Files in nmatzke/BioGeoBEARS
BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

.DS_Store
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/.DS_Store
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/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/.DS_Store
inst/CITATION
inst/extdata/.DS_Store
inst/extdata/Hawaii_abbreviations_table.txt
inst/extdata/Psychotria_5.2.newick
inst/extdata/Psychotria_controls_v1.txt
inst/extdata/Psychotria_detections_v1.txt
inst/extdata/Psychotria_geog.data
inst/extdata/Psychotria_geog_noAreaNames.data
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/examples/.DS_Store
inst/extdata/examples/BSM_3taxa/.DS_Store
inst/extdata/examples/BSM_3taxa/M0/.DS_Store
inst/extdata/examples/BSM_3taxa/M0/areas_allowed_noC.txt
inst/extdata/examples/BSM_3taxa/M0/areas_allowed_noC2.txt
inst/extdata/examples/BSM_3taxa/M0/areas_allowed_noZeros.txt
inst/extdata/examples/BSM_3taxa/M0/geog.data
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/M0/timeperiods.txt
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inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/.Rapp.history
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inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/BSM_inputs_file.Rdata
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inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_BAYAREALIKE+J_M3areas_allowed_v1.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_BAYAREALIKE_M3areas_allowed_v1.Rdata
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+J_M3areas_allowed_v1.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_DEC_M3areas_allowed_v1.Rdata
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+J_M3areas_allowed_v1.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/Psychotria_DIVALIKE_M3areas_allowed_v1.Rdata
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/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/RES_ana_events_tables.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/RES_ana_events_tables_PARTIAL.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/RES_clado_events_tables.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/a_counts_fromto_means.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/a_counts_fromto_sds.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/all_dispersals_counts_fromto_means.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/all_dispersals_counts_fromto_sds.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/ana_dispersals_counts_fromto_means.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/ana_dispersals_counts_fromto_sds.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/areas_allowed.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/areas_allowed_all1s.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/d_counts_fromto_means.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/d_counts_fromto_sds.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/e_counts_rectangle.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/founder_counts_fromto_means.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/founder_counts_fromto_sds.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/geog.data
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/input_files.zip
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/phytools_simmap.pdf
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/restable.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/restable_AIC_rellike.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/restable_AIC_rellike_formatted.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/restable_v1.Rdata
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/summary_counts_BSMs.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/teststable.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/teststable_v1.Rdata
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/timeperiods.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/tree.newick
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/tree.pdf
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/unique_sub_counts.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/unique_sym_counts.txt
inst/extdata/examples/Psychotria_M3strat/BSM_to_simmap/unique_vic_counts.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3_stratified.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3_stratified.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.results.txt
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.results.txt
inst/extdata/examples/_generic_run/BGB/geog.data
inst/extdata/examples/_generic_run/BGB/tree.newick
inst/extdata/examples/_generic_run/LGcpp/geog.data
inst/extdata/examples/_generic_run/LGcpp/lg_controls.lg
inst/extdata/examples/_generic_run/LGcpp/tree.newick
inst/extdata/examples/_process_Lagrange_outputs_v1.R
inst/extdata/examples/_run_LAGRANGE_examples_v1.txt
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/geog.data
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/geog_1area.data
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/geog_sim_observed.txt
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/params_inferred.txt
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/simtr_observed.newick
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/tipranges_observed_1area.data
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/traits.data
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/traits_sim_observed.txt
inst/extdata/examples/trait_examples/BAYAREALIKE_wTraits/tree.newick
inst/extdata/examples/trait_examples/DEC_wTraits/geog.data
inst/extdata/examples/trait_examples/DEC_wTraits/geog_1area.data
inst/extdata/examples/trait_examples/DEC_wTraits/geog_sim_complete.txt
inst/extdata/examples/trait_examples/DEC_wTraits/geog_sim_observed.txt
inst/extdata/examples/trait_examples/DEC_wTraits/simtr_complete.newick
inst/extdata/examples/trait_examples/DEC_wTraits/simtr_observed.newick
inst/extdata/examples/trait_examples/DEC_wTraits/tipranges_observed_1area.data
inst/extdata/examples/trait_examples/DEC_wTraits/tipranges_simulated_1area.data
inst/extdata/examples/trait_examples/DEC_wTraits/traits.data
inst/extdata/examples/trait_examples/DEC_wTraits/traits_sim_complete.txt
inst/extdata/examples/trait_examples/DEC_wTraits/traits_sim_observed.txt
inst/extdata/examples/trait_examples/DEC_wTraits/tree.newick
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/geog.data
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/geog_1area.data
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/geog_sim_observed.txt
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/params_inferred.txt
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/simtr_observed.newick
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/tipranges_observed_1area.data
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/traits.data
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/traits_sim_observed.txt
inst/extdata/examples/trait_examples/DIVALIKE_wTraits/tree.newick
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/.DS_Store
tests/testthat.R
tests/testthat/.DS_Store
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/2018-09-26_checks_passed.txt
tests/testthat/z_old/test-numstates_from_numareas.R
tests/testthat/z_tmp/.DS_Store
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
nmatzke/BioGeoBEARS documentation built on July 12, 2019, 12:27 p.m.