| AICstats_2models |
Source code
|
| AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_r |
Source code
|
| AkaikeWeights_on_summary_table |
Source code
|
| BioGeoBEARS_model_defaults |
Source code
|
| BioGeoBEARS_model_object_to_est_params |
Source code
|
| BioGeoBEARS_model_object_to_init_params |
Source code
|
| BioGeoBEARS_model_object_to_params_lower |
Source code
|
| BioGeoBEARS_model_object_to_params_upper |
Source code
|
| ChromoBEARS_model_defaults |
Source code
|
| DIVA_NEXUS_MacClade_block |
Source code
|
| DIVA_NEXUS_header |
Source code
|
| LGcpp_MLstate_per_node |
Source code
|
| LGcpp_splits_fn_to_table |
Source code
|
| LGcpp_splits_fn_to_table2 |
Source code
|
| LGcpp_states_fn_to_table |
Source code
|
| LGpy_MLsplit_per_node |
Source code
|
| LGpy_splits_fn_to_table |
Source code
|
| ML_yule_birthRate |
Source code
|
| ML_yule_birthRate_wRoot |
Source code
|
| Mk_Qmat |
Source code
|
| Pdata_given_rangerow |
Source code
|
| Pdata_given_rangerow_dp |
Source code
|
| Pmat_to_Qmat |
Source code
|
| Qmat_chromo_add_subtract |
Source code
|
| Qmat_chromo_alpha |
Source code
|
| Qmat_chromo_beta |
Source code
|
| Qmat_chromo_delta |
Source code
|
| Qmat_chromo_ep |
Source code
|
| Qmat_chromo_rho |
Source code
|
| Qmat_chromoploid |
Source code
|
| Qmat_ploidy |
Source code
|
| Qmat_to_Rmat |
Source code
|
| Qmat_to_Rmat_COO |
Source code
|
| Rmat_perfect_to_Qmat |
Source code
|
| Rmat_to_Qmat |
Source code
|
| Rmat_to_Qmat_noScaling |
Source code
|
| Rmat_to_Qmat_noScaling_COO |
Source code
|
| SSEsim_results_processed_into_res |
Source code
|
| SSEsim_results_processed_to_anagenetic_events_table |
Source code
|
| SSEsim_results_processed_to_cladogenetic_events_table |
Source code
|
| SSEsim_run |
Source code
|
| SSEsim_setup_inputs |
Source code
|
| SSEsim_to_files |
Source code
|
| add_cladogenetic_events_to_trtable |
Source code
|
| add_fossil_randomly |
Source code
|
| add_fossils_from_xls_randomly |
Source code
|
| add_fossils_to_many_trees |
Source code
|
| add_hook |
Source code
|
| add_hooks |
Source code
|
| add_jts_to_BioGeoBEARS_run_object |
Source code
|
| add_list_of_fossil_tips_to_tipranges |
Source code
|
| add_random_direct_ancestor_hook |
Source code
|
| add_random_side_branch |
Source code
|
| add_statum_boundaries_to_phylo_plot |
Source code
|
| add_to_downpass_labels |
Source code
|
| add_trait_to_BioGeoBEARS_run_object |
Source code
|
| addslash |
Source code
|
| adf |
Source code
|
| adf2 |
Source code
|
| allQs |
Source code
|
| ann |
Source code
|
| areas_list_to_states_list_new |
Source code
|
| assign_rates_asym |
Source code
|
| assign_rates_sym |
Source code
|
| average_tr_tips |
Source code
|
| basefreqs_to_basefreqs_mat |
Source code
|
| bd_liks |
Source code
|
| bears_optim_run |
Source code
|
| binary_range_to_letter_code_list |
Source code
|
| binary_range_to_letter_code_txt |
Source code
|
| binary_ranges_to_letter_codes |
Source code
|
| calcP_n |
Source code
|
| calcZ_part |
Source code
|
| calc_AIC_column |
Source code
|
| calc_AIC_vals |
Source code
|
| calc_AICc_column |
Source code
|
| calc_AICc_vals |
Source code
|
| calc_BSM_mean_node_states |
Source code
|
| calc_independent_likelihoods_on_each_branch_prebyte |
Source code
|
| calc_linked_params_BioGeoBEARS_model_object |
Source code
|
| calc_loglike_for_optim |
Source code
|
| calc_loglike_for_optim_neg |
Source code
|
| calc_loglike_for_optim_stratified |
Source code
|
| calc_loglike_for_optim_stratified_neg |
Source code
|
| calc_loglike_sp_prebyte |
Source code
|
| calc_loglike_sp_stratified |
Source code
|
| calc_obs_like |
Source code
|
| calc_post_prob_presence |
Source code
|
