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DAISIE (version 4.5.0)

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) .

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Install

install.packages('DAISIE')

Monthly Downloads

277

Version

4.5.0

License

GPL (>= 3) | file LICENSE

Issues

21

Pull Requests

1

Stars

9

Forks

11

Maintainer

Rampal Etienne

Last Published

February 5th, 2025

Functions in DAISIE (4.5.0)

DAISIE_IC

Calculates information criterion from DAISIE ML estimates?
DAISIE_ML

Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence
DAISIE_IW_num_threads

IW concurrency control
DAISIE_CS_max_steps

CS iteration control
Bats_GreaterAntilles

Colonization and branching times of Noctilionoid bats from the Greater Antilles.
DAISIE_ML2

Computes MLE for multiple islands under a clade specific scenario
DAISIE_ML1

Computes MLE for single type species under a clade specific scenario
Biwa_datalist

Colonization and branching times of 68 fish clades.
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_abm_factor

Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers.
DAISIE_ML4

Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution
DAISIE_SR_sim_core

DEPRECATED - Algorithm component of DAISIE_SR_sim.
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_ML_IW

Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence
DAISIE_ONEcolonist

Convert intermediate output to final simulation output
DAISIE_SR_ML

Maximization of the loglikelihood under the DAISIE model with clade-specific 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_format_CS_sampled_stt

Formats clade-specific simulation output into standard DAISIE list output
DAISIE_format_IW_full_stt

Formats clade-specific simulation output into standard DAISIE list output with complete STT table
DAISIE_format_CS_full_stt

Formats clade-specific simulation output into standard DAISIE list output with complete STT table
DAISIE_format_CS

Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt
DAISIE_loglik_CS

Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters
DAISIE_create_island

Converts simulation output into island output
DAISIE_dataprep

Prepare colonisation and branching time data to run in DAISIE.
DAISIE_format_GW

Formats guild-wide simulation output into standard DAISIE list output
DAISIE_format_IW_sampled_stt

Formats island-wide simulation output into standard DAISIE list output
DAISIE_extract_stt_median

Extract the STT median from the output of DAISIE_sim functions
DAISIE_make_global

Does something
DAISIE_loglik_IW

Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters
DAISIE_make_archipelago

Does some things
DAISIE_margprobdist

The marginal distribution of endemics and non-endemics under the DAISIE model
DAISIE_plot_age_diversity

Plot clade age against clade diversity.
DAISIE_plot_area

Plots island area function through time
DAISIE_loglik_integrate

Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution
DAISIE_loglik_integrand

Integrand to be integrated to calculate the log likelihood for the relaxed rate model.
DAISIE_numcol

The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model
DAISIE_logp0

Computes the log probability of no species present under the DAISIE model with clade-specific diversity-dependence
DAISIE_plot_cladogenesis

Plot cladogenesis rate through time
DAISIE_plot_island

Plot colonisation and branching time of species found on an island dataset.
DAISIE_plot_extinction

Plots extinction rate function through time
DAISIE_sample_event_cr

Samples what event to happen next
DAISIE_plot_input

DAISIE tree plot
DAISIE_plot_sims

Plot island species-through-time (STT) plots
DAISIE_plot_immigration

Plot immigration rate through time
DAISIE_plot_stt

Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions
DAISIE_probdist

The joint distribution of endemics and non-endemics under the DAISIE model
DAISIE_plot_pc_rates

Plot per capita STT and per-capita rate change thourgh simulation
DAISIE_sample_event_time_dep

Samples what event to happen next
DAISIE_sim_core_time_dep

Internal function of the DAISIE simulation
DAISIE_sim

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_core_cr_shift

Internal function of the DAISIE simulation
DAISIE_sim_MW

Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters
DAISIE_sim_cr_gw

Simulates island replicates with an guild-wide (GW) diversity-dependent process
DAISIE_sim_core_cr

Internal function of the DAISIE simulation
DAISIE_sim_core_trait_dep

Internal function of the DAISIE simulation
DAISIE_sample_event_trait_dep

Samples what event to happen next
DAISIE_sim_trait_dep

Simulate islands with given trait-dependent parameters.
DAISIE_sim_time_dep_gw

Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process
DAISIE_sim_relaxed_rate

Simulate (non-)oceanic islands with given parameters under a relaxed-rate model
DAISIE_sim_cr_iw

Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process
DAISIE_sim_time_dep_iw

Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process
DAISIE_sim_time_dep_cs

Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process
DAISIE_sim_cr_shift

Simulate (non-)oceanic islands with given parameters under a rate-shift regime
DAISIE_sim_trait_dep_2K

Simulate islands with given trait-dependent parameters.
DAISIE_sim_min_type2

Internal function of the DAISIE simulation
DAISIE_sim_time_dep

Simulate (non-)oceanic islands with given parameters under a time-dependent regime
add_column_to_dataframe

Add a column to a data frame
Galapagos_datalist_2types

Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
DAISIE_sim_update_state_trait_dep

Updates state of island given sampled event with two trait states.
Galapagos_datatable

Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.
DAISIE_sim_update_state_cr

Updates state of island given sampled event for a constant rate case.
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
archipelago_data

Physical data on 41 archipelagos
NewZealand_birds_datalist

Colonization and branching times of New Zealand birds.
DAISIE_sim_update_state_time_dep

Updates state of island given sampled event
create_CS_version

Creates the list object for CS_version argument in DAISIE_ML_CS
create_area_pars

Create named list of area parameters
countspecies

Count the number of species
create_full_CS_stt

Unsampled CS full STT
calc_next_timeval

Calculates when the next timestep will be.
calc_Abeta

Calculates the area at a point in time from a beta function
calc_next_timeval_shift

Calculates when the next timestep will be, and if a shift has occured.
Galapagos_datalist

Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
calc_peak

Calculates the peak of ontogeny curve (beta function)
archipelagos41

DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos
are_rates

Determines if object rates are rates
default_params_doc

Default parameter documentation
daisie_odeint_iw

Driver for the boost::odeint solver for the IW model
create_hyper_pars

Create list of hyperparameters
create_trait_pars

Create named list of trait state parameters
create_pars

Create vector of model parameters
daisie_odeint_cs

Driver for the boost::odeint solver for the CS model
create_trait_pars_2K

Create named list of trait state parameters
frogs_datatable

Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.
frogs_datalist

Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
cum_rho

Cumulative Gamma distribution parameterised with mean and standard deviation
get_immig_rate

Calculate immigration rate
frogs_sim_datalist

Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalist
island_area_vector

Computes island_area, but takes vector as argument (needed by )
get_ext_rate

Calculate extinction rate
get_ana_rate

Calculate anagenesis rate
island_area

Function to describe changes in area through time.
get_clado_rate

Calculate cladogenesis rate
islands_10reps_RAW

1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.
integral_peak

Computes integral of a very peaked function, modified from the SADISA package
get_trans_rate

Calculate transition rate
islands_1type_1000reps

1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data
sample_relaxed_rate

Samples from distribution when parameter is relaxed
update_rates

Calculates algorithm rates
transform_gamma_pars

Transforms mean and standard deviation to shape and scale gamma parameters
rho

Gamma distribution density parameterised with mean and standard deviation
remove_empty_elements

Remove superfluous lines in empty simulations
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)
update_max_rates

Calculates the maximum rates for a Gillespie simulation
stac_table

Explanatory table on meaning and use of stac settings
DAISIE_ExpEIN

The expected number of endemics and non-endemics under the DAISIE model
DAISIE-package

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