API for uqrmaie1/admixtools
Inferring demographic history from genetic data
| Global functions | |
|---|---|
| add_indivs | Source code |
| add_pairs | Source code |
| admixtools | Man page |
| afs_to_counts | Man page Source code |
| afs_to_f2 | Man page Source code |
| afs_to_f2_blocks | Man page Source code |
| agraph_to_igraph | Man page |
| alert_danger | Source code |
| alert_info | Source code |
| alert_success | Source code |
| alert_warning | Source code |
| anygeno_to_aftable | Source code |
| arr3d_to_mat | Source code |
| arr3d_to_pairmat | Source code |
| block_arr_mean | Source code |
| block_arr_sum | Source code |
| block_mat_mean | Source code |
| block_mat_sum | Source code |
| boo_list | Man page Source code |
| boo_list_cons | Source code |
| boot_dat_stats | Source code |
| catalan | Source code |
| compare_fits | Man page |
| compare_fits2 | Man page |
| compare_fits4 | Man page |
| count_snps | Man page |
| count_zero_edges | Man page |
| cpp_aftable_to_dstatden | Source code |
| cpp_aftable_to_dstatnum | Source code |
| cpp_aftable_to_dstatnum_old | Source code |
| cpp_eigenstrat_to_afs | Source code |
| cpp_fill_pwts | Source code |
| cpp_get_block_lengths | Source code |
| cpp_get_pairindex | Source code |
| cpp_get_weights_covariance | Source code |
| cpp_is_polymorphic | Source code |
| cpp_jack_vec_stats | Source code |
| cpp_mats_to_f2_arr | Source code |
| cpp_opt_A | Source code |
| cpp_opt_B | Source code |
| cpp_opt_edge_lengths | Source code |
| cpp_optimweightsfun | Source code |
| cpp_outer_array_minus | Source code |
| cpp_outer_array_mul | Source code |
| cpp_outer_array_plus | Source code |
| cpp_packedancestrymap_ploidy | Source code |
| cpp_packedancestrymap_to_afs | Source code |
| cpp_plink_ploidy | Source code |
| cpp_plink_to_afs | Source code |
| cpp_qpadm_weights | Source code |
| cpp_read_eigenstrat | Source code |
| cpp_read_packedancestrymap | Source code |
| cpp_read_plink | Source code |
| decomposed_tree_neighbors | Man page |
| delete_admix | Man page |
| delete_groups | Man page |
| delete_leaf | Man page |
| desimplify_graph | Man page |
| diag_3d | Source code |
| discard_from_aftable | Source code |
| discard_from_geno | Source code |
| discard_snps | Source code |
| doublefactorial | Source code |
| edges_to_igraph | Man page Source code |
| eigenstrat_ploidy | Source code |
| eigenstrat_to_afs | Man page Source code |
| eigenstrat_to_afs_old | Source code |
| eigenstrat_to_plink | Man page |
| est_to_boo | Man page Source code |
| est_to_boo_dat | Source code |
| est_to_loo | Man page Source code |
| est_to_loo_dat | Source code |
| est_to_loo_nafix | Source code |
| example_anno | Man page |
| example_f2_blocks | Man page |
| example_graph | Man page |
| example_igraph | Man page |
| example_opt | Man page |
| example_qpgraph_ref_results | Man page |
| example_triples | Man page |
| extract_afs | Man page Source code |
| extract_afs_simple | Man page Source code |
| extract_counts | Man page Source code |
| extract_counts_large | Source code |
| extract_f2 | Man page Source code |
| extract_f2_large | Man page Source code |
| extract_f2_subset | Man page Source code |
| extract_more_counts | Source code |
| extract_samples | Man page |
| f2 | Man page Source code |
| f2_f3 | Source code |
| f2_f4 | Source code |
| f2_from_geno | Man page Source code |
| f2_from_geno_indivs | Source code |
| f2_from_msprime | Man page |
| f2_from_precomp | Man page Source code |
| f2_from_precomp_indivs | Source code |
| f2blocks_to_f4blocks | Source code |
| f2blocks_to_f4stats | Source code |
| f2dat_f4dat | Man page |
| f3 | Man page |
| f3blockdat_from_geno | Man page |
| f4 | Man page |
| f4_from_afdat | Man page |
| f4_from_f2 | Man page |
| f4blockdat_from_geno | Man page |
| f4blockdat_to_f4blocks | Man page Source code |