| calc_prob_forward_onebranch_dense |
Source code
|
| calc_prob_forward_onebranch_sparse |
Source code
|
| calc_uppass_probs_new2 |
Source code
|
| calc_uppass_probs_new2_example_DEC |
Source code
|
| calc_uppass_probs_new2_example_DECj |
Source code
|
| calc_uppass_scenario_probs_new2 |
Source code
|
| catdf |
Source code
|
| cft |
Source code
|
| chainsaw2 |
Source code
|
| check_BioGeoBEARS_run |
Source code
|
| check_ML_vs_BSM |
Source code
|
| check_for_ana_events_table |
Source code
|
| check_if_state_is_allowed |
Source code
|
| check_if_state_is_allowed_by_adjacency |
Source code
|
| check_tipranges_for_allQs |
Source code
|
| check_tree |
Source code
|
| check_trfn |
Source code
|
| checktree |
Source code
|
| chromoploid_tiplikes |
Source code
|
| cls.df |
Source code
|
| combine_3matrices |
Source code
Source code
|
| combine_3matrices2 |
Source code
Source code
|
| combine_matrices_into_supermatrix |
Source code
|
| combine_matrices_into_supermatrix_w_names |
Source code
|
| compare_two_name_lists |
Source code
|
| conditional_format_cell |
Source code
|
| conditional_format_table |
Source code
|
| convert_SSEsim_to_stochastic_mapping_results_format |
Source code
|
| convert_clado_1desc_to_anagenetic |
Source code
|
| convert_full_simtree_nodenums_to_observed_simtree_nodenums |
Source code
|
| convert_simtr_observed_events_to_prelim_stochastic_mapping_forma |
Source code
|
| coo2crs |
Source code
|
| correct_de_events_on_observed_tree |
Source code
|
| count_ana_clado_events |
Source code
|
| count_ana_dispersal_events |
Source code
|
| count_clado_dispersal_events |
Source code
|
| count_clado_events_nonjump |
Source code
|
| count_events_huge_tables |
Source code
|
| counts_of_each_rate |
Source code
|
| counts_of_each_rate_minus_rowcol |
Source code
|
| define_BioGeoBEARS_model_object |
Source code
|
| define_BioGeoBEARS_run |
Source code
|
| define_ChromoBEARS_model_object |
Source code
|
| define_tipranges_object |
Source code
|
| df_to_numeric |
Source code
|
| dfn2n |
Source code
|
| dfnums_to_numeric |
Source code
|
| diri_probs |
Source code
|
| dispersal_multipliers_matrix_from_BioGeoBEARS_run_object |
Source code
|
| dist_between_direct_ancestors |
Source code
|
| divide_probs_by_number_of_options_nums |
Source code
|
| divide_probs_by_number_of_options_txt |
Source code
|
| edges_existing_at_correct_time_bp_TF |
Source code
|
| edges_table_to_tipranges_object |
Source code
|
| empcdf |
Source code
|
| enn |
Source code
|
| error_checks_for_fossils_xls |
Source code
|
| event_txt_into_events_row |
Source code
|
| events_table_into_txt |
Source code
|
| events_table_row_into_txt |
Source code
|
| events_txt_into_events_table |
Source code
|
| events_txt_list_into_events_table |
Source code
|
| example_ana_events_table |
Source code
|
| exp_SparseM |
Source code
|
| exp_cmdstr |
Source code
|
| exp_cmdstr_list |
Source code
|
| expand.grid.alt |
Source code
|
| expand.grid.jc |
Source code
|
| expokit_dgpadm_Qmat2_prebyte |
Source code
|
| exponentiate_sparse_matrix_w_lots_of_zeros |
Source code
|
| extend_tips_to_ultrametricize |
Source code
|
| extract_numbers |
Source code
|
| extract_param_inference |
Source code
|
| extract_params_from_BioGeoBEARS_results_object |
Source code
|
| figure_out_step_val |
Source code
Source code
|
| find_instring |
Source code
|
| find_str_inlist |
Source code
|
| findall |
Source code
|
| fix_BioGeoBEARS_params_minmax |
Source code
|
| geog_ancstates_from_both |
Source code
|
| getAIC |
Source code
|
| getAIC_weight_for_model1 |
Source code
|
| getAICc |
Source code
|
| get_AICweight_ratio_model1_over_model2 |
Source code
|
| get_APE_nodenums |
Source code
