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

Description Details Author(s) References See Also

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: 1.4
Date: 2017-04-12
License: GPL 2.0

DAISIE_ML computes the parameters that maximizes the loglikelihood computed by DAISIE_loglik_all for one island/archipelago

DAISIE_ML2 computes the parameters that maximizes the loglikelihood for a set of islands / archipelagoes

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

DAISIE_probdist calculates the joint distribution of the number of endemics and non-endemics for a given set of parameter values, a given mainland species pool size and a given set of times

DAISIE_margprobdist calculates the marginal distribution of the number of endemics and non-endemics and their sum for a given set of parameter values, a given mainland species pool size and a given set of times

DAISIE_numcol calculates expectation and marginal distribution of the number of colonizations (lineages) for a given set of parameter values, a given mainland species pool size and a given set of times

Author(s)

Rampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart Haegeman
Maintainer: Rampal S. Etienne <[email protected]>rep(0:(D1 - 1), each = D2)

References

Valente, L., A.B. Phillimore & R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852, <DOI:10.1111/ele.12461>.

Valente, L., R.S. Etienne & L. Davalos (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology and Evolution 1: 0026. <DOI:10.1038/s41559-016-0026>.

See Also

DDD


DAISIE documentation built on May 1, 2019, 8:06 p.m.