Files in nmatzke/BioGeoBEARS

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

R/BioGeoBEARS-package.R R/BioGeoBEARS_SSEsim_makePlots_v1.R R/BioGeoBEARS_SSEsim_v1.R R/BioGeoBEARS_add_fossils_randomly_v1.R R/BioGeoBEARS_basics_v1.R R/BioGeoBEARS_calc_transition_matrices_v1.R R/BioGeoBEARS_classes_v1.R R/BioGeoBEARS_detection_v1.R R/BioGeoBEARS_extract_Qmat_COOmat_v1.R R/BioGeoBEARS_on_multiple_trees_v1.R R/BioGeoBEARS_plots_v1.R R/BioGeoBEARS_readwrite_v1.R R/BioGeoBEARS_simulate_v1.R R/BioGeoBEARS_stochastic_mapping_v1.R R/BioGeoBEARS_stratified_v1.R R/BioGeoBEARS_traits_v1.R R/BioGeoBEARS_univ_model_v1.R R/ChromoBEARS_v1.R R/aa_generics_v1.R R/aa_tree_basics_v1.R R/calc_loglike_sp_v01.R R/calc_uppass_probs_v1.R R/get_stratified_subbranch_top_downpass_likelihoods_v1.R R/matrix_utils_v1.R R/runBSM_v1.R R/stochastic_map_given_inputs.R R/summarize_BSM_tables_v1.R README.md inst/extdata/Phylowiki_M0_2023_v1.R inst/extdata/Phylowiki_M3_2023_v1.R inst/extdata/a_scripts/03_BGB_Psychotria_script_DECvDEC+J_wBSM_v1.R inst/extdata/a_scripts/03_M1_Psychotria_maxareas2.R inst/extdata/a_scripts/03_M2_Psychotria_dispersal_multipliers.R inst/extdata/a_scripts/03_M3_Psychotria_time-strat_v2.R inst/extdata/a_scripts/03_M4_Psychotria_distances.R inst/extdata/a_scripts/BioGeoBEARS_LaplacesDemon_v1.R inst/extdata/a_scripts/compare_LAGRANGE_w_BEARS_2param_v01.R inst/extdata/a_scripts/per_area_probs_plot_v1.R inst/extdata/a_scripts/plot_phylo3_nodecoords.R inst/extdata/a_scripts/testrun.R inst/extdata/examples/395lab/395_lab_setup_v4.R inst/extdata/examples/395lab/Psychotria_M0_equalRates/Psychotria_M0_v1.R inst/extdata/examples/395lab/Psychotria_M2_oneWayDispersal/Psychotria_M2_oneWayDispersal_v1.R inst/extdata/examples/395lab/Psychotria_M4_DistanceDispersal/Psychotria_M4_DistanceDispersal_v1.R inst/extdata/examples/395lab/Psychotria_slides_v1.pdf inst/extdata/examples/395lab/conifer_DEC+x_traits_models/conifer_DEC+x_traits_models_v1_makePDFs.R inst/extdata/examples/395lab/conifer_DEC+x_traits_models/conifer_DEC+x_traits_models_v3.R inst/extdata/examples/395lab/conifer_DEC+x_traits_models/conifer_DEC+x_traits_models_v3_wAnswers.R inst/extdata/examples/395lab/conifer_DEC_traits_models/conifer_DEC_traits_models_v1_makePDFs.R inst/extdata/examples/395lab/conifer_DEC_traits_models/conifer_DEC_traits_models_v3.R inst/extdata/examples/395lab/conifer_DEC_traits_models/conifer_DEC_traits_models_v3_wAnswers.R inst/extdata/examples/395lab/distance+x_models.pdf inst/extdata/examples/BSM_3taxa/M0/script_BSM_to_phytools_v1.R inst/extdata/examples/BSM_3taxa/M0/script_BSM_to_phytools_v2.R inst/extdata/examples/BSM_3taxa/M0/script_v1.R inst/extdata/examples/BSM_3taxa/M3areas_allowed/DEC_BSM_v1.R inst/extdata/examples/BSM_3taxa/M3areas_allowed/script_BSM_to_phytools_v2strat.R inst/extdata/examples/BSM_3taxa/M3areas_allowed/script_BSM_to_phytools_v3strat.R inst/extdata/examples/BSM_3taxa/M3areas_allowed/script_v1.R inst/extdata/examples/BSM_3taxa/M3areas_allowed_wFossilBranch/DEC_BSM_time-strat_v1.R inst/extdata/examples/Psychotria_M0_BSM_to_simmap/BSM_to_simmap/script_BSM_to_phytools_v3strat.R inst/extdata/examples/Psychotria_M0_BSM_to_simmap/BSM_to_simmap/tree.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/50BSMs_in_phytools_simmap_format.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/BSM_in_phytools_simmap_format.