Files in Neves-P/DAISIErobustness

Test the Robustness of DAISIE to Geodynamics and Traits

CONTRIBUTING.md LICENSE.md NEWS.md R/DAISIErobustness-package.R R/all_endemic.R R/all_endemic_clades.R R/any_recols.R R/append_factor_key.R R/calc_ed95_for_plots.R R/calc_ed95_param_set.R R/calc_error.R R/calc_error_metrics.R R/calc_max_spec.R R/calc_ml.R R/calc_runtime_ed95_cor.R R/data.R R/default_params_doc.R R/extract_param_set.R R/get_runtime_params.R R/input-output.R R/is_integration_error.R R/is_param_space_name.R R/load_param_space.R R/ml_constraints.R R/plot_cor.R R/read_log_file.R R/read_param_set_log.R R/read_param_space_log.R R/read_runtime_log.R R/read_status_log.R R/run_novel_sim.R R/run_oceanic_sim.R R/run_robustness.R R/utils.R README.md data-raw/generate_continental_cs_param_space.R data-raw/generate_continental_di_param_space.R data-raw/generate_continental_iw_param_space.R data-raw/generate_continental_land_bridge_cs_param_space.R data-raw/generate_continental_land_bridge_di_param_space.R data-raw/generate_continental_land_bridge_iw_param_space.R data-raw/generate_ontogeny_cs_param_space.R data-raw/generate_ontogeny_di_param_space.R data-raw/generate_ontogeny_iw_param_space.R data-raw/generate_ontogeny_sea_level_cs_param_space.R data-raw/generate_ontogeny_sea_level_di_param_space.R data-raw/generate_ontogeny_sea_level_iw_param_space.R data-raw/generate_sea_level_cs_param_space.R data-raw/generate_sea_level_di_param_space.R data-raw/generate_sea_level_iw_param_space.R data-raw/generate_trait_2K_param_space.R data-raw/generate_trait_no_trans_param_space.R data-raw/generate_trait_param_space.R doc/pipeline_outline.md doc/robustness_specs.md man/DAISIErobustness-package.Rd man/all_endemic.Rd man/all_endemic_clades.Rd man/any_recols.Rd man/append_factor_key.Rd man/calc_ed95_for_plots.Rd man/calc_ed95_param_set.Rd man/calc_error.Rd man/calc_error_metrics.Rd man/calc_max_spec.Rd man/calc_ml.Rd man/calc_runtime_ed95_cor.Rd man/check_calc_error_metrics_input.Rd man/check_create_folders.Rd man/continental_cs.Rd man/continental_di.Rd man/continental_iw.Rd man/continental_land_bridge_cs.Rd man/continental_land_bridge_di.Rd man/continental_land_bridge_iw.Rd man/create_output_file_name.Rd man/default_params_doc.Rd man/extract_param_set.Rd man/get_runtime_params.Rd man/is_integration_error_log.Rd man/is_novel_sim_outputs.Rd man/is_param_space_name.Rd man/load_param_space.Rd man/ml_constraints.Rd man/oceanic_ontogeny_cs.Rd man/oceanic_ontogeny_di.Rd man/oceanic_ontogeny_iw.Rd man/oceanic_ontogeny_sea_level_cs.Rd man/oceanic_ontogeny_sea_level_di.Rd man/oceanic_ontogeny_sea_level_iw.Rd man/oceanic_sea_level_cs.Rd man/oceanic_sea_level_di.Rd man/oceanic_sea_level_iw.Rd man/plot_cor.Rd man/read_log_file.Rd man/read_param_set_log.Rd man/read_param_space_name_log.Rd man/read_runtime_log.Rd man/read_status_log.Rd man/run_novel_sim.Rd man/run_oceanic_sim.Rd man/run_robustness.Rd man/save_output.Rd man/trait_CES.Rd scripts/analysis/run_robustness_peregrine.R scripts/plots/all_scenarios_stripchart.R scripts/plots/area_through_time.R scripts/plots/continental_land_bridge_multiplier_stripchart.R scripts/plots/continental_land_bridge_sample_pars_stripchart.R scripts/plots/continental_sample_pars_stripchart.R scripts/plots/ed95_histograms.R scripts/plots/functions/compile_ed95s.R scripts/plots/functions/generate_paper_stripchart_plots.R scripts/plots/functions/plot_areas.R scripts/plots/functions/plot_error_dists.R scripts/plots/functions/plot_error_stripchart.R scripts/plots/functions/plot_error_stripchart_grouped.R scripts/plots/functions/save_faceted.R scripts/plots/functions/tidy_data.R scripts/plots/generate_all_plots.R scripts/plots/oceanic_sea_level_island_gradient_stripchart.R scripts/plots/ontogeny_sea_level_hyperpars_stripchart.R scripts/plots/runtime_correlation_plots.R scripts/trait/calc_clade_size_sd.R scripts/trait/calc_cssd_ctsd.R scripts/trait/calc_hellinger_dist.R scripts/trait/calc_stat_diff_trait.R scripts/trait/calc_tip_rates.R scripts/trait/create_dataframe.R scripts/trait/plot_2K.R scripts/trait/plot_combine_7ss.R scripts/trait/plot_est.R scripts/trait/plot_est_error.R scripts/trait/plot_hell_dist_RRD.R scripts/trait/plot_oceanic.R scripts/trait/plot_rate_ed95.R scripts/trait/plot_ss_vs_hdss.R tests/testthat.R tests/testthat/test-calc_ed95_for_plots.R tests/testthat/test-calc_ed95_param_set.R tests/testthat/test-calc_error.R tests/testthat/test-calc_error_metrics.R tests/testthat/test-calc_max_spec.R tests/testthat/test-calc_ml.R tests/testthat/test-calc_runtime_ed95_cor.R tests/testthat/test-create_output_file_name.R tests/testthat/test-extract_param_set.R tests/testthat/test-get_runtime_params.R tests/testthat/test-is_novel_sim_outputs.R tests/testthat/test-load_param_space.R tests/testthat/test-ml_constraints.R tests/testthat/test-novel_sim.R tests/testthat/test-oceanic_sim.R tests/testthat/test-plot_cor.R tests/testthat/test-read_param_set_log.R tests/testthat/test-read_param_space_log.R tests/testthat/test-read_runtime_log.R tests/testthat/test-run_robustness.R tests/testthat/test-style.R vignettes/robustness_vignette.Rmd vignettes/robustness_vignette.md