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.
| 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
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>.
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