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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
DAISIE_IC()
Calculates information criterion from DAISIE ML estimates?
DAISIE_IW_num_threads()
IW concurrency control
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_SR_ML_CS()
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_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_cr()
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.
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