Files in BioGeoBEARS

BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

inst/extdata/examples/_process_Lagrange_outputs_v1.R inst/extdata/a_scripts/BioGeoBEARS_LaplacesDemon_v1.R inst/extdata/a_scripts/compare_LAGRANGE_w_BEARS_2param_v01.R inst/extdata/a_scripts/plot_phylo3_nodecoords.R inst/extdata/a_scripts/testrun.R R/BioGeoBEARS_simulate_v1.R R/calc_loglike_sp_v01.R R/BioGeoBEARS_models_v1.R R/BioGeoBEARS_classes_v1.R R/BioGeoBEARS_readwrite_v1.R R/BioGeoBEARS_basics_v1.R R/BioGeoBEARS_plots_v1.R R/BioGeoBEARS_detection_v1.R R/BioGeoBEARS_univ_model_v1.R R/BioGeoBEARS-package.R R/BioGeoBEARS_generics_v1.R R/BioGeoBEARS_stratified_v1.R man/calc_loglike_for_optim_stratified.Rd man/make_spmat_row.Rd man/traverse_up.Rd man/make_relprob_txtmatrix_sp1.Rd man/expokit_dgpadm_Qmat2.Rd man/axisPhylo2.Rd man/bears_2param_standard_fast_symOnly_simp.Rd man/get_infparams_optimx_nosim.Rd man/parse_lagrange_python_output_old.Rd man/binary_range_to_letter_code_list.Rd man/get_ML_probs.Rd man/get_all_daughter_tips_of_a_node.Rd man/get_ML_states.Rd man/binary_range_to_letter_code_txt.Rd man/post_prob_states.Rd man/bears_3param_standard_fast.Rd man/unlist_df3.Rd man/get_ML_state_indices.Rd man/return_items_not_NA.Rd man/BioGeoBEARS_model_defaults.Rd man/BioGeoBEARS_model_object_to_params_upper.Rd man/bears_3param_standard_fast_noJ.Rd man/order_tipranges_by_tr.Rd man/unlist_df.Rd man/calc_loglike_sp.Rd man/calc_AICc_vals.Rd man/read_area_of_areas_fn.Rd man/get_deltaAIC.Rd man/plot_BioGeoBEARS_model.Rd man/relative_probabilities_of_subsets.Rd man/read_PHYLIP_data.Rd man/calc_AICc_column.Rd man/nodenums_bottom_up.Rd man/define_BioGeoBEARS_run.Rd man/bears_4param_standard_fast.Rd man/states_list_indexes_to_areastxt.Rd man/lrttest.Rd man/calcP_n.Rd man/get_nodenums.Rd man/size_species_matrix.Rd man/merge_words_nonwords.Rd man/get_deltaAIC_pairwise_w_ref_model.Rd man/bears_5param_standard_fast_diffstart.Rd man/get_daughters.Rd man/remove_null_rowcols_from_mat.Rd man/parse_lagrange_python_output.Rd man/get_nodenum_structural_root.Rd man/simulated_indexes_to_tipranges_object.Rd man/order_tipranges_by_tree_tips.Rd man/prflag.Rd man/maxsize.Rd man/BioGeoBEARS_model_object_to_est_params.Rd man/lrttest_on_summary_table.Rd man/printall.Rd man/section_the_tree.Rd man/get_parent.Rd man/get_TF_tips.Rd man/simulated_indexes_to_tipranges_file.Rd man/symbolic_to_P_matrix.Rd man/moref.Rd man/post_prob_states_matrix.Rd man/get_APE_nodenums.Rd man/symbolic_to_relprob_matrix_sp.Rd man/AICstats_2models.Rd man/get_level.Rd man/readfiles_BioGeoBEARS_run.Rd man/rangestxt_to_colors.Rd man/bears_2param_standard_fast.Rd man/colors_legend.Rd man/tipranges_to_area_strings.Rd man/symbolic_cell_to_relprob_cell.Rd man/read_distances_fn.Rd man/mapply_likelihoods.Rd man/get_Akaike_weights_from_rel_likes_pairwise.Rd man/bears_2param_DIVA_fast.Rd man/prob_of_states_from_prior_prob_areas.Rd man/relative_probabilities_of_vicariants.Rd man/match_list1_in_list2.Rd man/get_relative_prob_model2old.Rd man/get_indices_of_tip_nodes.Rd man/map_LG_MLsplits_to_tree_corners.Rd man/getAICc.Rd man/process_optim.Rd man/BioGeoBEARS-package.Rd man/get_inf_LgL_etc_optimx.Rd man/extend_tips_to_ultrametricize.Rd man/mapply_likelihoods_prebyte.Rd man/get_perEvent_probs.Rd man/calc_prob_forward_onebranch_dense.Rd man/read_times_fn.Rd man/calc_prob_forward_onebranch_sparse.Rd man/AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref.Rd man/LGpy_MLsplit_per_node.Rd man/get_simstates.Rd man/get_indices_where_list1_occurs_in_list2_noNA.Rd man/get_edge_times_before_present.Rd man/read_detections.Rd man/conditional_format_cell.Rd man/LGpy_splits_fn_to_table.Rd man/add_to_downpass_labels.Rd man/get_indices_where_list1_occurs_in_list2.Rd man/adf2.Rd man/adf.Rd man/order_LGnodes.Rd man/mapply_calc_post_prob_presence.Rd man/define_BioGeoBEARS_model_object.Rd man/prt_tree_to_phylo4.Rd man/read_areas_allowed_fn.Rd man/getAIC_weight_for_model1.Rd man/BioGeoBEARS_model_object_to_params_lower.Rd man/LGcpp_MLstate_per_node.Rd man/read_controls.Rd