Man pages for xieshu95/Trait_dependent_TraiSIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction
| are_area_params | Test if list has area parameters |
| are_rates | Determines if object x are rates |
| are_trait_state_params | Test if list has trait state parameters |
| Biwa_datalist | Colonization and branching times of 68 fish clades in list... |
| calc_next_timeval | Calculates when the next timestep will be. |
| compare_diff | Comparing simulated results from DAISIE and TRASIE |
| countspecies | Count the number of species |
| create_area_params | Create named list of area parameters |
| create_daisie_params | Create a full-blown DAISIE parameter structure |
| create_rates | Create the rates per ?island |
| create_test_daisie_params | Create a sunction to test full-blown DAISIE parameter... |
| create_test_simulation_outputs | Creates the output of a as-short-as-possible simulation run |
| create_trait_state_params | Create named list of trait state parameters |
| DAISIE_calc_clade_ana_rate | Calculate the clade-wide effective anagenesis rate. With... |
| DAISIE_calc_clade_clado_rate | Calculate the clade-wide cladogenesis rate. |
| DAISIE_calc_clade_ext_rate | Calculate the clade-wide extinction rate |
| DAISIE_calc_clade_imm_rate | Calculate the clade-wide immigration rate. |
| DAISIE_calc_sumstats_pcrates | Calculate summary statistics of per capita rates |
| DAISIE_convertprobdist | Converts the joint distribution of endemics and non-endemics... |
| DAISIE_convert_to_classic_plot | Prepare input for DAISIE_stt |
| DAISIE_create_island | Converts simulation output into island output |
| DAISIE_dataprep | Prepare colonisation and branching time data to run in... |
| DAISIE_ExpEIN | The expected number of endemics and non-endemics under the... |
| DAISIE_extract_stt_median | Extract the STT median from the output of 'DAISIE_sim' |
| DAISIE_format_CS | Formats clade-specific simulation output into standard DAISIE... |
| DAISIE_format_IW | Formats island-wide simulation output into standard DAISIE... |
| DAISIE_get_brts_mya | Extract the sorted branching times, in million years ago.... |
| DAISIE_loglik_CS | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_loglik_IW | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_margprobdist | The marginal distribution of endemics and non-endemics under... |
| DAISIE_ML | Maximization of the loglikelihood under the DAISIE model with... |
| DAISIE_ML_IW | Maximization of the loglikelihood under the DAISIE model with... |
| DAISIE_MW_ML | Maximization of the loglikelihood under the DAISIE model with... |
| DAISIE_numcol | The expectation and marginal distribution of the number of... |
| DAISIE_ONEcolonist | Does something |
| DAISIE_plot_age_diversity | Plot clade age against clade diversity. |
| DAISIE_plot_area | Plots island area function through time |
| DAISIE_plot_cladogenesis | Plot cladogenesis rate through time |
| DAISIE_plot_comparison_stts | Plot STT and overlay additional STT curves. |
| DAISIE_plot_extinction | Plots extinction rate function through time |
| DAISIE_plot_immigration | Plot immigration rate through time |
| DAISIE_plot_island | Plot colonisation and branching time of species found on an... |
| DAISIE_plot_pc_rates | Plot per capita STT and per-capita rate change thourgh... |
| DAISIE_plot_sims | Plot island species-through-time (STT) plots |
| DAISIE_plot_stt | Create the Species-Through-Time plot. This is used to... |
| DAISIE_probdist | The joint distribution of endemics and non-endemics under the... |
| DAISIE_sample_event | Samples what event to happen next |
| DAISIE_sim | Simulate islands with given parameters. |
| DAISIE_sim_core | Internal function of the DAISIE simulation |
| DAISIE_sim_core_1_4 | Internal function of the DAISIE simulation Taken from CRAN,... |
| DAISIE_sim_core_checked | Runs one DAISIE simulation with a clade-specific carrying... |
| DAISIE_sim_core_checked_1_4 | Runs one DAISIE simulation with a clade-specific carrying... |
| DAISIE_sim_update_state | Updates state of island given sampled event |
| DAISIE_sim_with_mainland | Simulate speciation, immigration and extinction on both... |
| DAISIE_sim_with_ontogeny | Internal function of the DAISIE simulation |
| DAISIE_SR_loglik_CS | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_SR_ML | Maximization of the loglikelihood under the DAISIE model with... |
| DAISIE_SR_sim | Simulate islands with given parameters. |
| DAISIE_tutorial | Opens DAISIE tutorial |
| default_params_doc | Defailt parameter documentation |
| Galapagos_datalist | Colonization and branching times of 8 terrestrial avifaunal... |
| Galapagos_datalist_2types | Colonization and branching times of 8 terrestrial avifaunal... |
| Galapagos_datatable | Colonization and branching times of 8 terrestrial avifaunal... |
| get_ana_rate | Calculate anagenesis rate |
| get_clado_rate | Calculate cladogenesis rate |
| get_ext_rate | Function to describe changes in extinction rate through time.... |
| get_immig_rate | Calculate immigration rate |
| get_t_hor | Function to calculate and update horizon for maximum... |
| get_trans_rate | Calculate transition rate |
| is_island_ontogeny_input | Check if island_ontogeny is correct after user input |
| is_island_ontogeny_runtime | Check if island_ontogeny is correct during runtime (i.e.... |
| island_area | Function to describe changes in area through time. Adapted... |
| island_area_vector | Computes island_area, but takes vector as argument (needed by... |
| islands_10reps_RAW | 1000 islands in RAW format simulated with the ML parameters... |
| islands_1type_1000reps | 1000 islands in DAISIE format simulated with the ML... |
| islands_2types_1000reps | 1000 islands in DAISIE format simulated with the ML... |
| is_numeric_list | Determine if list has only numerical values. |
| is.odd | Determine if the value is odd. |
| is_simulation_outputs | Measures if the input is a valid collection of simulation... |
| Macaronesia_datalist | Colonization and branching times of terrestrial avifaunal... |
| translate_island_ontogeny | Translate user-friendly ontogeny codes to numerics |
| update_rates | Calculates algorithm rates |
