Bats_GreaterAntilles    Colonization and branching times of
                        Noctilionoid bats from the Greater Antilles.
Biwa_datalist           Colonization and branching times of 68 fish
                        clades.
DAISIE_CS_max_steps     CS iteration control
DAISIE_ExpEIN           The expected number of endemics and
                        non-endemics under the DAISIE model with no
                        diversity-dependence
DAISIE_ExpEIN2          The expected number of endemics and
                        non-endemics under the DAISIE model
DAISIE_IC               Calculates information criterion from DAISIE ML
                        estimates?
DAISIE_IW_num_threads   IW concurrency control
DAISIE_ML               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_SR_ML            Maximization of the loglikelihood under the
                        DAISIE model with clade-specific
                        diversity-dependence
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_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_dataprep         Prepare colonisation and branching time data to
                        run in DAISIE.
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_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_margprobdist2    The probability distribution of the number of
                        endemics and non-endemics under the DAISIE
                        model
DAISIE_numcol           The expectation and marginal distribution of
                        the number of colonizations (lineages) under
                        the DAISIE 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_MW           Simulate multiple islands based on
                        hyperparameters that describe relationships
                        between area, isolation and local parameters
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_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.
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.
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.
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 physical data for 41
                        archipelagos
create_CS_version       Creates the list object for CS_version argument
                        in DAISIE_ML_CS
create_area_pars        Create named list of area parameters
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_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
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.
frogs_sim_datalist      Colonization and branching times of a data set
                        simulated with the MLE parameters of
                        frogs_datalist
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)
stac_table              Explanatory table on meaning and use of 'stac'
                        settings
