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DAISIE (version 1.0.2)

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. Ecology Letters 18: 844-852.

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Version

Install

install.packages('DAISIE')

Monthly Downloads

306

Version

1.0.2

License

GPL-2

Maintainer

Rampal Etienne

Last Published

September 29th, 2015

Functions in DAISIE (1.0.2)

DAISIE-internal

Internal DAISIE Functions

DAISIE-package

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

islands_1type_1000reps

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

DAISIE_loglik_all

Computes the loglikelihood of the DAISIE model given data and a set of model parameters

DAISIE_sim

Simulate islands with given parameters.

Galapagos_datalist

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

DAISIE_format_sim

Converting simulation output from RAW to DAISIE format

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)

DAISIE_ExpEIN

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

DAISIE_dataprep

Prepare colonisation and branching time data to run in DAISIE.

DAISIE_ML

Maximization of the loglikelihood under the DAISIE model

Galapagos_datatable

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

DAISIE_plot_sims

Plot island species-through-time (STT) plots

islands_10reps_RAW

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

DAISIE_tutorial

Opens DAISIE tutorial

Galapagos_datalist_2types

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