| f4blocks_to_f4stats | Source code |
| find_admixedges | Man page |
| find_graphs | Man page |
| find_graphs_old | Man page |
| find_newedges | Man page |
| find_normedges | Man page |
| flip_node | Source code |
| flipadmix_random | Man page |
| format_info | Source code |
| fst | Man page Source code |
| fstat_get_popcombs | Source code |
| generate_all_graphs | Man page |
| generate_all_trees | Man page |
| get_block_lengths | Man page Source code |
| get_dist_to_nmig | Source code |
| get_f | Source code |
| get_f2 | Man page |
| get_leafnames | Man page Source code |
| get_leaves | Source code |
| get_leaves2 | Source code |
| get_outpop | Man page Source code |
| get_root | Source code |
| get_rootname | Man page Source code |
| get_weights_covariance | Source code |
| gg_color_hue | Source code |
| graph_addleaf | Man page |
| graph_distances | Man page |
| graph_equations | Man page |
| graph_f2_function | Man page |
| graph_flipadmix | Man page |
| graph_hash | Man page |
| graph_minusone | Man page |
| graph_minusplus | Man page |
| graph_plusone | Man page |
| graph_splittrees | Man page |
| graph_to_afs | Man page |
| graph_to_pcs | Man page |
| graph_to_pwts | Source code |
| graph_to_qpadm | Man page |
| graphmod_pavel | Man page |
| group_samples | Man page Source code |
| group_samples_onepop | Source code |
| igraph_to_agraph | Man page |
| indpairs_to_f2blocks | Source code |
| insert_admix | Man page |
| insert_admix_n | Man page |
| insert_admix_old | Man page |
| insert_leaf | Man page |
| interleave | Source code |
| is_simplified | Source code |
| is_valid | Man page Source code |
| isomorphism_classes | Man page |
| isomorphism_classes2 | Man page |
| jack_arr_stats | Source code |
| jack_dat_stats | Source code |
| jack_mat_stats | Source code |
| jack_mat_stats2 | Source code |
| jack_pairarr_stats | Source code |
| jack_vec_stats | Source code |
| jack_vec_stats2 | Source code |
| joint_sfs | Man page |
| joint_spectrum | Man page |
| lazadm | Man page |
| loo_list | Man page Source code |
| loo_to_est | Man page Source code |
| loo_to_est_dat | Source code |
| make_bootfun | Source code |
| make_chunks | Source code |
| make_pseudohaploid | Source code |
| make_resample_snps_fun | Source code |
| mat_to_2rep1 | Source code |
| mat_to_arr3d | Source code |
| mat_to_rep21 | Source code |
| match_samples | Source code |
| mats_to_aparr | Source code |
| mats_to_ctarr | Source code |
| mats_to_f2arr | Source code |
| mats_to_fstarr | Source code |
| mean_impute | Source code |
| move_admixedge_once | Man page |
| msprime_genome | Man page |
| msprime_sim | Man page |
| mutate_n | Man page |
| namedList | Source code |
| newick_to_edges | Man page |
| node_counts | Man page |
| node_signature | Man page |
| numadmix | Man page Source code |
| numadmixplacements | Source code |
| numdags | Source code |
| numtrees | Source code |
| numtreesadmix | Source code |
| opt_A | Source code |
| opt_B | Source code |
| outer_array | Source code |
| packedancestrymap_to_afs | Man page Source code |
| packedancestrymap_to_plink | Man page |
| parse_dot | Man page |
| parse_fstats | Source code |
| parse_qp3pop_output | Man page |
| parse_qpadm_output | Man page |
| parse_qpdstat_output | Man page |
| parse_qpf4ratio_output | Man page |
| parse_qpgraph_graphfile | Man page |
| parse_qpgraph_output | Man page |
| permute_leaves | Man page |
| place_root_random | Man page |
| plink_to_afs | Man page Source code |
| plot_comparison | Man page Source code |
| plot_comparison_qpgraph | Source code |
| plot_cov | Source code |
| plot_cov_internal | Source code |
| plot_graph | Man page |
| plot_graph_map | Man page |
| plot_graph_treemix | Source code |
| plot_map | Man page |
| plot_modelcov | Source code |
| plot_resid | Source code |
