Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Documentation for package ‘DAISIE’ version 1.0.2

DAISIE-package	Dynamical Assembly of Islands by Speciation, Immigration and Extinction
DAISIE	Dynamical Assembly of Islands by Speciation, Immigration and Extinction
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_format_sim	Converting simulation output from RAW to DAISIE format
DAISIE_loglik_all	Computes the loglikelihood of the DAISIE model given data and a set of model parameters
DAISIE_ML	Maximization of the loglikelihood under the DAISIE model
DAISIE_plot_sims	Plot island species-through-time (STT) plots
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)