|
| get_Akaike_weight_ratio_from_Akaike_pairwise_weights |
Source code
|
| get_Akaike_weights_from_rel_likes |
Source code
|
| get_Akaike_weights_from_rel_likes_pairwise |
Source code
|
| get_Cevent_probs_df_from_mats |
Source code
|
| get_Cevent_probs_df_from_res |
Source code
|
| get_LnL_from_BioGeoBEARS_results_object |
Source code
|
| get_LnL_from_GenSA |
Source code
|
| get_LnL_from_optim |
Source code
|
| get_LnL_from_optim_result |
Source code
|
| get_LnL_from_optimx2012 |
Source code
|
| get_LnL_from_optimx2013 |
Source code
|
| get_ML_probs |
Source code
|
| get_ML_state_indices |
Source code
|
| get_ML_states |
Source code
|
| get_ML_states_from_relprobs |
Source code
|
| get_MLsplitprobs_from_results |
Source code
|
| get_Qmat_COOmat_from_BioGeoBEARS_run_object |
Source code
|
| get_Qmat_COOmat_from_res |
Source code
|
| get_TF_tips |
Source code
|
| get_all_daughter_tips_of_a_node |
Source code
|
| get_all_node_ages |
Source code
|
| get_bigmatrix_dim |
Source code
|
| get_clado_perEvent_weights |
Source code
|
| get_daughter_nodes |
Source code
|
| get_daughter_tipnames |
Source code
|
| get_daughter_tipnums |
Source code
|
| get_daughters |
Source code
|
| get_dej_params_row_from_SSEsim_results_processed |
Source code
|
| get_deltaAIC |
Source code
|
| get_deltaAIC_pairwise_w_ref_model |
Source code
|
| get_distribution_of_range_sizes_in_states_list |
Source code
|
| get_distribution_of_range_sizes_in_tipranges |
Source code
|
| get_dmat_times_from_BioGeoBEARS_run_object |
Source code
|
| get_dmat_times_from_res |
Source code
|
| get_edge_times_before_present |
Source code
|
| get_fn_prefix |
Source code
|
| get_geog_from_traitgeog_results |
Source code
|
| get_huge_events_tables_from_BSM_Rdata |
Source code
|
| get_huge_events_tables_from_clado_ana_events_tables |
Source code
|
| get_indices_of_branches_under_tips |
Source code
|
| get_indices_of_tip_nodes |
Source code
|
| get_indices_where_list1_occurs_in_list2 |
Source code
|
| get_indices_where_list1_occurs_in_list2_noNA |
Source code
|
| get_inf_LgL_etc_optimx |
Source code
|
| get_inf_ML_stateprobs |
Source code
|
| get_infparams_optimx |
Source code
|
| get_infparams_optimx_nosim |
Source code
|
| get_infprobs_of_simstates |
Source code
|
| get_inputs_for_stochastic_mapping |
Source code
|
| get_inputs_for_stochastic_mapping_from_results_object |
Source code
|
| get_inputs_for_stochastic_mapping_stratified |
Source code
|
| get_lagrange_nodenums |
Source code
|
| get_leftright_nodes_matrix_from_results |
Source code
|
| get_level |
Source code
|
| get_max_height_tree |
Source code
|
| get_node_ages_of_tips |
Source code
|
| get_nodenum_structural_root |
Source code
|
| get_nodenums |
Source code
|
| get_params_from_GenSA |
Source code
|
| get_params_from_optim |
Source code
|
| get_params_from_optim_or_optimx_result |
Source code
|
| get_params_from_optimx2012 |
Source code
|
| get_params_from_optimx2013 |
Source code
|
| get_parent |
Source code
|
| get_parent_for_trace_parents_up |
Source code
|
| get_path_first |
Source code
|
| get_path_last |
Source code
|
| get_possible_branches_to_add_fossils_to |
Source code
|
| get_probvals |
Source code
|
| get_pruningwise_nodenums |
Source code
|
| get_rangesize_prior_by_observed_rangesize |
Source code
|
| get_root_age |
Source code
|
| get_rownum_ref_model |
Source code
|
| get_simparams |
Source code
|
| get_simstates |
Source code
|
| get_simtr_full_to_observed_node_translation |
Source code
|
| get_sister_node |
Source code
|
| get_spPmat_inputs_from_BGB |
Source code
|
| get_tip_likelihoods_of_subbranch_from_resCondlikes_given_master_ |
Source code
|
| get_tiplabel_ranges |
