Files in DAISIE

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

NEWS.md R/RcppExports.R R/DAISIE_ML_IW.R R/DAISIE_sim_update_state_cr.R R/DAISIE_sim_relaxed_rate.R R/DAISIE_sim_cr_shift.R R/DAISIE_plot_stt.R R/DAISIE_plot_age_diversity.R R/DAISIE_utils.R R/DAISIE_sim_core_cr.R R/DAISIE_format_CS_trait.R R/DAISIE_ONEcolonist.R R/DAISIE_sample_event_time_dep.R R/DAISIE_data.R R/DAISIE_sim_time_dep_iw.R R/DAISIE_ML1.R R/DAISIE_ML2.R R/DAISIE_check_format.R R/DAISIE_format_GW.R R/DAISIE_sim_time_dep.R R/DAISIE_sim_time_dep_cs.R R/DAISIE_plot_input.R R/DAISIE_loglik_CS_shift.R R/DAISIE-package.R R/DAISIE_sim_MW.R R/DAISIE_make_archipelago.R R/DAISIE_MW_ML.R R/DAISIE_loglik_high_lambda.R R/DAISIE_sim_update_state_trait_dep.R R/DAISIE_sim_trait_dep_2K.R R/DAISIE_format_IW_full_stt.R R/DAISIE_sample_event_cr.R R/DAISIE_format_IW.R R/DAISIE_loglik_integrate.R R/default_params_doc.R R/DAISIE_max_rates.R R/DAISIE_ML4.R R/DAISIE_ExpEIN.R R/DAISIE_sim_update_state_time_dep.R R/DAISIE_sim_cr_gw.R R/DAISIE_format_CS_sampled_stt.R R/DAISIE_plot_sims.R R/DAISIE_dataprep.R R/DAISIE_PEI.R R/DAISIE_sim_core_trait_dep.R R/DAISIE_sumstats_rates.R R/DAISIE_sim_min_type2.R R/DAISIE_loglik_CS.R R/remove_empty_elements.R R/DAISIE_extract_stt_median.R R/DAISIE_SR_sim_core.R R/DAISIE_format_CS.R R/DAISIE_sim_cr_iw.R R/DAISIE_loglik_IW.R R/DAISIE_sim_cr_cs.R R/DAISIE_SR_ML_CS.R R/DAISIE_plot_params.R R/DAISIE_create_island.R R/DAISIE_SR_loglik_CS.R R/DAISIE_loglik_CS_time.R R/DAISIE_sample_event_trait_dep.R R/DAISIE_plot_comparison_stts.R R/DAISIE_sim_core_cr_shift.R R/DAISIE_rates.R R/DAISIE_IC.R R/DAISIE_sim_cr.R R/DAISIE_loglik_IW0.R R/DAISIE_count_species.R R/DAISIE_format_IW_sampled_stt.R R/DAISIE_plot_pc_rates.R R/create_pars.R R/DAISIE_SR_sim.R R/DAISIE_sim_trait_dep.R R/DAISIE_plot_island.R R/DAISIE_format_CS_full_stt.R R/DAISIE_sim_time_dep_gw.R R/DAISIE_ML_CS.R R/DAISIE_sim_core_time_dep.R inst/doc/demo_sim.R inst/doc/demo_optimize.Rmd inst/doc/stac_key.R inst/doc/demo_CSvsIW.R inst/doc/demo_optimize.R inst/doc/stac_key.Rmd inst/doc/demo_sim.Rmd inst/doc/demo_CSvsIW.Rmd tests/testthat.R tests/testthat/test-DAISIE_loglik_integrate.R tests/testthat/test-DAISIE_convert_to_classic_plot.R tests/testthat/test-get_ana_rate.R tests/testthat/test-DAISIE_max_rates.R tests/testthat/test-DAISIE_ML4.R tests/testthat/test-DAISIE_dataprep.R tests/testthat/test-is_island_ontogeny_input.R tests/testthat/test-get_clado_rate.R tests/testthat/test-DAISIE_format_IW.R tests/testthat/test-DAISIE_sumstats_rates.R tests/testthat/test-get_immig_rate.R tests/testthat/test-DAISIE_loglik_CS_M1.R