Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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Documentation for package ‘DAISIE’ version 4.4.1

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add_column_to_dataframe Add a column to a data frame
archipelagos41 DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos
archipelago_data Physical data on 41 archipelagos
Bats_GreaterAntilles Colonization and branching times of Noctilionoid bats from the Greater Antilles.
Biwa_datalist Colonization and branching times of 68 fish clades.
create_area_pars Create named list of area parameters
create_CS_version Creates the list object for CS_version argument in DAISIE_ML_CS
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
DAISIE_abm_factor Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers.
DAISIE_convertprobdist Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format
DAISIE_count_species Count number of species in DAISIE datalist or simulated data.
DAISIE_CS_max_steps CS iteration control
DAISIE_dataprep Prepare colonisation and branching time data to run in DAISIE.
DAISIE_ExpEIN The expected number of endemics and non-endemics under the DAISIE model
DAISIE_format_CS_full_stt Formats clade-specific simulation output into standard DAISIE list output with complete STT table
DAISIE_format_IW_full_stt Formats clade-specific simulation output into standard DAISIE list output with complete STT table
DAISIE_IC Calculates information criterion from DAISIE ML estimates?
DAISIE_IW_num_threads IW concurrency control
DAISIE_loglik_IW Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters
DAISIE_margprobdist The marginal distribution of endemics and non-endemics under the DAISIE model
DAISIE_ML Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence
DAISIE_ML_CS Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence
DAISIE_ML_IW Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence
DAISIE_MW_ML Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson
DAISIE_numcol The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model
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_plot_age_diversity Plot clade age against clade diversity.
DAISIE_plot_input DAISIE tree plot
DAISIE_plot_island Plot colonisation and branching time of species found on an island dataset.
DAISIE_plot_sims Plot island species-through-time (STT) plots
DAISIE_probdist The joint distribution of endemics and non-endemics under the DAISIE model
DAISIE_sim Simulate (non-)oceanic islands with given parameters under time-constant rates
DAISIE_sim_cr Simulate (non-)oceanic islands with given parameters under time-constant rates
DAISIE_sim_cr_cs Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process
DAISIE_sim_cr_gw Simulates island replicates with an guild-wide (GW) diversity-dependent process
DAISIE_sim_cr_iw Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process
DAISIE_sim_cr_shift Simulate (non-)oceanic islands with given parameters under a rate-shift regime
DAISIE_sim_MW Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters
DAISIE_sim_relaxed_rate Simulate (non-)oceanic islands with given parameters under a relaxed-rate model
DAISIE_sim_time_dep Simulate (non-)oceanic islands with given parameters under a time-dependent regime
DAISIE_sim_time_dep_cs Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process
DAISIE_sim_time_dep_gw Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process
DAISIE_sim_time_dep_iw Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process
DAISIE_sim_trait_dep Simulate islands with given trait-dependent parameters.
DAISIE_sim_trait_dep_2K Simulate islands with given trait-dependent parameters.
DAISIE_SR_loglik_all Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time
DAISIE_SR_loglik_CS Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time
DAISIE_SR_ML Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence
DAISIE_SR_ML_CS Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence
frogs_datalist Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
frogs_datatable Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.
Galapagos_datalist Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
Galapagos_datalist_2types Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
Galapagos_datatable Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.
islands_10reps_RAW 1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.
islands_1type_1000reps 1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data
islands_2types_1000reps 1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)
Macaronesia_datalist Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all
NewZealand_birds_datalist Colonization and branching times of New Zealand birds.
stac_table Explanatory table on meaning and use of 'stac' settings