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
mailund/admixture_graph documentation built on April 3, 2018, 9:28 p.m.