tests/testthat/test-DAISIE_sim_core.R tests/testthat/test-DAISIE_ExpEIN.R tests/testthat/test-DAISIE_sim_time_dep.R tests/testthat/test-time_dep_vs_cr.R tests/testthat/test-DAISIE_loglik_IW_solver.R tests/testthat/test-odeint.R tests/testthat/test-create_trait_pars.R tests/testthat/test-DAISIE_loglik_CS.R tests/testthat/test-update_rates.R tests/testthat/test-are_max_rates_gt_rates.R tests/testthat/test-DAISIE_plot_comparison_stts.R tests/testthat/test-DAISIE_ML_CS.R tests/testthat/test-DAISIE_ONEcolonist.R tests/testthat/test-are_area_pars.R tests/testthat/test-DAISIE_min_rates.R tests/testthat/test-DAISIE_sim_trait_dep.R tests/testthat/test-DAISIE_extract_stt_median.R tests/testthat/test-DAISIE_SR_loglik.R tests/testthat/test-DAISIE_sim_core_cr.R tests/testthat/test-DAISIE_format_IW_sampled_stt.R tests/testthat/test-DAISIE_MW_ML.R tests/testthat/test-are_rates.R tests/testthat/test-DAISIE_plot_stt.R tests/testthat/test-DAISIE_sim_core_cr_shift.R tests/testthat/test-rosenbrock_abm1_steppers.R tests/testthat/test-printing.R tests/testthat/test-DAISIE_utils.R tests/testthat/test-DAISIE_ML1.R tests/testthat/test-is_simulation_outputs.R tests/testthat/test-are_trait_pars.R tests/testthat/Rplots.pdf tests/testthat/test-DAISIE_format_GW.R tests/testthat/test-DAISIE_sim_core_time_dep.R tests/testthat/test-DAISIE_sim_MW.R tests/testthat/test-DAISIE_sim_core_trait_dep.R tests/testthat/test-DAISIE_ML2.R tests/testthat/test-DAISIE_format_CS_full_stt.R tests/testthat/test-DAISIE_sim_relaxed_rate.R tests/testthat/test-is_sea_level_input.R tests/testthat/test-DAISIE_plot_sims.R tests/testthat/test-update_max_rates.R tests/testthat/test-DAISIE_format_CS_sampled_stt.R tests/testthat/test-DAISIE_format_CS_trait.R tests/testthat/test-are_max_rates.R tests/testthat/test-get_ext_rate.R tests/testthat/test-integration_DAISIE.R tests/testthat/test-create_area_pars.R tests/testthat/test-DAISIE_format_CS.R tests/testthat/test-DAISIE_format_IW_full_stt.R tests/testthat/test-island_area.R tests/testthat/test-DAISIE_sim_cr_shift.R tests/testthat/test-DAISIE_sim_cr.R vignettes/demo_optimize.Rmd vignettes/stac_key.Rmd vignettes/demo_sim.Rmd vignettes/demo_CSvsIW.Rmd man/DAISIE_sim_time_dep_iw.Rd man/DAISIE_ONEcolonist.Rd man/DAISIE_sim_update_state_time_dep.Rd man/update_max_rates.Rd man/DAISIE_sim_min_type2.Rd man/integral_peak.Rd man/DAISIE_SR_loglik_CS.Rd man/create_pars.Rd man/DAISIE_plot_area.Rd man/update_rates.Rd man/islands_10reps_RAW.Rd man/DAISIE_loglik_integrate.Rd man/DAISIE_IW_num_threads.Rd man/DAISIE_sim_core_cr_shift.Rd man/create_full_CS_stt.Rd man/calc_next_timeval.Rd