Files in BioGeoBEARS
BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
inst
inst/CITATION
inst/REFERENCES.bib
inst/extdata
inst/extdata/examples
inst/extdata/examples/Cyrtandra_M0
inst/extdata/examples/Cyrtandra_M0/LGcpp
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgkey.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgstates.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0.lg
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgsplits.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_geog.data
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0_lgcpp_out.txt
inst/extdata/examples/Cyrtandra_M0/BGB
inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2013
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.lagrange.py
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results-1.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2012
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.lagrange.py
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results-1.txt
inst/extdata/examples/Psychotria_M1strat
inst/extdata/examples/Psychotria_M1strat/LGcpp
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1_stratified.txt
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat.lg
inst/extdata/examples/Psychotria_M1strat/BGB
inst/extdata/examples/Psychotria_M1strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGpy_2013
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.lagrange.py
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.results.txt
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGpy_2012
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.lagrange.py
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.results.txt
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/_run_LAGRANGE_examples_v1.txt
inst/extdata/examples/Psychotria_M1
inst/extdata/examples/Psychotria_M1/LGcpp
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1.lg
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1_lgcpp_out.txt
inst/extdata/examples/Psychotria_M1/BGB
inst/extdata/examples/Psychotria_M1/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGpy_2013
inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.results.txt
inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.lagrange.py
inst/extdata/examples/Psychotria_M1/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGpy_2012
inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.results.txt
inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.lagrange.py
inst/extdata/examples/Psychotria_M1/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat
inst/extdata/examples/Psychotria_M2strat/LGcpp
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2_stratified.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat.lg
inst/extdata/examples/Psychotria_M2strat/BGB
inst/extdata/examples/Psychotria_M2strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2013
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.lagrange.py
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.results.txt
inst/extdata/examples/Psychotria_M2strat/LGpy_2012
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.lagrange.py
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.results.txt
inst/extdata/examples/Psychotria_M0
inst/extdata/examples/Psychotria_M0/LGcpp
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0_lgcpp_out.txt
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0.lg
inst/extdata/examples/Psychotria_M0/BGB
inst/extdata/examples/Psychotria_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGpy_2013
inst/extdata/examples/Psychotria_M0/LGpy_2013/psychotria_M0.lagrange.py
inst/extdata/examples/Psychotria_M0/LGpy_2013/psychotria_M0.results.txt
inst/extdata/examples/Psychotria_M0/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGpy_2012
inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.lagrange.py
inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.results.txt
inst/extdata/examples/Psychotria_M0/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/_generic_run
inst/extdata/examples/_generic_run/LGcpp
inst/extdata/examples/_generic_run/LGcpp/tree.newick
inst/extdata/examples/_generic_run/LGcpp/lg_controls.lg
inst/extdata/examples/_generic_run/LGcpp/geog.data
inst/extdata/examples/_generic_run/BGB
inst/extdata/examples/_generic_run/BGB/tree.newick
inst/extdata/examples/_generic_run/BGB/geog.data
inst/extdata/examples/Psychotria_M0strat
inst/extdata/examples/Psychotria_M0strat/LGcpp
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat.lg
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0_stratified.txt
inst/extdata/examples/Psychotria_M0strat/BGB
inst/extdata/examples/Psychotria_M0strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M0strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M0strat/BGB/areas_allowed_all1s.txt
inst/extdata/examples/Psychotria_M0strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0strat/LGpy_2013
inst/extdata/examples/Psychotria_M0strat/LGpy_2013/psychotria_M0_strat.lagrange.py
inst/extdata/examples/Psychotria_M0strat/LGpy_2013/psychotria_M0_strat.results.txt
inst/extdata/examples/Psychotria_M0strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0strat/LGpy_2012
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.lagrange.py
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.results.txt
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/LAGRANGE_example_param_LnL_results.txt
inst/extdata/examples/Lonicera_M0
inst/extdata/examples/Lonicera_M0/LGcpp
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0.lg
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out.txt
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out_orig.txt
inst/extdata/examples/Lonicera_M0/BGB
inst/extdata/examples/Lonicera_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Lonicera_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Lonicera_M0/LGpy_2013
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results-1.txt
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.lagrange.py
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results-1.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.lagrange.py
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results_orig.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results.txt
inst/extdata/examples/Psychotria_M2
inst/extdata/examples/Psychotria_M2/LGcpp
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2.lg
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2_lgcpp_out.txt
inst/extdata/examples/Psychotria_M2/BGB
inst/extdata/examples/Psychotria_M2/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M2/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2/LGpy_2013
inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.results.txt
inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.lagrange.py
inst/extdata/examples/Psychotria_M2/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2/LGpy_2012
inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.results.txt
inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.lagrange.py
inst/extdata/examples/Psychotria_M2/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat
inst/extdata/examples/Psychotria_M3strat/LGcpp
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3_stratified.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3_stratified.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/BGB
inst/extdata/examples/Psychotria_M3strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed.txt
inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed_all1s.txt
inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2013
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.results.txt
inst/extdata/examples/Psychotria_M3strat/LGpy_2012
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.results.txt
inst/extdata/examples/_process_Lagrange_outputs_v1.R
inst/extdata/Psychotria_detections_v1.txt
inst/extdata/Psychotria_geog_noAreaNames.data
inst/extdata/Psychotria_geog.data
inst/extdata/Psychotria_controls_v1.txt
inst/extdata/a_scripts
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
inst/extdata/Psychotria_5.2.newick
NAMESPACE
NEWS
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
MD5
DESCRIPTION
man
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
