# Dynamical Assembly of Islands by Speciation, Immigration and Extinction

## Documentation for package ‘DAISIE’ version 1.4

- DESCRIPTION file.

## Help Pages

DAISIE-package | Dynamical Assembly of Islands by Speciation, Immigration and Extinction
DAISIE | Dynamical Assembly of Islands by Speciation, Immigration and Extinction
DAISIE_convertprobdist | Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format
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_loglik_all | Computes the loglikelihood of the DAISIE model given data and a set of model parameters
DAISIE_loglik_CS | Computes the loglikelihood of the DAISIE model 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
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_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 islands with given parameters.
DAISIE_tutorial | Opens DAISIE tutorial
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 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