Man pages for DAISIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction
| add_column_to_dataframe | Add a column to a data frame |
| archipelago_data | Physical data on 41 archipelagos |
| archipelagos41 | DAISIE datalist object including bird phylogenetic data and... |
| are_rates | Determines if object rates are rates |
| Bats_GreaterAntilles | Colonization and branching times of Noctilionoid bats from... |
| Biwa_datalist | Colonization and branching times of 68 fish clades. |
| calc_Abeta | Calculates the area at a point in time from a beta function |
| calc_next_timeval | Calculates when the next timestep will be. |
| calc_next_timeval_shift | Calculates when the next timestep will be, and if a shift has... |
| calc_peak | Calculates the peak of ontogeny curve (beta function) |
| countspecies | Count the number of species |
| create_area_pars | Create named list of area parameters |
| create_CS_version | Creates the list object for CS_version argument in... |
| create_full_CS_stt | Unsampled CS full STT |
| create_hyper_pars | Create list of hyperparameters |
| create_pars | Create vector of model parameters |
| create_trait_pars | Create named list of trait state parameters |
| create_trait_pars_2K | Create named list of trait state parameters |
| cum_rho | Cumulative Gamma distribution parameterised with mean and... |
| DAISIE_abm_factor | Sets or retrieves the factor to calculate the step-size used... |
| DAISIE_convertprobdist | Converts the joint distribution of endemics and non-endemics... |
| DAISIE_count_species | Count number of species in DAISIE datalist or simulated data. |
| DAISIE_create_island | Converts simulation output into island output |
| DAISIE_CS_max_steps | CS iteration control |
| DAISIE_dataprep | Prepare colonisation and branching time data to run in... |
| DAISIE_ExpEIN | The expected number of endemics and non-endemics under the... |
| DAISIE_ExpEIN2 | 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_full_stt | Formats clade-specific simulation output into standard DAISIE... |
| DAISIE_format_IW_sampled_stt | Formats island-wide simulation output into standard DAISIE... |
| DAISIE_IC | Calculates information criterion from DAISIE ML estimates? |
| DAISIE_IW_num_threads | IW concurrency control |
| DAISIE_loglik_CS | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_loglik_integrand | Integrand to be integrated to calculate the log likelihood... |
| DAISIE_loglik_integrate | Integrates the loglikelihood of a single clade across a... |
| DAISIE_loglik_IW | Computes the loglikelihood of the DAISIE model with... |
| DAISIE_loglik_MC | function to calculate the log likelihood for the relaxed rate... |
| DAISIE_logp0 | Computes the log probability of no species present under the... |
| DAISIE_make_archipelago | Does some things |
| DAISIE_make_global | Does something |
| DAISIE_margprobdist | The marginal distribution of endemics and non-endemics under... |
| DAISIE_margprobdist2 | The probability distribution of the number of endemics and... |
| 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 multiple islands under a clade specific... |
| DAISIE_ML4 | 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_numcol | The expectation and marginal distribution of the number of... |
| daisie_odeint_cs | Driver for the boost::odeint solver for the CS model |
| daisie_odeint_iw | Driver for the boost::odeint solver for the IW model |
| DAISIE_ONEcolonist | Convert intermediate output to final simulation output |
| DAISIE-package | DAISIE: Dynamical Assembly of Islands by Speciation,... |
| 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_extinction | Plots extinction rate function through time |
| DAISIE_plot_immigration | Plot immigration rate through time |
| DAISIE_plot_input | DAISIE tree plot |
| 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_cr | Samples what event to happen next |
| DAISIE_sample_event_time_dep | Samples what event to happen next |
| DAISIE_sample_event_trait_dep | Samples what event to happen next |
| DAISIE_sim | Simulate (non-)oceanic islands with given parameters under... |
| DAISIE_sim_core_cr | Internal function of the DAISIE simulation |
| DAISIE_sim_core_cr_shift | Internal function of the DAISIE simulation |
| DAISIE_sim_core_time_dep | Internal function of the DAISIE simulation |
| DAISIE_sim_core_trait_dep | Internal function of the DAISIE simulation |
| DAISIE_sim_cr_cs | Simulates island replicates with an clade-specific (CS)... |
| DAISIE_sim_cr_gw | Simulates island replicates with an guild-wide (GW)... |
| DAISIE_sim_cr_iw | Simulates island replicates with an island-wide (IW)... |
| DAISIE_sim_cr_shift | Simulate (non-)oceanic islands with given parameters under a... |
| DAISIE_sim_min_type2 | Internal function of the DAISIE simulation |
| DAISIE_sim_MW | Simulate multiple islands based on hyperparameters that... |
| DAISIE_sim_relaxed_rate | Simulate (non-)oceanic islands with given parameters under a... |
| DAISIE_sim_time_dep | Simulate (non-)oceanic islands with given parameters under a... |
| DAISIE_sim_time_dep_cs | Simulates island replicates with an clade-specific (CS)... |
| DAISIE_sim_time_dep_gw | Simulates island replicates with an guild-wide (GW)... |
| DAISIE_sim_time_dep_iw | Simulates island replicates with an island-wide (IW)... |
| DAISIE_sim_trait_dep | Simulate islands with given trait-dependent parameters. |
| DAISIE_sim_trait_dep_2K | Simulate islands with given trait-dependent parameters. |
| DAISIE_sim_update_state_cr | Updates state of island given sampled event for a constant... |
| DAISIE_sim_update_state_time_dep | Updates state of island given sampled event |
| DAISIE_sim_update_state_trait_dep | Updates state of island given sampled event with two trait... |
| 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_core | DEPRECATED - Algorithm component of DAISIE_SR_sim. |
| default_params_doc | Default parameter documentation |
| frogs_datalist | Colonization and branching times of 5 Eleutherodactylus... |
| frogs_datatable | Colonization and branching times of 5 Eleutherodactylus... |
| frogs_sim_datalist | Colonization and branching times of a data set simulated with... |
| 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 | Calculate extinction rate |
| get_immig_rate | Calculate immigration rate |
| get_trans_rate | Calculate transition rate |
| integral_peak | Computes integral of a very peaked function, modified from... |
| island_area | Function to describe changes in area through time. |
| 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... |
| Macaronesia_datalist | Colonization and branching times of terrestrial avifaunal... |
| NewZealand_birds_datalist | Colonization and branching times of New Zealand birds. |
| remove_empty_elements | Remove superfluous lines in empty simulations |
| rho | Gamma distribution density parameterised with mean and... |
| sample_relaxed_rate | Samples from distribution when parameter is relaxed |
| stac_table | Explanatory table on meaning and use of 'stac' settings |
| transform_gamma_pars | Transforms mean and standard deviation to shape and scale... |
| update_max_rates | Calculates the maximum rates for a Gillespie simulation |
| update_rates | Calculates algorithm rates |
