island: Stochastic Island Biogeography Theory Made Easy
Tools to develop stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) and extensions. The package allows the calculation of colonization and extinction rates (including environmental variables) given presence-absence data, the simulation of community assembly and model selection.
In the simplest stochastic model of Island Biogeography, there is a
pool of species that potentially can colonize a system of islands. When we
sample an island in time, we obtain a time-series of presence-absence
vectors for the different species of the pool, which allows us to estimate
colonization (c) and extinction (e) rates under perfect
detectability. These are actual rates (in time^-1 units).
The simplest stochastic model of island biogeography assumes a single colonization-extinction pair for the whole community. This model implictly assumes: first, neutrality of the species in the community, that is, all species in the community share the same values for those rates; and second, all species colonize and become extinct indepently from each other. The "species neutrality assumption" can be relaxed easily, for example, calculating different rates for different groups or on a per-species basis. In addition, we can make these rates depend on environmental variables measured at the same time that we took our samples. For more information of the basic model, please see the references.
The data should be organized in dataframes with consecutive presence-absence data of each sample ordered cronologically, being the data associated with a single species in a row. Additional columns can contain the filiations of every species to a group, i. e. a phylogenetic group or a guild.
Alonso, D., Pinyol-Gallemi, A., Alcoverro T. and Arthur, R..
(2015) Fish community reassembly after a coral mass mortality: higher
trophic groups are subject to increased rates of extinction. Ecology
Letters, 18, 451–461.
Simberloff, D. S., and Wilson, E. O.. (1969). Experimental Zoogeography of Islands: The Colonization of Empty Islands. Ecology, 50(2), 278–296. http://doi.org/10.2307/1934856
Simberloff, D. S.. (1969). Experimental Zoogeography of Islands: A Model for Insular Colonization. Ecology, 50(2), 296–314. http://doi.org/10.2307/1934857