R: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

# Dynamical Assembly of Islands by Speciation, Immigration and Extinction

## Documentation for package ‘DAISIE’ version 4.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 with no diversity-dependence
DAISIE_ExpEIN2 | 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_margprobdist2 | The probability distribution of the number 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.
frogs_sim_datalist | Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalist
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