API for DAISIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction
| Global functions | |
|---|---|
| Bats_GreaterAntilles | Man page |
| Biwa_datalist | Man page |
| DAISIE | Man page |
| DAISIE-package | Man page |
| DAISIE_CS_max_steps | Man page Source code |
| DAISIE_ExpEIN | Man page Source code |
| DAISIE_IC | Man page Source code |
| DAISIE_IW_num_threads | Man page Source code |
| DAISIE_IW_pars | Source code |
| DAISIE_KLdist | Source code |
| DAISIE_ML | Man page Source code |
| DAISIE_ML1 | Man page Source code |
| DAISIE_ML2 | Man page Source code |
| DAISIE_ML4 | Man page Source code |
| DAISIE_ML_CS | Man page |
| DAISIE_ML_IW | Man page Source code |
| DAISIE_MW_ML | Man page Source code |
| DAISIE_MW_loglik_choosepar | Source code |
| DAISIE_ONEcolonist | Man page Source code |
| DAISIE_SR_ML | Man page Source code |
| DAISIE_SR_ML_CS | Man page |
| DAISIE_SR_loglik | Source code |
| DAISIE_SR_loglik_CS | Man page |
| DAISIE_SR_loglik_all | Man page Source code |
| DAISIE_SR_loglik_all_choosepar | Source code |
| DAISIE_SR_sim | Source code |
| DAISIE_SR_sim_core | Man page Source code |
| DAISIE_abm_factor | Man page Source code |
| DAISIE_calc_sumstats_pcrates | Source code |
| DAISIE_convert_to_classic_plot | Source code |
| DAISIE_convertprobdist | Man page Source code |
| DAISIE_count_species | Man page Source code |
| DAISIE_create_island | Man page Source code |
| DAISIE_create_island_trait | Source code |
| DAISIE_dataprep | Man page Source code |
| DAISIE_eq | Source code |
| DAISIE_extract_stt_median | Man page Source code |
| DAISIE_format_CS | Man page Source code |
| DAISIE_format_CS_full_stt | Man page Source code |
| DAISIE_format_CS_sampled_stt | Man page Source code |
| DAISIE_format_CS_trait | Source code |
| DAISIE_format_GW | Man page Source code |
| DAISIE_format_IW | Source code |
| DAISIE_format_IW_full_stt | Man page Source code |
| DAISIE_format_IW_sampled_stt | Man page Source code |
| DAISIE_format_IW_trait | Source code |
| DAISIE_integrate | Source code |
| DAISIE_integrate_const | Source code |
| DAISIE_integrate_shift | Source code |
| DAISIE_integrate_time | Source code |
| DAISIE_loglik | Source code |
| DAISIE_loglik_CS | Man page |
| DAISIE_loglik_CS_choice | Source code |
| DAISIE_loglik_CS_shift | Source code |
| DAISIE_loglik_IW | Man page Source code |
| DAISIE_loglik_IW_M1 | Source code |
| DAISIE_loglik_IW_choosepar | Source code |
| DAISIE_loglik_all | Man page Source code |
| DAISIE_loglik_all_choosepar | Source code |
| DAISIE_loglik_all_choosepar2 | Source code |
| DAISIE_loglik_all_choosepar4 | Source code |
| DAISIE_loglik_high_lambda | Source code |
| DAISIE_loglik_integrand | Man page Source code |
| DAISIE_loglik_integrate | Man page Source code |
| DAISIE_loglik_rhs | Source code |
| DAISIE_loglik_rhs1 | Source code |
| DAISIE_loglik_rhs2 | Source code |
| DAISIE_loglik_rhs_IW | Source code |
| DAISIE_loglik_rhs_precomp | Source code |
| DAISIE_loglik_rhs_time | Source code |
| DAISIE_loglik_rhs_time1 | Source code |
| DAISIE_loglik_rhs_time2 | Source code |
| DAISIE_make_archipelago | Man page Source code |
| DAISIE_make_global | Man page Source code |
| DAISIE_margprobdist | Man page Source code |
| DAISIE_nonoceanic_spec | Source code |
| DAISIE_numcol | Man page Source code |
| DAISIE_numcol_dist | Source code |
| DAISIE_ode_cs | Source code |
| DAISIE_plot_age_diversity | Man page Source code |
| DAISIE_plot_area | Man page Source code |
| DAISIE_plot_cladogenesis | Man page Source code |
| DAISIE_plot_comparison_stts | Source code |
| DAISIE_plot_extinction | Man page Source code |
| DAISIE_plot_immigration | Man page Source code |
| DAISIE_plot_input | Man page Source code |
| DAISIE_plot_island | Man page |
| DAISIE_plot_pc_rates | Man page Source code |
| DAISIE_plot_sims | Man page Source code |
| DAISIE_plot_stt | Man page Source code |
| DAISIE_probdist | Man page Source code |
| DAISIE_probdist_rhs | Source code |
| DAISIE_sample_event_cr | Man page Source code |
| DAISIE_sample_event_time_dep | Man page Source code |
| DAISIE_sample_event_trait_dep | Man page Source code |
| DAISIE_sim | Man page Source code |
| DAISIE_sim_MW | Man page |
| DAISIE_sim_core_cr | Man page Source code |
| DAISIE_sim_core_cr_shift | Man page Source code |
| DAISIE_sim_core_time_dep | Man page Source code |
| DAISIE_sim_core_trait_dep | Man page Source code |
