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 |

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