Source code
|
| get_tipranges_from_detects_df |
Source code
|
| get_tr_height |
Source code
|
| get_trait_from_traitgeog_results |
Source code
|
| get_tree_height |
Source code
|
| get_treeheight |
Source code
|
| get_trht |
Source code
|
| getareanames_from_tipranges_object |
Source code
|
| getareas_from_tipranges_object |
Source code
|
| getname |
Source code
|
| getranges_from_LagrangePHYLIP |
Source code
|
| given_a_starting_state_get_prob_of_each_split_scenario |
Source code
|
| given_a_starting_state_simulate_branch_end |
Source code
|
| given_a_starting_state_simulate_split |
Source code
|
| hist_event_counts |
Source code
|
| hist_sim_v_inf_vals |
Source code
|
| impose_min_brlen |
Source code
|
| infprobs_to_probs_of_each_area |
Source code
|
| infprobs_to_probs_of_each_area_from_relprobs |
Source code
|
| infprobs_to_probs_of_each_rangesize |
Source code
|
| inn |
Source code
|
| is.not.na |
Source code
|
| is_list_not_dataframe |
Source code
|
| isblank_TF |
Source code
|
| label_nodes_postorder_phylo3 |
Source code
|
| label_table_of_anagenetic_events |
Source code
|
| label_table_of_cladogenetic_events |
Source code
|
| letter_string_to_binary |
Source code
|
| letter_strings_to_tipranges_df |
Source code
|
| level_tree_tips |
Source code
|
| linear_regression_plot |
Source code
|
| list2str |
Source code
|
| little_Qmats_to_big_Qmat |
Source code
|
| lrttest |
Source code
|
| lrttest_on_summary_table |
Source code
|
| make_BSMs |
Source code
|
| make_BioGeoBEARS_manytrees_results_object |
Source code
|
| make_dispersal_multiplier_matrix |
Source code
|
| make_list_of_indices_from_2_lists |
Source code
Source code
|
| make_lotsa_sparse_matrices |
Source code
|
| make_relprob_matrix_bi |
Source code
|
| make_relprob_matrix_de |
Source code
|
| make_relprob_nummatrix_sp1 |
Source code
|
| make_relprob_txtmatrix_sp1 |
Source code
|
| make_sparse_matrix |
Source code
|
| make_sparse_matrix_by_i |
Source code
|
| make_spmat_row |
Source code
|
| mapply_calc_obs_like |
Source code
|
| mapply_calc_post_prob_presence |
Source code
|
| mapply_likelihoods_prebyte |
Source code
|
| mat2q |
Source code
|
| mat_to_Qmat_as_list |
Source code
|
| match_list1_in_list2 |
Source code
|
| matpow |
Source code
|
| matpow2 |
Source code
|
| matpowfast |
Source code
|
| matpowfast2 |
Source code
|
| matrix_to_spam |
Source code
|
| merge_words_nonwords |
Source code
|
| meval |
Source code
|
| minmax_pretty |
Source code
|
| modify_Qmat_with_trait |
Source code
|
| modify_a_rate |
Source code
|
| modify_rate_matrix_categories |
Source code
|
| moref |
Source code
|
| motA_tree_example |
Source code
|
| n |
Source code
|
| nesting_mats |
Source code
|
| nesting_mats_w_names |
Source code
|
| nodenums_DIVA |
Source code
|
| nodenums_bottom_up |
Source code
|
| normat |
Source code
Source code
|
| np |
Source code
|
| nparams_from_optimx2013 |
Source code
|
| nullsym_to_NA |
Source code
|
| ones |
Source code
|
| opd |
Source code
|
| openwd |
Source code
|
| order_tipranges_by_tr |
Source code
|
| order_tipranges_by_tree_tips |
Source code
|
| params_into_BioGeoBEARS_model_object |
Source code
|
| parse_lagrange_output |
Source code
|
| parse_lagrange_output_old |
Source code
|
| parse_lagrange_python_output |
Source code
|
| parse_lagrange_python_output_old |
Source code
|
| paste_rows_without_zeros |
Source code
|
| plot_BSM_fns |
Source code
|
| plot_BioGeoBEARS_results |
Source code
|
| plot_inf_accuracy_vs_SSEsims_v2 |
Source code
|
| plot_nodelabels_on_edges |
Source code
|
| plot_nodelabels_on_nodes |
Source code
|
| plot_nodelabels_on_nodes_right |
Source code
|
| plot_params_from_multiple_trees |
Source code