| plot_resid_internal | Source code |
| plot_tree | Source code |
| plot_tree_internal | Source code |
| plotly_comparison | Man page Source code |
| plotly_graph | Man page |
| pop_indices | Source code |
| power_set | Source code |
| prodarray | Source code |
| pseudo_dates | Man page |
| qp3pop | Man page Source code |
| qp3pop_resample_inds | Man page |
| qp3pop_resample_snps | Man page |
| qp3pop_wrapper | Man page Source code |
| qpadm | Man page Source code |
| qpadm_dof | Source code Source code Source code |
| qpadm_models | Man page |
| qpadm_models_old | Man page |
| qpadm_multi | Man page |
| qpadm_p | Man page |
| qpadm_resample_inds | Man page |
| qpadm_resample_snps | Man page |
| qpadm_rotate | Man page |
| qpadm_weights | Source code |
| qpadm_wrapper | Man page Source code |
| qpdstat | Man page Source code |
| qpdstat_resample_inds | Man page |
| qpdstat_resample_snps | Man page |
| qpdstat_wrapper | Man page Source code |
| qpf4diff | Man page |
| qpf4ratio | Man page |
| qpf4ratio_wrapper | Man page Source code |
| qpfstats | Man page |
| qpfstats_wrapper | Source code |
| qpgraph | Man page |
| qpgraph_precompute_f3 | Man page |
| qpgraph_resample_inds | Man page |
| qpgraph_resample_multi | Man page |
| qpgraph_resample_snps | Man page |
| qpgraph_resample_snps2 | Man page |
| qpgraph_wrapper | Man page Source code |
| qpgraph_wrapper2 | Source code |
| qpsolve | Source code |
| qpwave | Man page Source code |
| qpwave_dof | Source code Source code Source code Source code |
| qpwave_pairs | Man page |
| qpwave_resample_inds | Man page |
| qpwave_resample_snps | Man page |
| qpwave_wrapper | Man page |
| random_admixturegraph | Man page |
| random_dates | Man page |
| random_newick | Man page |
| random_sim | Man page |
| read_anygeno | Source code |
| read_eigenstrat | Man page Source code |
| read_f2 | Man page Source code |
| read_indivs | Source code |
| read_packedancestrymap | Man page Source code |
| read_pairs | Source code |
| read_plink | Man page Source code |
| resample_inds | Man page |
| resample_snps | Man page |
| rotate_models | Man page |
| row_prods | Source code |
| run_admixtools | Source code |
| run_shiny_admixtools | Man page Source code |
| satisfies_constraints | Man page |
| satisfies_eventorder | Man page |
| satisfies_nonzerof4 | Man page |
| satisfies_numadmix | Man page |
| satisfies_zerof4 | Man page |
| scale_ap_blocks | Source code |
| set_mig_coords | Source code |
| set_x_coord | Source code |
| set_x_coords | Source code |
| set_y_coord | Source code |
| set_y_coords | Source code |
| shortest_unique_prefixes | Man page |
| simplify_graph | Man page |
| split_mat | Man page Source code |
| split_multifurcations | Man page |
| spr_all | Man page |
| spr_leaves | Man page |
| summarize_descendants | Man page |
| summarize_descendants_list | Man page |
| summarize_eventorder | Man page |
| summarize_eventorder_list | Man page |
| summarize_fits | Man page |
| summarize_numadmix | Man page |
| summarize_numadmix_list | Man page |
| summarize_proxies | Man page |
| summarize_proxies_list | Man page |
| summarize_triples | Man page |
| summarize_zerof4 | Man page |
| summarize_zerof4_list | Man page |
| swap_leaves | Man page |
| test_cladality | Man page |
| tree_in_graph | Man page |
| tree_neighbors | Man page |
| tree_to_pwts | Source code |
| unidentifiable_edges | Man page |
| unify_vertex_names | Source code |
| unify_vertex_names_rec | Source code |
| weighted_row_means | Source code |
| write_dot | Man page |
| write_f2 | Man page Source code |
| write_indiv | Source code |
| write_pairdat | Source code |
| write_pairdat2 | Source code |
| write_split_inddat | Source code |
| xmat_to_inddat | Source code |
| xmat_to_pairdat | Source code |
| xmats_to_pairarrs | Source code |
| yesno | Source code |
| ztop | Source code |
