DAISIE (version 1.0.2)

DAISIE-package: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

DAISIE is an island biogeography model that assumes island biota assembly is governed by immigration, extinction and speciation through cladogenesis and anagenesis. This likelihood-based statistical package can simulate islands and estimate parameters of the DAISIE model based on phylogenetic/phylogeographic data. Cladogenesis and immigration rates can be dependent on diversity.

Details

Package:

DAISIE

Type:

Package

Version:

1.0.2

Date:

2015-09-25

License:

GPL 2.0

DAISIE_ML computes the parameters that maximizes the loglikelihood computes by DAISIE_loglik_all

DAISIE_sim simulates islands with given parameters

DAISIE_tutorial opens a step-by-step tutorial with example from Galapagos islands

DAISIE_loglik_all computes the loglikelihood of a given parameterization of the DAISIE model for a data set of colonization and branching times

DAISIE_plot_sims produces species-through-time plots based on simulated islands

DAISIE_dataprep converts data in table format to the list format accepted by DAISIE_loglik_all and DAISIE_ML

DAISIE_ExpEIN computes the expected number of endemics, non-endemics and their sum for a given time and set of parameters

References

Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.

See Also

DDD