Man pages for xieshu95/DAISIE_new
Dynamical Assembly of Islands by Speciation, Immigration and Extinction
| are_area_pars | Test if list has area parameters |
| are_dist_pars | Create list of distance parameters |
| are_hyper_pars | Test if a list has hyperparameters |
| are_max_rates | Determines if object max_rates are max_rates |
| are_max_rates_gt_rates | Check if maximum rates are greater or equal to rates |
| are_rates | Determines if object rates are rates |
| are_trait_pars | 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. |
| countimmi | Title |
| countspecies | Counts the number of species |
| countspeciestype1 | Title |
| countstac | Title |
| counttype1 | Counts the number of type 1 species |
| create_area_pars | Create named list of area parameters |
| create_default_pars | Creates standard metaparameters to defaults when NULL |
| create_dist_pars | Create list of distance pars |
| create_full_CS_stt | Unsampled CS full STT |
| create_hyper_pars | Create list of hyperparameters |
| create_singleton_phylo | Create an empty phylogeny |
| create_trait_pars | Create named list of trait state parameters |
| 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 | Wrapper function around for the DAISIE_format_CS_full_stt and... |
| DAISIE_format_CS_full_stt | Formats clade-specific simulation output into standard DAISIE... |
| DAISIE_format_CS_sampled_stt | Formats clade-specific simulation output into standard DAISIE... |
| DAISIE_format_GW | Formats guild-wide 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_IC | Calculates information criterion from DAISIE ML estimates? |
| DAISIE_loglik_CS | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_loglik_IW | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_make_archipelago | Does somethings |
| DAISIE_make_global | Does something |
| DAISIE_margprobdist | The marginal distribution of endemics and non-endemics under... |
| DAISIE_ML | Maximization of the loglikelihood under the DAISIE model with... |
| DAISIE_ML1 | Computes MLE for single type species under a clade specific... |
| DAISIE_ML2 | Computes MLE for two sets of species under a clade specific... |
| DAISIE_ML3 | Computes MLE for single type species under a clade specific... |
| 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_nonoceanic_spec | Calculates the species on the island initially when... |
| DAISIE_numcol | The expectation and marginal distribution of the number of... |
| DAISIE_ONEcolonist | Title |
| 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_constant_rate | Samples what event to happen next |
| DAISIE_sample_event_time_dependent | Samples what event to happen next |
| DAISIE_sample_event_trait_dependent | Samples what event to happen next |
| DAISIE_sim_constant_rate | Simulate islands with given parameters. |
| DAISIE_sim_constant_rate_shift | Simulate islands with given parameters. |
| DAISIE_sim_core_constant_rate | Internal function of the DAISIE simulation |
| DAISIE_sim_core_constant_rate_shift | Internal function of the DAISIE simulation |
| DAISIE_sim_core_time_dependent | Internal function of the DAISIE simulation |
| DAISIE_sim_core_trait_dependent | Internal function of the DAISIE simulation |
| DAISIE_sim_min_type2 | Internal function of the DAISIE simulation |
| DAISIE_sim_time_dependent | Simulate islands with given parameters. |
| DAISIE_sim_trait_dependent | Simulate islands with given parameters. |
| DAISIE_sim_update_state_constant_rate | Updates state of island given sampled event for a constant... |
| DAISIE_sim_update_state_time_dependent | Updates state of island given sampled event |
| DAISIE_SR_loglik_CS | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_SR_ML | Maximization of the loglikelihood under the DAISIE model with... |
| 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_global_max_area_time | Get the time of maximum area |
| get_global_min_area_time | Get the time when area is minimum |
| get_immig_rate | Calculate immigration rate |
| get_trans_rate | Calculate transition rate |
| is_island_ontogeny_input | Check if island_ontogeny is correct after user input |
| 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_sea_level_input | Check if sea_level is correct after user input |
| 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 |
| translate_sea_level | Translate user-friendly sea-level codes to numerics |
| update_max_rates | Calculates the maximum rates for a Gillespie simulation |
| update_rates | Calculates algorithm rates |