|
| plot_simDEC_DECJ_inferences |
Source code
|
| plot_tiplabels_on_tips |
Source code
|
| plot_tree_nodenums_tipnums |
Source code
|
| post_prob_states |
Source code
|
| post_prob_states_matrix |
Source code
|
| postorder_nodes_phylo4_return_table |
Source code
|
| postorder_nodes_phylo4_return_table2 |
Source code
|
| prflag |
Source code
|
| print_counts_lists_to_file |
Source code
|
| printall |
Source code
|
| prob_each_split_scenario_to_uppass_probs |
Source code
|
| prob_of_states_from_prior_prob_areas |
Source code
|
| process_DIVA_output |
Source code
|
| process_optim |
Source code
|
| prt |
Source code
|
| prt_tree_to_phylo4 |
Source code
|
| prune_specimens_to_species |
Source code
|
| prune_states_list |
Source code
|
| prune_states_list_by_adjacency |
Source code
|
| put_jcol_after_ecol |
Source code
|
| put_params_into_optim_or_optimx_result |
Source code
|
| read_PHYLIP_data |
Source code
|
| read_area_of_areas_fn |
Source code
|
| read_areas_adjacency_fn |
Source code
|
| read_areas_allowed_fn |
Source code
|
| read_controls |
Source code
|
| read_detections |
Source code
|
| read_dispersal_multipliers_fn |
Source code
|
| read_distances_fn |
Source code
|
| read_envdistances_fn |
Source code
|
| read_times_fn |
Source code
|
| readfiles_BioGeoBEARS_run |
Source code
|
| rel_likes_from_deltaAICs |
Source code
|
| rel_likes_from_deltaAICs_pairwise |
Source code
|
| relative_probabilities_of_subsets |
Source code
|
| relative_probabilities_of_vicariants |
Source code
|
| remove_multiple_commas_from_strings_in_list |
Source code
|
| remove_null_rowcols_from_mat |
Source code
|
| rerun_optimization_w_HiLow |
Source code
|
| return_items_not_NA |
Source code
|
| rn |
Source code
|
| runBSM |
Source code
|
| run_all_exponentiation_methods |
Source code
|
| run_bears_optim_on_multiple_trees |
Source code
|
| run_exp_timetests |
Source code
|
| run_lotsa_exp_functions |
Source code
|
| run_lotsa_exponentiations |
Source code
|
| sample_split_scenario |
Source code
|
| sample_split_scenario2 |
Source code
|
| sample_uppass_split_scenario_given_probs_ancstate |
Source code
|
| save_tipranges_to_LagrangePHYLIP |
Source code
|
| scale_BGB_params |
Source code
|
| section_the_tree |
Source code
|
| sfunc |
Source code
|
| simstates_to_probs_of_each_area |
Source code
|
| simulate_biogeog_history |
Source code
|
| simulate_source_area_ana |
Source code
|
| simulate_source_area_clado |
Source code
|
| simulate_source_areas_ana_clado |
Source code
|
| simulated_indexes_to_tipranges_file |
Source code
|
| simulated_indexes_to_tipranges_object |
Source code
|
| size_half_tri_nodiag |
Source code
|
| size_species_matrix |
Source code
|
| slashslash |
Source code
|
| sort_list_of_lists_of_numbers |
Source code
|
| sourceall |
Source code
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| sourceall_git |
Source code
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| spPmat_inputs_from_BioGeoBEARS_model_object |
Source code
|
| spPmat_inputs_to_COO_weights_columnar |
Source code
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| split_key_item |
Source code
|
| states_list_0based_to_ranges_txt_list |
Source code
|
| states_list_indexes_to_areastxt |
Source code
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| stochastic_map_branch |
Source code
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| stochastic_map_given_inputs |
Source code
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| stochastic_mapping_on_stratified |
Source code
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| strsplit2 |
Source code
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| strsplit_whitespace |