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/DEC_1BSMs_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/DEC_50BSMs_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/DEC_ML_vs_BSM.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/DEC_histograms_of_event_counts.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/DEC_single_stochastic_map_n1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_BAYAREALIKE_vs_BAYAREALIKE+J_M3areas_allowed_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_DEC_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_DEC_vs_DEC+J_M3areas_allowed_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_DIVALIKE_vs_DIVALIKE+J_M3areas_allowed_v1.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/phytools_simmap.pdf inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/script_BSM_to_phytools_v3strat.R inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/script_BSM_to_phytools_v3strat_OLD.R inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/tree.pdf inst/extdata/examples/_process_Lagrange_outputs_v1.R inst/extdata/examples/apes_SSE/apes_BAYAREALIKE_vs_BAYAREALIKE+J_M0_unconstrained_v1.pdf inst/extdata/examples/apes_SSE/apes_DEC_vs_DEC+J_M0_unconstrained_v1.pdf inst/extdata/examples/apes_SSE/apes_DIVALIKE_vs_DIVALIKE+J_M0_unconstrained_v1.pdf inst/extdata/examples/apes_SSE/apes_M0_v1.R inst/extdata/examples/apes_SSE/tree.pdf inst/extdata/examples/check_strat/M0/3taxa_DEC_vs_DEC+J_M0_unconstrained_v1.pdf inst/extdata/examples/check_strat/M0/script_v1.R inst/extdata/examples/check_strat/M0/tree.pdf inst/extdata/examples/check_strat/M3/script_timestrat_v1.R inst/extdata/examples/check_strat2/M0/3taxa_DEC_vs_DEC+J_M0_unconstrained_v1.pdf inst/extdata/examples/check_strat2/M0/script_v1.R inst/extdata/examples/check_strat2/M0/tree.pdf inst/extdata/examples/check_strat2/M3/script_timestrat_v1.R inst/extdata/examples/check_strat3/M0/script_v1.R inst/extdata/examples/check_strat3/M3/script_timestrat_v1.R inst/extdata/examples/check_strat4_ML/M0/script_v1.R inst/extdata/examples/check_strat4_ML/M3/script_timestrat_v1.R inst/extdata/examples/check_strat5_ML/M0/script_v1.R inst/extdata/examples/check_strat5_ML/M3/script_timestrat_v1.R inst/extdata/examples/check_strat6_MLmax2/M0/script_v1.R inst/extdata/examples/check_strat6_MLmax2/M3/script_timestrat_v1.R inst/extdata/z_old_code/BioGeoBEARS_DNA_cladogenesis_sim_v1.R inst/extdata/z_old_code/BioGeoBEARS_models_v1.R inst/extdata/z_old_code/dead_BioGeoBEARS_v1.R tests/sum_branchlengths_by_timebin_fossils.R tests/test_calc_uppass_probs_new2_example_v1.R tests/testthat.R tests/testthat/test-3taxa_M3_areas_allowed.R tests/testthat/test-likelihoods.R tests/testthat/test-numstates_from_numareas.R tests/testthat/test-trait_example_script_BAYAREALIKE_v1.R tests/testthat/test-trait_example_script_DEC_v1.R tests/testthat/test-trait_example_script_DIVALIKE_v1.R tests/testthat/test-trait_independent_from_DEC_v1.R tests/testthat/z_old/test-numstates_from_numareas.R tests/testthat/z_tmp/example_6models_M0_GenSA.R tests/testthat/z_tmp/example_6models_M0_optimx.R tests/testthat/z_tmp/example_6models_M3areas_GenSA.R tests/testthat/z_tmp/example_6models_M3areas_optimx.R tests/testthat/z_tmp/example_6models_M3strat_GenSA.R tests/testthat/z_tmp/example_6models_M3strat_optimx.R tests/testthat/z_tmp/example_script_BAYAREALIKE_v1.R tests/testthat/z_tmp/example_script_DIVALIKE_v1.R