man/DAISIE_format_CS.Rd man/DAISIE_ML_IW.Rd man/daisie_odeint_cs.Rd man/DAISIE_CS_max_steps.Rd man/get_clado_rate.Rd man/island_area.Rd man/DAISIE_ExpEIN.Rd man/DAISIE_sim_update_state_trait_dep.Rd man/create_CS_version.Rd man/islands_1type_1000reps.Rd man/DAISIE_format_IW_sampled_stt.Rd man/archipelago_data.Rd man/DAISIE_IC.Rd man/Biwa_datalist.Rd man/DAISIE_sim_core_cr.Rd man/cum_rho.Rd man/get_immig_rate.Rd man/Galapagos_datalist.Rd man/Macaronesia_datalist.Rd man/rho.Rd man/DAISIE_loglik_CS.Rd man/NewZealand_birds_datalist.Rd man/DAISIE_numcol.Rd man/DAISIE_ML.Rd man/Bats_GreaterAntilles.Rd man/DAISIE_plot_stt.Rd man/DAISIE_plot_extinction.Rd man/calc_peak.Rd man/frogs_datatable.Rd man/DAISIE_plot_cladogenesis.Rd man/island_area_vector.Rd man/calc_next_timeval_shift.Rd man/DAISIE_format_CS_full_stt.Rd man/DAISIE_sim_trait_dep.Rd man/DAISIE_plot_sims.Rd man/DAISIE_sim_core_trait_dep.Rd man/create_hyper_pars.Rd man/DAISIE_create_island.Rd man/countspecies.Rd man/DAISIE_abm_factor.Rd man/get_ext_rate.Rd man/DAISIE_plot_immigration.Rd man/DAISIE-package.Rd man/DAISIE_sample_event_time_dep.Rd man/DAISIE_make_archipelago.Rd man/DAISIE_sim_time_dep_cs.Rd man/DAISIE_sim_update_state_cr.Rd man/remove_empty_elements.Rd man/DAISIE_ML2.Rd man/daisie_odeint_iw.Rd man/DAISIE_margprobdist.Rd man/Galapagos_datatable.Rd man/DAISIE_sim_cr_shift.Rd man/default_params_doc.Rd man/DAISIE_sample_event_cr.Rd man/DAISIE_loglik_IW.Rd man/DAISIE_convertprobdist.Rd man/DAISIE_make_global.Rd man/DAISIE_ML4.Rd man/DAISIE_sim_trait_dep_2K.Rd man/are_rates.Rd man/create_trait_pars_2K.Rd man/DAISIE_format_IW_full_stt.Rd man/archipelagos41.Rd man/DAISIE_extract_stt_median.Rd man/DAISIE_format_CS_sampled_stt.Rd man/DAISIE_sim_cr_iw.Rd man/create_area_pars.Rd man/DAISIE_SR_sim_core.Rd man/calc_Abeta.Rd man/frogs_datalist.Rd man/DAISIE_format_GW.Rd man/DAISIE_SR_ML.Rd man/Galapagos_datalist_2types.Rd man/islands_2types_1000reps.Rd man/DAISIE_MW_ML.Rd man/DAISIE_ML1.Rd man/DAISIE_sim_cr_gw.Rd man/DAISIE_plot_age_diversity.Rd man/stac_table.Rd man/sample_relaxed_rate.Rd man/DAISIE_plot_island.Rd man/transform_gamma_pars.Rd man/DAISIE_sim_relaxed_rate.Rd man/DAISIE_sim_time_dep_gw.Rd man/add_column_to_dataframe.Rd man/DAISIE_sim_core_time_dep.Rd man/get_trans_rate.Rd man/DAISIE_sim_cr_cs.Rd man/create_trait_pars.Rd man/get_ana_rate.Rd man/DAISIE_sim_time_dep.Rd man/DAISIE_plot_input.Rd man/DAISIE_sim_MW.Rd man/DAISIE_probdist.Rd man/DAISIE_sample_event_trait_dep.Rd man/DAISIE_loglik_integrand.Rd man/DAISIE_dataprep.Rd man/DAISIE_plot_pc_rates.Rd man/DAISIE_count_species.Rd man/DAISIE_sim.Rd