Source code
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| subset_distmats |
Source code
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| sum_nodes_branchlengths_by_timeperiod |
Source code
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| sumdiag |
Source code
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| summarize_Qmats |
Source code
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| summarize_stateprobs_on_master_tree |
Source code
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| sumoffdiag |
Source code
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| symbolic_cell_to_relprob_cell |
Source code
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| symbolic_cell_to_relprob_cell_sp |
Source code
|
| symbolic_to_P_matrix |
Source code
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| symbolic_to_Q_matrix |
Source code
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| symbolic_to_Q_matrix_exper |
Source code
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| symbolic_to_relprob_matrix_sp |
Source code
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| table2 |
Source code
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| testexp |
Source code
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| testexp2 |
Source code
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| testexp_sub |
Source code
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| tiplikes_wDetectionModel |
Source code
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| tipranges_from_BGB_run_object |
Source code
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| tipranges_from_detects_fn |
Source code
|
| tipranges_to_DIVA_DATAblock_format |
Source code
|
| tipranges_to_area_strings |
Source code
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| tipranges_to_tip_condlikes_of_data_on_each_state |
Source code
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| tnn |
Source code
|
| trace_parents_up |
Source code
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| trait_ancstates_from_both |
Source code
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| traits_results_to_geogOnly_traitsOnly |
Source code
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| traverse_up |
Source code
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| tree_to_DIVA_TREE_block |
Source code
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| trim2 |
Source code
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| uniq_rates |
Source code
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| uniqs_of_each_rate_minus_rowcol |
Source code
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| uniquify_clado_events |
Source code
|
| unlist_df |
Source code
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| unlist_df2 |
Source code
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| unlist_df3 |
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| unlist_df4 |
Source code
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| unlist_dtf_cols |
Source code
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| unscale_BGB_params |
Source code
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| update_BioGeoBEARS_model_object_w_optimx_result |
Source code
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| vfunc |
Source code
|
| write_DIVA_cmds |
Source code
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| write_distances_to_fn |
Source code
|
| yfunc |
Source code
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| zeros_diag_ones_offdiag |
Source code
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| zerosmat |
Source code
|
