| AICstats_2models |
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| AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_r |
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| AkaikeWeights_on_summary_table |
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| BioGeoBEARS |
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| BioGeoBEARS-package |
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| BioGeoBEARS_model |
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| BioGeoBEARS_model_defaults |
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| BioGeoBEARS_model_object_to_est_params |
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| BioGeoBEARS_model_object_to_init_params |
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| BioGeoBEARS_model_object_to_params_lower |
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| BioGeoBEARS_model_object_to_params_upper |
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| BioGeoBEARS_run |
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| LGcpp_MLstate_per_node |
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| LGcpp_splits_fn_to_table |
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| LGcpp_splits_fn_to_table2 |
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| LGcpp_states_fn_to_table |
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| LGpy_MLsplit_per_node |
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| LGpy_splits_fn_to_table |
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| Pdata_given_rangerow |
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| Pdata_given_rangerow_dp |
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| add_corners |
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| add_to_downpass_labels |
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| addslash |
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| adf |
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| adf2 |
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| areas_list_to_states_list_new |
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| average_tr_tips |
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| axisPhylo2 |
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| bears_2param_DIVA_fast |
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| bears_2param_standard_fast |
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| bears_2param_standard_fast_fixnode |
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| bears_2param_standard_fast_fortest |
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| bears_2param_standard_fast_symOnly |
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| bears_2param_standard_fast_symOnly_simp |
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| bears_2param_standard_slowQ_slowSP |
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| bears_3param_standard_fast |
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| bears_3param_standard_fast_fixnode |
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| bears_3param_standard_fast_noJ |
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| bears_4param_standard_fast |
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| bears_5param_standard_fast |
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| bears_5param_standard_fast_diffstart |
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| bears_5param_standard_fast_v |
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| bears_6param_standard_fast_ys_v |
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| bears_9param_standard_fast_ys_v_cb |
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| bears_optim_run |
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| binary_range_to_letter_code_list |
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| binary_range_to_letter_code_txt |
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| binary_ranges_to_letter_codes |
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| calcP_n |
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| calcZ_part |
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| calc_AIC_column |
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| calc_AIC_vals |
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| calc_AICc_column |
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| calc_AICc_vals |
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| calc_linked_params_BioGeoBEARS_model_object |
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| calc_loglike_for_optim |
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| calc_loglike_for_optim_stratified |
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| calc_loglike_sp |
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| calc_loglike_sp_prebyte |
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| calc_loglike_sp_stratified |
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| calc_obs_like |
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| calc_post_prob_presence |
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| calc_prob_forward_onebranch_dense |
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| calc_prob_forward_onebranch_sparse |
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| chainsaw2 |
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| check_BioGeoBEARS_run |
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| check_if_state_is_allowed |
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| cls.df |
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| colors_legend |
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| conditional_format_cell |
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| conditional_format_table |
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| corner_coords |
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| cornerlabels |
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| cornerpies |
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| default_states_list |
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| define_BioGeoBEARS_model_object |
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| define_BioGeoBEARS_run |
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| define_tipranges_object |
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| dfnums_to_numeric |
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| divide_probs_by_number_of_options_nums |
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| divide_probs_by_number_of_options_txt |
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| expand.grid.alt |
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| expand.grid.jc |
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| expokit_dgpadm_Qmat2 |
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| expokit_dgpadm_Qmat2_prebyte |
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| extend_tips_to_ultrametricize |
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| extract_numbers |
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| findall |
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| getAIC |
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| getAIC_weight_for_model1 |
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| getAICc |
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| get_AICweight_ratio_model1_over_model2 |
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| get_APE_nodenums |
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| get_Akaike_weight_ratio_from_Akaike_pairwise_weights |
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| get_Akaike_weights_from_rel_likes |
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| get_Akaike_weights_from_rel_likes_pairwise |
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| get_ML_probs |
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| get_ML_state_indices |
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| get_ML_states |
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| get_ML_states_from_relprobs |
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| get_MLsplitprobs_from_results |
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| get_TF_tips |
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| get_all_daughter_tips_of_a_node |
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| get_all_node_ages |
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| get_colors_for_numareas |
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| get_daughters |
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| get_deltaAIC |
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| get_deltaAIC_pairwise_w_ref_model |
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| get_edge_times_before_present |
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| get_fn_prefix |
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| get_indices_of_branches_under_tips |
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| get_indices_of_tip_nodes |
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| get_indices_where_list1_occurs_in_list2 |
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| get_indices_where_list1_occurs_in_list2_noNA |
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| get_inf_LgL_etc_optimx |
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| get_infparams_optimx |
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| get_infparams_optimx_nosim |
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| get_infprobs_of_simstates |
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| get_lagrange_nodenums |
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| get_leftright_nodes_matrix_from_results |
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| get_level |
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| get_max_height_tree |
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| get_node_ages_of_tips |
