Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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Documentation for package ‘DAISIE’ version 1.4

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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