
| symmetry_6_XVI | Source code |
| symmetry_6_XVII | Source code |
| symmetry_6_XVIII | Source code |
| symmetry_7_I | Source code |
| symmetry_7_II | Source code |
| symmetry_7_III | Source code |
| symmetry_7_IV | Source code |
| symmetry_7_V | Source code |
| symmetry_8_I | Source code |
| symmetry_8_II | Source code |
| symmetry_8_III | Source code |
| symmetry_8_IV | Source code |
| thinning | Man page Source code |
| try_to_add | Source code |
| unpack_environment | Source code |
| update_cycle_orientation | Source code |
| vector_to_graph | Man page Source code |