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| get_nodenum_structural_root |
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| get_nodenums |
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| get_parent |
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| get_path_first |
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| get_path_last |
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| get_perEvent_probs |
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| get_probvals |
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| get_pruningwise_nodenums |
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| get_relative_prob_model1old |
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| get_relative_prob_model2old |
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| get_rownum_ref_model |
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| get_simparams |
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| get_simstates |
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| get_sister_node |
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| get_statesColors_table |
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| get_tiplabel_ranges |
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| getareas_from_tipranges_object |
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| getname |
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| getranges_from_LagrangePHYLIP |
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| given_a_starting_state_simulate_branch_end |
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| given_a_starting_state_simulate_split |
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| infprobs_to_probs_of_each_area |
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| infprobs_to_probs_of_each_area_from_relprobs |
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| is.not.na |
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| label_nodes_postorder_phylo3 |
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| letter_string_to_binary |
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| letter_strings_to_tipranges_df |
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| list2str |
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| lrttest |
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| lrttest_on_summary_table |
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| make_dispersal_multiplier_matrix |
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| make_relprob_matrix_bi |
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| make_relprob_matrix_de |
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| make_relprob_nummatrix_sp1 |
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| make_relprob_txtmatrix_sp1 |
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| make_spmat_row |
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| map_LG_MLsplits_to_tree |
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| map_LG_MLsplits_to_tree_corners |
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| map_LG_MLstates_to_tree |
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| map_LGpy_MLsplits_to_tree |
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| mapply_calc_obs_like |
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| mapply_calc_post_prob_presence |
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| mapply_likelihoods |
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| mapply_likelihoods_prebyte |
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| match_list1_in_list2 |
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| maxsize |
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| merge_words_nonwords |
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| meval |
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| mix_colors_for_states |
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| moref |
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| nodenums_bottom_up |
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| normat |
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| np |
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| nullsym_to_NA |
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| order_LGnodes |
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| order_tipranges_by_tr |
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| order_tipranges_by_tree_tips |
Man page
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| params_into_BioGeoBEARS_model_object |
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| parse_lagrange_output |
Man page
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| parse_lagrange_output_old |
Man page
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| parse_lagrange_python_output |
Man page
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| parse_lagrange_python_output_old |
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| paste_rows_without_zeros |
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| pdfit |
Man page
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| pdftable |
Man page
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| plot_BioGeoBEARS_model |
Man page
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| plot_BioGeoBEARS_results |
Man page
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| plot_cladogenesis_size_probabilities |
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| post_prob_states |
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| post_prob_states_matrix |
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| postorder_nodes_phylo4_return_table |
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| prflag |
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| printall |
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| prob_of_states_from_prior_prob_areas |
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| process_optim |
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| prt |
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| prt_tree_to_phylo4 |
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| prune_specimens_to_species |
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| prune_states_list |
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| rangestxt_to_colors |
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| read_PHYLIP_data |
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| read_area_of_areas_fn |
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| read_areas_allowed_fn |
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| read_controls |
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| read_detections |
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| read_dispersal_multipliers_fn |
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| read_distances_fn |
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| read_times_fn |
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| readfiles_BioGeoBEARS_run |
Man page
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| rel_likes_from_deltaAICs |
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| rel_likes_from_deltaAICs_pairwise |
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| relative_probabilities_of_subsets |
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| relative_probabilities_of_vicariants |
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| remove_null_rowcols_from_mat |
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| return_items_not_NA |
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| save_tipranges_to_LagrangePHYLIP |
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| section_the_tree |
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| sfunc |
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| simstates_to_probs_of_each_area |
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| simulate_biogeog_history |
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| simulated_indexes_to_tipranges_file |
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| simulated_indexes_to_tipranges_object |
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| size_species_matrix |
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| slashslash |
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| sourceall |
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| states_list_indexes_to_areastxt |
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| strsplit2 |
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| strsplit_whitespace |
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| symbolic_cell_to_relprob_cell |
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| symbolic_cell_to_relprob_cell_sp |
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| symbolic_to_P_matrix |
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| symbolic_to_Q_matrix |
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| symbolic_to_Q_matrix_exper |
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| symbolic_to_relprob_matrix_sp |
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| tiplikes_wDetectionModel |
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| tipranges |
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| tipranges_to_area_strings |
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| tipranges_to_tip_condlikes_of_data_on_each_state |
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| traverse_up |
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| unlist_df |
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| unlist_df2 |
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| unlist_df3 |
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| unlist_df4 |
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| unlist_dtf_cols |
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| vfunc |
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| yfunc |
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