| DAISIE_sim_cr | Man page |
| DAISIE_sim_cr_cs | Man page Source code |
| DAISIE_sim_cr_gw | Man page Source code |
| DAISIE_sim_cr_iw | Man page Source code |
| DAISIE_sim_cr_shift | Man page Source code |
| DAISIE_sim_global | Source code |
| DAISIE_sim_min_type2 | Man page Source code |
| DAISIE_sim_relaxed_rate | Man page Source code |
| DAISIE_sim_time_dep | Man page Source code |
| DAISIE_sim_time_dep_cs | Man page Source code |
| DAISIE_sim_time_dep_gw | Man page Source code |
| DAISIE_sim_time_dep_iw | Man page Source code |
| DAISIE_sim_trait_dep | Man page Source code |
| DAISIE_sim_trait_dep_2K | Man page Source code |
| DAISIE_sim_update_state_cr | Man page Source code |
| DAISIE_sim_update_state_time_dep | Man page Source code |
| DAISIE_sim_update_state_trait_dep | Man page Source code |
| DAISIE_spec_tables | Source code |
| Galapagos_datalist | Man page |
| Galapagos_datalist_2types | Man page |
| Galapagos_datatable | Man page |
| Macaronesia_datalist | Man page |
| NewZealand_birds_datalist | Man page |
| add_brt_table | Source code |
| add_column_to_dataframe | Man page Source code |
| antidiagSums | Source code |
| approximate_logp0 | Source code |
| archipelago_data | Man page |
| archipelagos41 | Man page |
| are_area_pars | Source code |
| are_hyper_pars | Source code |
| are_max_rates | Source code |
| are_max_rates_gt_rates | Source code |
| are_rates | Man page Source code |
| are_trait_pars | Source code |
| bin2dec | Source code |
| calcMN | Source code |
| calc_Abeta | Man page Source code |
| calc_next_timeval | Man page Source code |
| calc_next_timeval_shift | Man page Source code |
| calc_peak | Man page Source code |
| checkprobs | Source code |
| checkprobs2 | Source code |
| convert_parameters_MW | Source code |
| countimmi | Source code |
| countspecies | Man page Source code |
| countspeciestype1 | Source code |
| countstac | Source code |
| counttype1 | Source code |
| create_CS_version | Man page Source code |
| create_area_pars | Man page Source code |
| create_full_CS_stt | Man page Source code |
| create_full_CS_stt_trait | Source code |
| create_hyper_pars | Man page Source code |
| create_l0ki | Source code |
| create_pars | Man page Source code |
| create_trait_pars | Man page Source code |
| create_trait_pars_2K | Man page Source code |
| cum_rho | Man page Source code |
| daisie_odeint_cs | Man page |
| daisie_odeint_iw | Man page |
| dec2bin | Source code |
| dec2binmat | Source code |
| default_params_doc | Man page Source code |
| distance_dep_options1_fun | Source code |
| divdepvec | Source code |
| divdepvec1 | Source code |
| divdepvecproc | Source code |
| f_sigmoidal_neg | Source code |
| f_sigmoidal_pos | Source code |
| fconstr13 | Source code |
| fconstr15 | Source code |
| frogs_datalist | Man page |
| frogs_datatable | Man page |
| get_ana_rate | Man page Source code |
| get_clado_rate | Man page Source code |
| get_clado_rate_per_capita | Source code |
| get_ext_rate | Man page Source code |
| get_ext_rate_per_capita | Source code |
| get_global_max_area | Source code |
| get_global_min_area | Source code |
| get_immig_rate | Man page Source code |
| get_immig_rate_per_capita | Source code |
| get_trans_rate | Man page Source code |
| integral_peak | Man page Source code |
| is_island_ontogeny_input | Source code |
| is_sea_level_input | Source code |
| is_simulation_outputs | Source code |
| island_area | Man page Source code |
| island_area_vector | Man page Source code |
| islands_10reps_RAW | Man page |
| islands_1type_1000reps | Man page |
| islands_2types_1000reps | Man page |
| kimat | Source code |
| nndivdep | Source code |
| odeproc | Source code |
| order_pars1 | Source code |
| par_shift | Source code |
| print_init_ll | Source code |
| print_ml_par_settings | Source code |
| print_parameters_and_loglik | Source code |
| quantiles | Source code |
| remove_empty_elements | Man page Source code |
| rho | Man page Source code |
| s1output | Source code |
| sample_relaxed_rate | Man page Source code |
| selectrows | Source code |
| shift_before_certain_brts | Source code |
| stac_table | Man page |
| transform_gamma_pars | Man page Source code |
| translate_island_ontogeny | Source code |
| translate_sea_level | Source code |
| update_max_rates | Man page Source code |
| update_rates | Man page Source code |
| update_rates_trait | Source code |