man/postorder_nodes_phylo4_return_table.Rd man/get_pruningwise_nodenums.Rd man/Pdata_given_rangerow_dp.Rd man/cornerlabels.Rd man/AkaikeWeights_on_summary_table.Rd man/get_Akaike_weight_ratio_from_Akaike_pairwise_weights.Rd man/check_if_state_is_allowed.Rd man/calcZ_part.Rd man/get_all_node_ages.Rd man/prt.Rd man/sourceall.Rd man/make_relprob_matrix_de.Rd man/calc_AIC_column.Rd man/read_dispersal_multipliers_fn.Rd man/is.not.na.Rd man/unlist_dtf_cols.Rd man/slashslash.Rd man/get_AICweight_ratio_model1_over_model2.Rd man/plot_BioGeoBEARS_results.Rd man/expokit_dgpadm_Qmat2_prebyte.Rd man/tipranges_to_tip_condlikes_of_data_on_each_state.Rd man/get_indices_of_branches_under_tips.Rd man/get_node_ages_of_tips.Rd man/pdfit.Rd man/get_lagrange_nodenums.Rd man/tiplikes_wDetectionModel.Rd man/make_relprob_nummatrix_sp1.Rd man/getranges_from_LagrangePHYLIP.Rd man/findall.Rd man/get_max_height_tree.Rd man/LGcpp_splits_fn_to_table.Rd man/get_fn_prefix.Rd man/calc_loglike_for_optim.Rd man/unlist_df2.Rd man/prune_specimens_to_species.Rd man/LGcpp_states_fn_to_table.Rd man/rel_likes_from_deltaAICs.Rd man/get_tiplabel_ranges.Rd man/parse_lagrange_output_old.Rd man/LGcpp_splits_fn_to_table2.Rd man/unlist_df4.Rd man/map_LGpy_MLsplits_to_tree.Rd man/calc_post_prob_presence.Rd man/cornerpies.Rd man/parse_lagrange_output.Rd man/expand.grid.alt.Rd man/make_dispersal_multiplier_matrix.Rd man/get_infprobs_of_simstates.Rd man/getAIC.Rd man/addslash.Rd man/average_tr_tips.Rd man/dfnums_to_numeric.Rd man/infprobs_to_probs_of_each_area.Rd man/mix_colors_for_states.Rd man/get_ML_states_from_relprobs.Rd man/meval.Rd man/check_BioGeoBEARS_run.Rd man/binary_ranges_to_letter_codes.Rd man/symbolic_cell_to_relprob_cell_sp.Rd man/expand.grid.jc.Rd man/calc_AIC_vals.Rd man/symbolic_to_Q_matrix_exper.Rd man/given_a_starting_state_simulate_branch_end.Rd man/nullsym_to_NA.Rd man/get_probvals.Rd man/get_statesColors_table.Rd man/calc_loglike_sp_stratified.Rd man/paste_rows_without_zeros.Rd man/calc_linked_params_BioGeoBEARS_model_object.Rd man/strsplit2.Rd man/get_leftright_nodes_matrix_from_results.Rd man/bears_3param_standard_fast_fixnode.Rd man/letter_string_to_binary.Rd man/prune_states_list.Rd man/simstates_to_probs_of_each_area.Rd man/tipranges-class.Rd man/mapply_calc_obs_like.Rd man/divide_probs_by_number_of_options_txt.Rd man/bears_2param_standard_fast_fortest.Rd man/BioGeoBEARS_run-class.Rd man/get_sister_node.Rd man/Pdata_given_rangerow.Rd man/divide_probs_by_number_of_options_nums.Rd man/calc_loglike_sp_prebyte.Rd man/corner_coords.Rd man/vfunc.Rd man/rel_likes_from_deltaAICs_pairwise.Rd man/bears_2param_standard_slowQ_slowSP.Rd man/get_relative_prob_model1old.Rd man/extract_numbers.Rd man/bears_9param_standard_fast_ys_v_cb.Rd man/get_path_last.Rd man/get_path_first.Rd man/bears_5param_standard_fast_v.Rd man/get_Akaike_weights_from_rel_likes.Rd man/bears_5param_standard_fast.Rd man/list2str.Rd man/letter_strings_to_tipranges_df.Rd man/bears_2param_standard_fast_fixnode.Rd man/chainsaw2.Rd man/plot_cladogenesis_size_probabilities.Rd man/normat.Rd man/get_rownum_ref_model.Rd man/infprobs_to_probs_of_each_area_from_relprobs.Rd man/make_relprob_matrix_bi.Rd man/sfunc.Rd man/params_into_BioGeoBEARS_model_object.Rd man/BioGeoBEARS_model-class.Rd man/BioGeoBEARS_model_object_to_init_params.Rd man/areas_list_to_states_list_new.Rd man/yfunc.Rd man/get_simparams.Rd man/save_tipranges_to_LagrangePHYLIP.Rd man/cls.df.Rd man/symbolic_to_Q_matrix.Rd man/get_MLsplitprobs_from_results.Rd man/default_states_list.Rd man/map_LG_MLsplits_to_tree.Rd man/simulate_biogeog_history.Rd man/label_nodes_postorder_phylo3.Rd man/add_corners.Rd man/get_infparams_optimx.Rd man/define_tipranges_object.Rd man/conditional_format_table.Rd man/given_a_starting_state_simulate_split.Rd man/get_colors_for_numareas.Rd man/bears_2param_standard_fast_symOnly.Rd man/bears_optim_run.Rd man/calc_obs_like.Rd man/np.Rd man/bears_6param_standard_fast_ys_v.Rd man/strsplit_whitespace.Rd man/getareas_from_tipranges_object.Rd man/getname.Rd man/pdftable.Rd man/map_LG_MLstates_to_tree.Rd